diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index 94990954496041803f05768c9e255cd11acf82de..2c7723ab5dd19f9816968c9a4d28145ed1d67092 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -171,7 +171,7 @@ set(LAMMPS_DEPS)
set(LAMMPS_API_DEFINES)
set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR
- KSPACE MANYBODY MC MEAM MESSAGE MISC MOLECULE PERI REAX REPLICA RIGID SHOCK
+ KSPACE MANYBODY MC MESSAGE MISC MOLECULE PERI REPLICA RIGID SHOCK
SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD
USER-BOCS USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION
USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD
@@ -191,11 +191,11 @@ endforeach()
######################################################
# packages with special compiler needs or external libs
######################################################
-if(PKG_REAX OR PKG_MEAM OR PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE OR PKG_USER-SCAFACOS)
+if(PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE OR PKG_USER-SCAFACOS)
enable_language(Fortran)
endif()
-if(PKG_MEAM OR PKG_USER-H5MD OR PKG_USER-QMMM OR PKG_USER-SCAFACOS)
+if(PKG_USER-H5MD OR PKG_USER-QMMM OR PKG_USER-SCAFACOS)
enable_language(C)
endif()
@@ -826,7 +826,7 @@ endforeach()
##############################################
# add lib sources of (simple) enabled packages
############################################
-foreach(SIMPLE_LIB REAX MEAM POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
+foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
USER-QMMM)
if(PKG_${SIMPLE_LIB})
string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}")
diff --git a/doc/src/Build_extras.txt b/doc/src/Build_extras.txt
index 58ae16a372bbadb69848f1531aa8fc47ef5d9286..e13165c7d267596fdf624e10aed1e42e47603260 100644
--- a/doc/src/Build_extras.txt
+++ b/doc/src/Build_extras.txt
@@ -36,7 +36,6 @@ This is the list of packages that may require additional steps.
"OPT"_#opt,
"POEMS"_#poems,
"PYTHON"_#python,
-"REAX"_#reax,
"VORONOI"_#voronoi,
"USER-ATC"_#user-atc,
"USER-AWPMD"_#user-awpmd,
@@ -536,45 +535,6 @@ build fails.
:line
-REAX package :h4,link(reax)
-
-NOTE: the use of the REAX package and its "pair_style
-reax"_pair_reax.html command is discouraged, as it is no longer
-maintained. Please use the USER-REAXC package and its "pair_style
-reax/c"_pair_reaxc.html command instead, and possibly its KOKKOS
-enabled variant (pair_style reax/c/kk), which has a more robust memory
-management. See the "pair_style reax/c"_pair_reaxc.html doc page for
-details.
-
-[CMake build]:
-
-No additional settings are needed besides "-D PKG_REAX=yes".
-
-[Traditional make]:
-
-Before building LAMMPS, you must build the REAX library in lib/reax.
-You can do this manually if you prefer; follow the instructions in
-lib/reax/README. You can also do it in one step from the lammps/src
-dir, using a command like these, which simply invoke the
-lib/reax/Install.py script with the specified args:
-
-make lib-reax # print help message
-make lib-reax args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
-make lib-reax args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
-make lib-reax args="-m ifort" # build with Intel ifort compiler :pre
-
-The build should produce two files: lib/reax/libreax.a and
-lib/reax/Makefile.lammps. The latter is copied from an existing
-Makefile.lammps.* and has settings needed to link C++ (LAMMPS) with
-Fortran (REAX library). Typically the two compilers used for LAMMPS
-and the REAX library need to be consistent (e.g. both Intel or both
-GNU compilers). If necessary, you can edit/create a new
-lib/reax/Makefile.machine file for your system, which should define an
-EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
-file.
-
-:line
-
VORONOI package :h4,link(voronoi)
To build with this package, you must download and build the "Voro++
diff --git a/doc/src/Build_package.txt b/doc/src/Build_package.txt
index 82833b867c0129e32c4cd82f1a3365bea16e38f0..01c82d724e51a9d452415a495cba9633e048678a 100644
--- a/doc/src/Build_package.txt
+++ b/doc/src/Build_package.txt
@@ -47,7 +47,6 @@ packages:
"OPT"_Build_extras.html#opt,
"POEMS"_Build_extras.html#poems,
"PYTHON"_Build_extras.html#python,
-"REAX"_Build_extras.html#reax,
"VORONOI"_Build_extras.html#voronoi,
"USER-ATC"_Build_extras.html#user-atc,
"USER-AWPMD"_Build_extras.html#user-awpmd,
diff --git a/doc/src/Commands_fix.txt b/doc/src/Commands_fix.txt
index fb4515b486c9d368b6273c9609b9de365b39c23d..678cc9ba0dd857151073ac52408bae68124d2f4e 100644
--- a/doc/src/Commands_fix.txt
+++ b/doc/src/Commands_fix.txt
@@ -169,8 +169,7 @@ OPT.
"qmmm"_fix_qmmm.html,
"qtb"_fix_qtb.html,
"rattle"_fix_shake.html,
-"reax/bonds"_fix_reax_bonds.html,
-"reax/c/bonds (k)"_fix_reax_bonds.html,
+"reax/c/bonds (k)"_fix_reaxc_bonds.html,
"reax/c/species (k)"_fix_reaxc_species.html,
"recenter"_fix_recenter.html,
"restrain"_fix_restrain.html,
diff --git a/doc/src/Commands_pair.txt b/doc/src/Commands_pair.txt
index bf2b2b4f396f811b5a6f788569419e929496541a..2691ccaebfde6b21904b968d420701617b9173e0 100644
--- a/doc/src/Commands_pair.txt
+++ b/doc/src/Commands_pair.txt
@@ -160,8 +160,7 @@ OPT.
"lubricateU/poly"_pair_lubricateU.html,
"mdpd"_pair_meso.html,
"mdpd/rhosum"_pair_meso.html,
-"meam"_pair_meam.html,
-"meam/c"_pair_meam.html,
+"meam/c"_pair_meamc.html,
"meam/spline (o)"_pair_meam_spline.html,
"meam/sw/spline"_pair_meam_sw_spline.html,
"mgpt"_pair_mgpt.html,
@@ -194,7 +193,6 @@ OPT.
"polymorphic"_pair_polymorphic.html,
"python"_pair_python.html,
"quip"_pair_quip.html,
-"reax"_pair_reax.html,
"reax/c (ko)"_pair_reaxc.html,
"rebo (io)"_pair_airebo.html,
"resquared (go)"_pair_resquared.html,
diff --git a/doc/src/Install_windows.txt b/doc/src/Install_windows.txt
index df87754c5fcfc84bf9f55bc99679ffe8e4b793dd..0f306ec64cd6da700d58c65723028d6302f3d341 100644
--- a/doc/src/Install_windows.txt
+++ b/doc/src/Install_windows.txt
@@ -23,8 +23,8 @@ install the Windows MPI package (MPICH2 from Argonne National Labs),
needed to run in parallel.
The LAMMPS binaries contain all optional packages included in the
-source distribution except: KIM, REAX, KOKKOS, USER-INTEL,
-and USER-QMMM. The serial version also does not include the MPIIO and
+source distribution except: KIM, KOKKOS, USER-INTEL, and USER-QMMM.
+The serial version also does not include the MPIIO and
USER-LB packages. GPU support is provided for OpenCL.
The installer site also has instructions on how to run LAMMPS under
diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt
index 364ff3fe3034de8a08f9d4c91cb169219fafeb3f..4768c50ca47d8ad2d9f8ec0634e4bf43f5ac2031 100644
--- a/doc/src/Packages_details.txt
+++ b/doc/src/Packages_details.txt
@@ -45,7 +45,6 @@ as contained in the file name.
"LATTE"_#PKG-LATTE,
"MANYBODY"_#PKG-MANYBODY,
"MC"_#PKG-MC,
-"MEAM"_#PKG-MEAM,
"MESSAGE"_#PKG-MESSAGE,
"MISC"_#PKG-MISC,
"MOLECULE"_#PKG-MOLECULE,
@@ -56,7 +55,6 @@ as contained in the file name.
"POEMS"_#PKG-POEMS,
"PYTHON"_#PKG-PYTHON,
"QEQ"_#PKG-QEQ,
-"REAX"_#PKG-REAX,
"REPLICA"_#PKG-REPLICA2,
"RIGID"_#PKG-RIGID,
"SHOCK"_#PKG-SHOCK,
@@ -533,37 +531,6 @@ http://lammps.sandia.gov/movies.html#gcmc :ul
:line
-MEAM package :link(PKG-MEAM),h4
-
-[Contents:]
-
-A pair style for the modified embedded atom (MEAM) potential.
-
-Please note that the use of the MEAM package is discouraged as
-it has been superseded by the "USER-MEAMC"_#PKG-USER-MEAMC package,
-which is a direct translation of the MEAM package to C++.
-USER-MEAMC contains additional optimizations making it run faster
-than MEAM on most machines, while providing the identical features
-and user interface.
-
-[Author:] Greg Wagner (Northwestern U) while at Sandia.
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/MEAM: filenames -> commands
-src/meam/README
-lib/meam/README
-"pair_style meam"_pair_meam.html
-examples/meam :ul
-
-:line
-
MESSAGE package :link(PKG-MESSAGE),h4
[Contents:]
@@ -834,38 +801,6 @@ examples/streitz :ul
:line
-REAX package :link(PKG-REAX),h4
-
-[Contents:]
-
-NOTE: the use of the REAX package is discouraged, as it is no longer
-maintained. Please use the "USER-REAXC"_#PKG-USER-REAXC package instead,
-and possibly the KOKKOS enabled variant of that, which has a more robust
-memory management.
-
-A pair style which wraps a Fortran library which implements the ReaxFF
-potential, which is a universal reactive force field. Also included is
-a "fix reax/bonds"_fix_reax_bonds.html command for monitoring molecules
-as bonds are created and destroyed.
-
-[Author:] Aidan Thompson (Sandia).
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/REAX: filenames -> commands
-lib/reax/README
-"pair_style reax"_pair_reax.html
-"fix reax/bonds"_fix_reax_bonds.html
-examples/reax :ul
-
-:line
-
REPLICA package :link(PKG-REPLICA2),h4
[Contents:]
@@ -1552,10 +1487,9 @@ USER-MEAMC package :link(PKG-USER-MEAMC),h4
[Contents:]
A pair style for the modified embedded atom (MEAM) potential
-translated from the Fortran version in the "MEAM"_#PKG-MEAM package
-to plain C++. In contrast to the MEAM package, no library
-needs to be compiled and the pair style can be instantiated
-multiple times.
+translated from the Fortran version in the (obsolete) "MEAM" package
+to plain C++. The USER-MEAMC fully replaces the MEAM package, which
+has been removed from LAMMPS after the 12 December 2018 version.
[Author:] Sebastian Huetter, (Otto-von-Guericke University Magdeburg)
based on the Fortran version of Greg Wagner (Northwestern U) while at
@@ -1565,8 +1499,8 @@ Sandia.
src/USER-MEAMC: filenames -> commands
src/USER-MEAMC/README
-"pair_style meam/c"_pair_meam.html
-examples/meam :ul
+"pair_style meam/c"_pair_meamc.html
+examples/meamc :ul
:line
@@ -1894,9 +1828,8 @@ USER-REAXC package :link(PKG-USER-REAXC),h4
[Contents:]
-A pair style which implements the ReaxFF potential in C/C++ (in
-contrast to the "REAX package"_#PKG-REAX and its Fortran library). ReaxFF
-is universal reactive force field. See the src/USER-REAXC/README file
+A pair style which implements the ReaxFF potential in C/C++. ReaxFF
+is a universal reactive force field. See the src/USER-REAXC/README file
for more info on differences between the two packages. Also two fixes
for monitoring molecules as bonds are created and destroyed.
@@ -1907,7 +1840,7 @@ for monitoring molecules as bonds are created and destroyed.
src/USER-REAXC: filenames -> commands
src/USER-REAXC/README
"pair_style reax/c"_pair_reaxc.html
-"fix reax/c/bonds"_fix_reax_bonds.html
+"fix reax/c/bonds"_fix_reaxc_bonds.html
"fix reax/c/species"_fix_reaxc_species.html
examples/reax :ul
diff --git a/doc/src/Packages_standard.txt b/doc/src/Packages_standard.txt
index 583ecf39fe39ab603168d2956c9c4f2c035860c2..7fb1d99174abdba6121cb7097528385082e69425 100644
--- a/doc/src/Packages_standard.txt
+++ b/doc/src/Packages_standard.txt
@@ -46,7 +46,6 @@ Package, Description, Doc page, Example, Library
"LATTE"_Packages_details.html#PKG-LATTE, quantum DFTB forces via LATTE, "fix latte"_fix_latte.html, latte, ext
"MANYBODY"_Packages_details.html#PKG-MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, no
"MC"_Packages_details.html#PKG-MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, n/a, no
-"MEAM"_Packages_details.html#PKG-MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int
"MESSAGE"_Packages_details.html#PKG-MESSAGE, client/server messaging, "message"_message.html, message, int
"MISC"_Packages_details.html#PKG-MISC, miscellaneous single-file commands, n/a, no, no
"MOLECULE"_Packages_details.html#PKG-MOLECULE, molecular system force fields, "Howto bioFF"_Howto_bioFF.html, peptide, no
@@ -57,7 +56,6 @@ Package, Description, Doc page, Example, Library
"POEMS"_Packages_details.html#PKG-POEMS, coupled rigid body motion, "fix poems"_fix_poems.html, rigid, int
"PYTHON"_Packages_details.html#PKG-PYTHON, embed Python code in an input script, "python"_python.html, python, sys
"QEQ"_Packages_details.html#PKG-QEQ, QEq charge equilibration, "fix qeq"_fix_qeq.html, qeq, no
-"REAX"_Packages_details.html#PKG-REAX, ReaxFF potential (Fortran), "pair_style reax"_pair_reax.html, reax, int
"REPLICA"_Packages_details.html#PKG-REPLICA2, multi-replica methods, "Howto replica"_Howto_replica.html, tad, no
"RIGID"_Packages_details.html#PKG-RIGID, rigid bodies and constraints, "fix rigid"_fix_rigid.html, rigid, no
"SHOCK"_Packages_details.html#PKG-SHOCK, shock loading methods, "fix msst"_fix_msst.html, n/a, no
diff --git a/doc/src/Packages_user.txt b/doc/src/Packages_user.txt
index 077a7ce69dbafade4446726fdbba5b1b19c3dac2..cea3db4377411c05272bae170c09625678e46cf0 100644
--- a/doc/src/Packages_user.txt
+++ b/doc/src/Packages_user.txt
@@ -53,7 +53,7 @@ Package, Description, Doc page, Example, Library
"USER-INTEL"_Packages_details.html#PKG-USER-INTEL, optimized Intel CPU and KNL styles,"Speed intel"_Speed_intel.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no
"USER-LB"_Packages_details.html#PKG-USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, no
"USER-MANIFOLD"_Packages_details.html#PKG-USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, no
-"USER-MEAMC"_Packages_details.html#PKG-USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meam.html, meam, no
+"USER-MEAMC"_Packages_details.html#PKG-USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meamc.html, meamc, no
"USER-MESO"_Packages_details.html#PKG-USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, no
"USER-MGPT"_Packages_details.html#PKG-USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, no
"USER-MISC"_Packages_details.html#PKG-USER-MISC, single-file contributions, USER-MISC/README, USER/misc, no
diff --git a/doc/src/Tools.txt b/doc/src/Tools.txt
index 9204ae992aea299ddf4ba8b626c14e4464208cda..4002e471cf9eb6a2740e37683ddae1df3bf0a432 100644
--- a/doc/src/Tools.txt
+++ b/doc/src/Tools.txt
@@ -486,8 +486,8 @@ README for more info on Pizza.py and how to use these scripts.
reax tool :h4,link(reax_tool)
The reax sub-directory contains stand-alone codes that can
-post-process the output of the "fix reax/bonds"_fix_reax_bonds.html
-command from a LAMMPS simulation using "ReaxFF"_pair_reax.html. See
+post-process the output of the "fix reax/c/bonds"_fix_reaxc_bonds.html
+command from a LAMMPS simulation using "ReaxFF"_pair_reaxc.html. See
the README.txt file for more info.
These tools were written by Aidan Thompson at Sandia.
diff --git a/doc/src/compute_pair.txt b/doc/src/compute_pair.txt
index 1ced6eecfc09cfe3bcd45118c02c15f9b6753129..c1bd4f74d982f5299f4999a1b0ffcaf5eeccf504 100644
--- a/doc/src/compute_pair.txt
+++ b/doc/src/compute_pair.txt
@@ -24,7 +24,7 @@ nsub = {n}-instance of a sub-style, if a pair style is used multiple times in a
compute 1 all pair gauss
compute 1 all pair lj/cut/coul/cut ecoul
compute 1 all pair tersoff 2 epair
-compute 1 all pair reax :pre
+compute 1 all pair reax/c :pre
[Description:]
@@ -60,8 +60,8 @@ corrections, even if they are enabled via the
"pair_modify"_pair_modify.html command.
Some pair styles tally additional quantities, e.g. a breakdown of
-potential energy into a dozen or so components is tallied by the
-"pair_style reax"_pair_reax.html command. These values (1 or more)
+potential energy into 14 components is tallied by the "pair_style
+reax/c"_pair_reaxc.html command. These values (1 or more)
are stored as a global vector by this compute. See the doc page for
"individual pair styles"_pair_style.html for info on these values.
diff --git a/doc/src/fix.txt b/doc/src/fix.txt
index 916e9887f9f389171f58879caa819c4faaec17d9..395f2ad7a964c899b53726b044c5800e96ddc885 100644
--- a/doc/src/fix.txt
+++ b/doc/src/fix.txt
@@ -312,9 +312,8 @@ accelerated styles exist.
"qmmm"_fix_qmmm.html -
"qtb"_fix_qtb.html -
"rattle"_fix_shake.html - RATTLE constraints on bonds and/or angles
-"reax/bonds"_fix_reax_bonds.html - write out ReaxFF bond information
-"reax/c/bonds"_fix_reax_bonds.html -
-"reax/c/species"_fix_reaxc_species.html -
+"reax/c/bonds"_fix_reaxc_bonds.html - write out ReaxFF bond information
+"reax/c/species"_fix_reaxc_species.html - write out ReaxFF molecule information
"recenter"_fix_recenter.html - constrain the center-of-mass position of a group of atoms
"restrain"_fix_restrain.html - constrain a bond, angle, dihedral
"rhok"_fix_rhok.html -
diff --git a/doc/src/fix_reax_bonds.txt b/doc/src/fix_reaxc_bonds.txt
similarity index 78%
rename from doc/src/fix_reax_bonds.txt
rename to doc/src/fix_reaxc_bonds.txt
index 06d30d871adbc423057799f1469aba3d50c505ff..9cd4ed7610cf926f6fe709f048ec77a4a19b576e 100644
--- a/doc/src/fix_reax_bonds.txt
+++ b/doc/src/fix_reaxc_bonds.txt
@@ -6,13 +6,12 @@
:line
-fix reax/bonds command :h3
fix reax/c/bonds command :h3
fix reax/c/bonds/kk command :h3
[Syntax:]
-fix ID group-ID reax/bonds Nevery filename :pre
+fix ID group-ID reaxc/bonds Nevery filename :pre
ID, group-ID are documented in "fix"_fix.html command
reax/bonds = style name of this fix command
@@ -21,16 +20,14 @@ filename = name of output file :ul
[Examples:]
-fix 1 all reax/bonds 100 bonds.tatb
fix 1 all reax/c/bonds 100 bonds.reaxc :pre
[Description:]
-Write out the bond information computed by the ReaxFF potential
-specified by "pair_style reax"_pair_reax.html or "pair_style
-reax/c"_pair_reaxc.html in the exact same format as the original
-stand-alone ReaxFF code of Adri van Duin. The bond information is
-written to {filename} on timesteps that are multiples of {Nevery},
+Write out the bond information computed by the ReaxFF potential specified
+by "pair_style reax/c"_pair_reaxc.html in the exact same format as the
+original stand-alone ReaxFF code of Adri van Duin. The bond information
+is written to {filename} on timesteps that are multiples of {Nevery},
including timestep 0. For time-averaged chemical species analysis,
please see the "fix reaxc/c/species"_fix_reaxc_species.html command.
@@ -94,12 +91,8 @@ more instructions on how to use the accelerated styles effectively.
[Restrictions:]
-The fix reax/bonds command requires that the "pair_style
-reax"_pair_reax.html be invoked. This fix is part of the REAX
-package. It is only enabled if LAMMPS was built with that package,
-which also requires the REAX library be built and linked with LAMMPS.
The fix reax/c/bonds command requires that the "pair_style
-reax/c"_pair_reaxc.html be invoked. This fix is part of the
+reax/c"_pair_reaxc.html is invoked. This fix is part of the
USER-REAXC package. It is only enabled if LAMMPS was built with that
package. See the "Build package"_Build_package.html doc page for more
info.
@@ -109,7 +102,6 @@ To write gzipped bond files, you must compile LAMMPS with the
[Related commands:]
-"pair_style reax"_pair_reax.html, "pair_style
-reax/c"_pair_reaxc.html, "fix reax/c/species"_fix_reaxc_species.html
+"pair_style reax/c"_pair_reaxc.html, "fix reax/c/species"_fix_reaxc_species.html
[Default:] none
diff --git a/doc/src/fix_reaxc_species.txt b/doc/src/fix_reaxc_species.txt
index 980384ff34c778e6ee3246c91762faff19b9e37e..60fa3a1d700bcec0162fa5b99cad54bfce738ae4 100644
--- a/doc/src/fix_reaxc_species.txt
+++ b/doc/src/fix_reaxc_species.txt
@@ -161,7 +161,7 @@ more instructions on how to use the accelerated styles effectively.
[Restrictions:]
-The fix species currently only works with "pair_style
+The "fix reax/c/species" currently only works with "pair_style
reax/c"_pair_reaxc.html and it requires that the "pair_style
reax/c"_pair_reaxc.html be invoked. This fix is part of the
USER-REAXC package. It is only enabled if LAMMPS was built with that
@@ -177,8 +177,7 @@ It should be possible to extend it to other reactive pair_styles (such as
[Related commands:]
-"pair_style reax/c"_pair_reaxc.html, "fix
-reax/bonds"_fix_reax_bonds.html
+"pair_style reax/c"_pair_reaxc.html, "fix reax/c/bonds"_fix_reaxc_bonds.html
[Default:]
diff --git a/doc/src/fixes.txt b/doc/src/fixes.txt
index eb52583dce95e217be8c397a261c8620757590a6..3853bb77a9655069cbf8176d96431821a6bc0663 100644
--- a/doc/src/fixes.txt
+++ b/doc/src/fixes.txt
@@ -135,7 +135,7 @@ Fixes :h1
fix_qeq_reax
fix_qmmm
fix_qtb
- fix_reax_bonds
+ fix_reaxc_bonds
fix_reaxc_species
fix_recenter
fix_restrain
diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index 3ec314e09e30e71da020a7b717c1a8cf3091a259..d752d2a929ddba2dec3544d58a71b54485840ad8 100644
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@@ -356,7 +356,7 @@ fix_qeq_comb.html
fix_qeq_reax.html
fix_qmmm.html
fix_qtb.html
-fix_reax_bonds.html
+fix_reaxc_bonds.html
fix_reaxc_species.html
fix_recenter.html
fix_restrain.html
@@ -598,7 +598,7 @@ pair_lj_soft.html
pair_lubricate.html
pair_lubricateU.html
pair_mdf.html
-pair_meam.html
+pair_meamc.html
pair_meam_spline.html
pair_meam_sw_spline.html
pair_meso.html
@@ -617,7 +617,6 @@ pair_peri.html
pair_polymorphic.html
pair_python.html
pair_quip.html
-pair_reax.html
pair_reaxc.html
pair_resquared.html
pair_sdk.html
diff --git a/doc/src/pair_hybrid.txt b/doc/src/pair_hybrid.txt
index 59af479b9fca19ff218a4ef40aef974b682b616b..4467ac1d51f00a6623153c6c3c45b715080bad01 100644
--- a/doc/src/pair_hybrid.txt
+++ b/doc/src/pair_hybrid.txt
@@ -70,15 +70,10 @@ other pairwise potential for several different atom type pairs in your
model, then you should just list the sub-style once and use the
pair_coeff command to assign parameters for the different type pairs.
-NOTE: There are two exceptions to this option to list an individual
-pair style multiple times. The first is for pair styles implemented
-as Fortran libraries: "pair_style meam"_pair_meam.html and "pair_style
-reax"_pair_reax.html ("pair_style reax/c"_pair_reaxc.html is OK).
-This is because unlike a C++ class, they can not be instantiated
-multiple times, due to the manner in which they were coded in Fortran.
-The second is for GPU-enabled pair styles in the GPU package. This is
-b/c the GPU package also currently assumes that only one instance of a
-pair style is being used.
+NOTE: There is one exception to this option to list an individual
+pair style multiple times: GPU-enabled pair styles in the GPU package.
+This is because the GPU package currently assumes that only one
+instance of a pair style is being used.
In the pair_coeff commands, the name of a pair style must be added
after the I,J type specification, with the remaining coefficients
diff --git a/doc/src/pair_meam_spline.txt b/doc/src/pair_meam_spline.txt
index 74adba243291f8d1f8afd86ce795b2e90a4befb5..7a185b4d55a5fbce4b467474f818bc3eda5308d8 100644
--- a/doc/src/pair_meam_spline.txt
+++ b/doc/src/pair_meam_spline.txt
@@ -152,7 +152,7 @@ info.
[Related commands:]
-"pair_coeff"_pair_coeff.html, "pair_style meam"_pair_meam.html
+"pair_coeff"_pair_coeff.html, "pair_style meam/c"_pair_meamc.html
[Default:] none
diff --git a/doc/src/pair_meam_sw_spline.txt b/doc/src/pair_meam_sw_spline.txt
index 77322953cf6557665436c304533107114ef7f423..a9ad3484d3f72dd15b0fdb28d24d51214d85affa 100644
--- a/doc/src/pair_meam_sw_spline.txt
+++ b/doc/src/pair_meam_sw_spline.txt
@@ -116,7 +116,7 @@ info.
[Related commands:]
-"pair_coeff"_pair_coeff.html, "pair_style meam"_pair_meam.html,
+"pair_coeff"_pair_coeff.html, "pair_style meam/c"_pair_meamc.html,
"pair_style meam/spline"_pair_meam_spline.html
[Default:] none
diff --git a/doc/src/pair_meam.txt b/doc/src/pair_meamc.txt
similarity index 95%
rename from doc/src/pair_meam.txt
rename to doc/src/pair_meamc.txt
index b4893d1db1381a7ed571f2ee68cdac1385816fce..b57339b1800d271c0be3e5b514743c130a0e8438 100644
--- a/doc/src/pair_meam.txt
+++ b/doc/src/pair_meamc.txt
@@ -6,18 +6,17 @@
:line
-pair_style meam command :h3
pair_style meam/c command :h3
[Syntax:]
pair_style style :pre
-style = {meam} or {meam/c}
+style = {meam/c}
[Examples:]
-pair_style meam
+pair_style meam/c
pair_coeff * * ../potentials/library.meam Si ../potentials/si.meam Si
pair_coeff * * ../potentials/library.meam Ni Al NULL Ni Al Ni Ni :pre
@@ -27,14 +26,16 @@ NOTE: The behavior of the MEAM potential for alloy systems has changed
as of November 2010; see description below of the mixture_ref_t
parameter
-Style {meam} computes pairwise interactions for a variety of materials
+Style {meam/c} computes pairwise interactions for a variety of materials
using modified embedded-atom method (MEAM) potentials
"(Baskes)"_#Baskes. Conceptually, it is an extension to the original
"EAM potentials"_pair_eam.html which adds angular forces. It is
thus suitable for modeling metals and alloys with fcc, bcc, hcp and
diamond cubic structures, as well as covalently bonded materials like
-silicon and carbon. Style {meam/c} is a translation of the {meam} code
-from (mostly) Fortran to C++. It is functionally equivalent to {meam}.
+silicon and carbon. Style {meam/c} is a translation of the (now obsolete)
+{meam} code from Fortran to C++. It is functionally equivalent to {meam}
+but more efficient, and thus {meam} has been removed from LAMMPS after
+the 12 December 2018 release.
In the MEAM formulation, the total energy E of a system of atoms is
given by:
@@ -352,13 +353,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
-The {meam} style is part of the MEAM package. It is only enabled if
-LAMMPS was built with that package, which also requires the MEAM
-library be built and linked with LAMMPS. The {meam/c} style is
-provided in the USER-MEAMC package. It is only enabled if LAMMPS was
-built with that package. In contrast to the {meam} style, {meam/c}
-does not require a separate library to be compiled and it can be
-instantiated multiple times in a "hybrid"_pair_hybrid.html pair style.
+The {meam/c} style is provided in the USER-MEAMC package. It is
+only enabled if LAMMPS was built with that package.
See the "Build package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_reax.txt b/doc/src/pair_reax.txt
deleted file mode 100644
index a3b84955cd058937fd28cb84732656e2f3f055ef..0000000000000000000000000000000000000000
--- a/doc/src/pair_reax.txt
+++ /dev/null
@@ -1,216 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-pair_style reax command :h3
-
-[Syntax:]
-
-pair_style reax hbcut hbnewflag tripflag precision :pre
-
-hbcut = hydrogen-bond cutoff (optional) (distance units)
-hbnewflag = use old or new hbond function style (0 or 1) (optional)
-tripflag = apply stabilization to all triple bonds (0 or 1) (optional)
-precision = precision for charge equilibration (optional) :ul
-
-[Examples:]
-
-pair_style reax
-pair_style reax 10.0 0 1 1.0e-5
-pair_coeff * * ffield.reax 3 1 2 2
-pair_coeff * * ffield.reax 3 NULL NULL 3 :pre
-
-[Description:]
-
-Style {reax} computes the ReaxFF potential of van Duin, Goddard and
-co-workers. ReaxFF uses distance-dependent bond-order functions to
-represent the contributions of chemical bonding to the potential
-energy. There is more than one version of ReaxFF. The version
-implemented in LAMMPS uses the functional forms documented in the
-supplemental information of the following paper:
-"(Chenoweth)"_#Chenoweth_20081. The version integrated into LAMMPS matches
-the most up-to-date version of ReaxFF as of summer 2010.
-
-WARNING: pair style reax is now deprecated and will soon be retired. Users
-should switch to "pair_style reax/c"_pair_reaxc.html. The {reax} style
-differs from the {reax/c} style in the lo-level implementation details.
-The {reax} style is a
-Fortran library, linked to LAMMPS. The {reax/c} style was initially
-implemented as stand-alone C code and is now integrated into LAMMPS as
-a package.
-
-LAMMPS requires that a file called ffield.reax be provided, containing
-the ReaxFF parameters for each atom type, bond type, etc. The format
-is identical to the ffield file used by van Duin and co-workers. The
-filename is required as an argument in the pair_coeff command. Any
-value other than "ffield.reax" will be rejected (see below).
-
-LAMMPS provides several different versions of ffield.reax in its
-potentials dir, each called potentials/ffield.reax.label. These are
-documented in potentials/README.reax. The default ffield.reax
-contains parameterizations for the following elements: C, H, O, N.
-
-NOTE: We do not distribute a wide variety of ReaxFF force field files
-with LAMMPS. Adri van Duin's group at PSU is the central repository
-for this kind of data as they are continuously deriving and updating
-parameterizations for different classes of materials. You can submit
-a contact request at the Materials Computation Center (MCC) website
-"https://www.mri.psu.edu/materials-computation-center/connect-mcc"_https://www.mri.psu.edu/materials-computation-center/connect-mcc,
-describing the material(s) you are interested in modeling with ReaxFF.
-They can tell
-you what is currently available or what it would take to create a
-suitable ReaxFF parameterization.
-
-The format of these files is identical to that used originally by van
-Duin. We have tested the accuracy of {pair_style reax} potential
-against the original ReaxFF code for the systems mentioned above. You
-can use other ffield files for specific chemical systems that may be
-available elsewhere (but note that their accuracy may not have been
-tested).
-
-The {hbcut}, {hbnewflag}, {tripflag}, and {precision} settings are
-optional arguments. If none are provided, default settings are used:
-{hbcut} = 6 (which is Angstroms in real units), {hbnewflag} = 1 (use
-new hbond function style), {tripflag} = 1 (apply stabilization to all
-triple bonds), and {precision} = 1.0e-6 (one part in 10^6). If you
-wish to override any of these defaults, then all of the settings must
-be specified.
-
-Two examples using {pair_style reax} are provided in the examples/reax
-sub-directory, along with corresponding examples for
-"pair_style reax/c"_pair_reaxc.html. Note that while the energy and force
-calculated by both of these pair styles match very closely, the
-contributions due to the valence angles differ slightly due to
-the fact that with {pair_style reax/c} the default value of {thb_cutoff_sq}
-is 0.00001, while for {pair_style reax} it is hard-coded to be 0.001.
-
-Use of this pair style requires that a charge be defined for every
-atom since the {reax} pair style performs a charge equilibration (QEq)
-calculation. See the "atom_style"_atom_style.html and
-"read_data"_read_data.html commands for details on how to specify
-charges.
-
-The thermo variable {evdwl} stores the sum of all the ReaxFF potential
-energy contributions, with the exception of the Coulombic and charge
-equilibration contributions which are stored in the thermo variable
-{ecoul}. The output of these quantities is controlled by the
-"thermo"_thermo.html command.
-
-This pair style tallies a breakdown of the total ReaxFF potential
-energy into sub-categories, which can be accessed via the "compute
-pair"_compute_pair.html command as a vector of values of length 14.
-The 14 values correspond to the following sub-categories (the variable
-names in italics match those used in the ReaxFF FORTRAN library):
-
-{eb} = bond energy
-{ea} = atom energy
-{elp} = lone-pair energy
-{emol} = molecule energy (always 0.0)
-{ev} = valence angle energy
-{epen} = double-bond valence angle penalty
-{ecoa} = valence angle conjugation energy
-{ehb} = hydrogen bond energy
-{et} = torsion energy
-{eco} = conjugation energy
-{ew} = van der Waals energy
-{ep} = Coulomb energy
-{efi} = electric field energy (always 0.0)
-{eqeq} = charge equilibration energy :ol
-
-To print these quantities to the log file (with descriptive column
-headings) the following commands could be included in an input script:
-
-compute reax all pair reax
-variable eb equal c_reax\[1\]
-variable ea equal c_reax\[2\]
-...
-variable eqeq equal c_reax\[14\]
-thermo_style custom step temp epair v_eb v_ea ... v_eqeq :pre
-
-Only a single pair_coeff command is used with the {reax} style which
-specifies a ReaxFF potential file with parameters for all needed
-elements. These are mapped to LAMMPS atom types by specifying N
-additional arguments after the filename in the pair_coeff command,
-where N is the number of LAMMPS atom types:
-
-filename
-N indices = mapping of ReaxFF elements to atom types :ul
-
-The specification of the filename and the mapping of LAMMPS atom types
-recognized by the ReaxFF is done differently than for other LAMMPS
-potentials, due to the non-portable difficulty of passing character
-strings (e.g. filename, element names) between C++ and Fortran.
-
-The filename has to be "ffield.reax" and it has to exist in the
-directory you are running LAMMPS in. This means you cannot prepend a
-path to the file in the potentials dir. Rather, you should copy that
-file into the directory you are running from. If you wish to use
-another ReaxFF potential file, then name it "ffield.reax" and put it
-in the directory you run from.
-
-In the ReaxFF potential file, near the top, after the general
-parameters, is the atomic parameters section that contains element
-names, each with a couple dozen numeric parameters. If there are M
-elements specified in the {ffield} file, think of these as numbered 1
-to M. Each of the N indices you specify for the N atom types of LAMMPS
-atoms must be an integer from 1 to M. Atoms with LAMMPS type 1 will
-be mapped to whatever element you specify as the first index value,
-etc. If a mapping value is specified as NULL, the mapping is not
-performed. This can be used when a ReaxFF potential is used as part
-of the {hybrid} pair style. The NULL values are placeholders for atom
-types that will be used with other potentials.
-
-NOTE: Currently the reax pair style cannot be used as part of the
-{hybrid} pair style. Some additional changes still need to be made to
-enable this.
-
-As an example, say your LAMMPS simulation has 4 atom types and the
-elements are ordered as C, H, O, N in the {ffield} file. If you want
-the LAMMPS atom type 1 and 2 to be C, type 3 to be N, and type 4 to be
-H, you would use the following pair_coeff command:
-
-pair_coeff * * ffield.reax 1 1 4 2 :pre
-
-:line
-
-[Mixing, shift, table, tail correction, restart, rRESPA info]:
-
-This pair style does not support the "pair_modify"_pair_modify.html
-mix, shift, table, and tail options.
-
-This pair style does not write its information to "binary restart
-files"_restart.html, since it is stored in potential files. Thus, you
-need to re-specify the pair_style and pair_coeff commands in an input
-script that reads a restart file.
-
-This pair style can only be used via the {pair} keyword of the
-"run_style respa"_run_style.html command. It does not support the
-{inner}, {middle}, {outer} keywords.
-
-[Restrictions:]
-
-The ReaxFF potential files provided with LAMMPS in the potentials
-directory are parameterized for real "units"_units.html. You can use
-the ReaxFF potential with any LAMMPS units, but you would need to
-create your own potential file with coefficients listed in the
-appropriate units if your simulation doesn't use "real" units.
-
-[Related commands:]
-
-"pair_coeff"_pair_coeff.html, "pair_style reax/c"_pair_reaxc.html,
-"fix_reax_bonds"_fix_reax_bonds.html
-
-[Default:]
-
-The keyword defaults are {hbcut} = 6, {hbnewflag} = 1, {tripflag} = 1,
-{precision} = 1.0e-6.
-
-:line
-
-:link(Chenoweth_20081)
-[(Chenoweth_2008)] Chenoweth, van Duin and Goddard,
-Journal of Physical Chemistry A, 112, 1040-1053 (2008).
diff --git a/doc/src/pair_reaxc.txt b/doc/src/pair_reaxc.txt
index e63f4a90eef6a957787fabcfa43084c00d090ff7..37482beacf90bd73a15d9723dc1dd64781a3f457 100644
--- a/doc/src/pair_reaxc.txt
+++ b/doc/src/pair_reaxc.txt
@@ -37,7 +37,7 @@ pair_coeff * * ffield.reax C H O N :pre
Style {reax/c} computes the ReaxFF potential of van Duin, Goddard and
co-workers. ReaxFF uses distance-dependent bond-order functions to
represent the contributions of chemical bonding to the potential
-energy. There is more than one version of ReaxFF. The version
+energy. There is more than one version of ReaxFF. The version
implemented in LAMMPS uses the functional forms documented in the
supplemental information of the following paper: "(Chenoweth et al.,
2008)"_#Chenoweth_20082. The version integrated into LAMMPS matches
@@ -56,11 +56,10 @@ consideration when using the {reax/c/kk} style is the choice of either
half or full neighbor lists. This setting can be changed using the
Kokkos "package"_package.html command.
-The {reax/c} style differs from the "pair_style reax"_pair_reax.html
-command in the lo-level implementation details. The {reax} style is a
-Fortran library, linked to LAMMPS. The {reax/c} style was initially
-implemented as stand-alone C code and is now integrated into LAMMPS as
-a package.
+The {reax/c} style differs from the (obsolete) "pair_style reax"
+command in the implementation details. The {reax} style was a
+Fortran library, linked to LAMMPS. The {reax} style has been removed
+from LAMMPS after the 12 December 2018 version.
LAMMPS provides several different versions of ffield.reax in its
potentials dir, each called potentials/ffield.reax.label. These are
@@ -98,9 +97,8 @@ correspond to those used by Adri van Duin's stand-alone serial
code. If these are changed by setting control variables in the control
file, the results from LAMMPS and the serial code will not agree.
-Two examples using {pair_style reax/c} are provided in the examples/reax
-sub-directory, along with corresponding examples for
-"pair_style reax"_pair_reax.html.
+Examples using {pair_style reax/c} are provided in the examples/reax
+sub-directory.
Use of this pair style requires that a charge be defined for every
atom. See the "atom_style"_atom_style.html and
@@ -193,8 +191,7 @@ where N is the number of LAMMPS atom types:
filename
N indices = ReaxFF elements :ul
-The filename is the ReaxFF potential file. Unlike for the {reax}
-pair style, any filename can be used.
+The filename is the ReaxFF potential file.
In the ReaxFF potential file, near the top, after the general
parameters, is the atomic parameters section that contains element
@@ -337,9 +334,8 @@ appropriate units if your simulation doesn't use "real" units.
[Related commands:]
"pair_coeff"_pair_coeff.html, "fix qeq/reax"_fix_qeq_reax.html, "fix
-reax/c/bonds"_fix_reax_bonds.html, "fix
-reax/c/species"_fix_reaxc_species.html, "pair_style
-reax"_pair_reax.html
+reax/c/bonds"_fix_reaxc_bonds.html, "fix
+reax/c/species"_fix_reaxc_species.html
[Default:]
diff --git a/doc/src/pair_style.txt b/doc/src/pair_style.txt
index 46a4f31dd4fc4a55661108ce41e95a381abc67f8..ea746f89438c1388cbc2ff608b4740e99cfc2745 100644
--- a/doc/src/pair_style.txt
+++ b/doc/src/pair_style.txt
@@ -226,8 +226,7 @@ accelerated styles exist.
"lubricateU/poly"_pair_lubricateU.html - hydrodynamic lubrication forces for Fast Lubrication with polydispersity
"mdpd"_pair_meso.html - mDPD particle interactions
"mdpd/rhosum"_pair_meso.html - mDPD particle interactions for mass density
-"meam"_pair_meam.html - modified embedded atom method (MEAM) in Fortran
-"meam/c"_pair_meam.html - modified embedded atom method (MEAM) in C
+"meam/c"_pair_meamc.html - modified embedded atom method (MEAM) in C
"meam/spline"_pair_meam_spline.html - splined version of MEAM
"meam/sw/spline"_pair_meam_sw_spline.html - splined version of MEAM with a Stillinger-Weber term
"mgpt"_pair_mgpt.html - simplified model generalized pseudopotential theory (MGPT) potential
@@ -260,7 +259,6 @@ accelerated styles exist.
"polymorphic"_pair_polymorphic.html - polymorphic 3-body potential
"python"_pair_python.html -
"quip"_pair_quip.html -
-"reax"_pair_reax.html - ReaxFF potential in Fortran
"reax/c"_pair_reaxc.html - ReaxFF potential in C
"rebo"_pair_airebo.html - 2nd generation REBO potential of Brenner
"resquared"_pair_resquared.html - Everaers RE-Squared ellipsoidal potential
diff --git a/doc/src/pairs.txt b/doc/src/pairs.txt
index ca7905105330f811f7d1388a5a3710dddb89191f..7a7ad86d0d80975c93e85cd0b84c19de51819ea6 100644
--- a/doc/src/pairs.txt
+++ b/doc/src/pairs.txt
@@ -63,7 +63,7 @@ Pair Styles :h1
pair_lubricate
pair_lubricateU
pair_mdf
- pair_meam
+ pair_meamc
pair_meam_spline
pair_meam_sw_spline
pair_meso
@@ -82,7 +82,6 @@ Pair Styles :h1
pair_polymorphic
pair_python
pair_quip
- pair_reax
pair_reaxc
pair_resquared
pair_sdk
diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt
index faa74ca0ddf9f3f76659f2e63634275768f4c3ab..b90df965e6bb7fc43f0c43f4776eb0a2742d9c7d 100644
--- a/doc/utils/sphinx-config/false_positives.txt
+++ b/doc/utils/sphinx-config/false_positives.txt
@@ -1522,6 +1522,7 @@ mdf
mdpd
mDPD
meam
+meamc
MEAMC
meamf
meanDist
diff --git a/examples/meam/in.meam b/examples/meam/in.meam
deleted file mode 100644
index b4463be365a3fe172a7f3f72f90080099560e25a..0000000000000000000000000000000000000000
--- a/examples/meam/in.meam
+++ /dev/null
@@ -1,30 +0,0 @@
-# Test of MEAM potential for SiC system
-
-units metal
-boundary p p p
-
-atom_style atomic
-
-read_data data.meam
-
-pair_style meam
-pair_coeff * * library.meam Si C SiC.meam Si C
-
-neighbor 0.3 bin
-neigh_modify delay 10
-
-fix 1 all nve
-thermo 10
-timestep 0.001
-
-#dump 1 all atom 50 dump.meam
-
-#dump 2 all image 10 image.*.jpg element element &
-# axes yes 0.8 0.02 view 60 -30
-#dump_modify 2 pad 3 element Si C
-
-#dump 3 all movie 10 movie.mpg element element &
-# axes yes 0.8 0.02 view 60 -30
-#dump_modify 3 pad 3 element Si C
-
-run 100
diff --git a/examples/meam/log.27Nov18.meam.g++.1 b/examples/meam/log.27Nov18.meam.g++.1
deleted file mode 100644
index 502d91992344fc312e6baf7ea66cab11bfdf77b9..0000000000000000000000000000000000000000
--- a/examples/meam/log.27Nov18.meam.g++.1
+++ /dev/null
@@ -1,96 +0,0 @@
-LAMMPS (27 Nov 2018)
- using 1 OpenMP thread(s) per MPI task
-# Test of MEAM potential for SiC system
-
-units metal
-boundary p p p
-
-atom_style atomic
-
-read_data data.meam
- orthogonal box = (-6 -6 -6) to (5.97232 5.97232 5.97232)
- 1 by 1 by 1 MPI processor grid
- reading atoms ...
- 128 atoms
-
-pair_style meam
-WARNING: THE pair_style meam COMMAND IS OBSOLETE AND WILL BE REMOVED VERY SOON. PLEASE USE meam/c (src/MEAM/pair_meam.cpp:51)
-pair_coeff * * library.meam Si C SiC.meam Si C
-Reading potential file library.meam with DATE: 2012-06-29
-Reading potential file SiC.meam with DATE: 2007-06-11
-
-neighbor 0.3 bin
-neigh_modify delay 10
-
-fix 1 all nve
-thermo 10
-timestep 0.001
-
-#dump 1 all atom 50 dump.meam
-
-#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
-#dump_modify 2 pad 3 element Si C
-
-#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
-#dump_modify 3 pad 3 element Si C
-
-run 100
-Neighbor list info ...
- update every 1 steps, delay 10 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 4.3
- ghost atom cutoff = 4.3
- binsize = 2.15, bins = 6 6 6
- 2 neighbor lists, perpetual/occasional/extra = 2 0 0
- (1) pair meam, perpetual
- attributes: full, newton on
- pair build: full/bin/atomonly
- stencil: full/bin/3d
- bin: standard
- (2) pair meam, perpetual, half/full from (1)
- attributes: half, newton on
- pair build: halffull/newton
- stencil: none
- bin: none
-Per MPI rank memory allocation (min/avg/max) = 8.103 | 8.103 | 8.103 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 0 -636.38121 0 -636.38121 -76571.819
- 10 1807.8862 -666.21959 0 -636.54126 -150571.49
- 20 1932.4467 -668.2581 0 -636.53498 -120223.52
- 30 1951.3652 -668.58139 0 -636.54771 -100508.4
- 40 2172.5974 -672.22715 0 -636.5617 -110753.34
- 50 2056.9149 -670.33108 0 -636.56468 -105418.07
- 60 1947.9564 -668.52788 0 -636.55015 -111413.04
- 70 1994.7712 -669.28849 0 -636.54225 -109645.76
- 80 2126.0903 -671.43755 0 -636.53557 -97475.831
- 90 2065.755 -670.4349 0 -636.52338 -95858.837
- 100 2051.4553 -670.20799 0 -636.53122 -107068.9
-Loop time of 0.0545483 on 1 procs for 100 steps with 128 atoms
-
-Performance: 158.392 ns/day, 0.152 hours/ns, 1833.239 timesteps/s
-99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.050821 | 0.050821 | 0.050821 | 0.0 | 93.17
-Neigh | 0.0026484 | 0.0026484 | 0.0026484 | 0.0 | 4.86
-Comm | 0.0006423 | 0.0006423 | 0.0006423 | 0.0 | 1.18
-Output | 0.00011492 | 0.00011492 | 0.00011492 | 0.0 | 0.21
-Modify | 0.00021195 | 0.00021195 | 0.00021195 | 0.0 | 0.39
-Other | | 0.0001101 | | | 0.20
-
-Nlocal: 128 ave 128 max 128 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 543 ave 543 max 543 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 1526 ave 1526 max 1526 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs: 3052 ave 3052 max 3052 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 3052
-Ave neighs/atom = 23.8438
-Neighbor list builds = 10
-Dangerous builds = 10
-Total wall time: 0:00:00
diff --git a/examples/meam/log.27Nov18.meam.g++.4 b/examples/meam/log.27Nov18.meam.g++.4
deleted file mode 100644
index d02591e1221594bf84bb2c991e762bd51cbd9966..0000000000000000000000000000000000000000
--- a/examples/meam/log.27Nov18.meam.g++.4
+++ /dev/null
@@ -1,96 +0,0 @@
-LAMMPS (27 Nov 2018)
- using 1 OpenMP thread(s) per MPI task
-# Test of MEAM potential for SiC system
-
-units metal
-boundary p p p
-
-atom_style atomic
-
-read_data data.meam
- orthogonal box = (-6 -6 -6) to (5.97232 5.97232 5.97232)
- 1 by 2 by 2 MPI processor grid
- reading atoms ...
- 128 atoms
-
-pair_style meam
-WARNING: THE pair_style meam COMMAND IS OBSOLETE AND WILL BE REMOVED VERY SOON. PLEASE USE meam/c (src/MEAM/pair_meam.cpp:51)
-pair_coeff * * library.meam Si C SiC.meam Si C
-Reading potential file library.meam with DATE: 2012-06-29
-Reading potential file SiC.meam with DATE: 2007-06-11
-
-neighbor 0.3 bin
-neigh_modify delay 10
-
-fix 1 all nve
-thermo 10
-timestep 0.001
-
-#dump 1 all atom 50 dump.meam
-
-#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
-#dump_modify 2 pad 3 element Si C
-
-#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
-#dump_modify 3 pad 3 element Si C
-
-run 100
-Neighbor list info ...
- update every 1 steps, delay 10 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 4.3
- ghost atom cutoff = 4.3
- binsize = 2.15, bins = 6 6 6
- 2 neighbor lists, perpetual/occasional/extra = 2 0 0
- (1) pair meam, perpetual
- attributes: full, newton on
- pair build: full/bin/atomonly
- stencil: full/bin/3d
- bin: standard
- (2) pair meam, perpetual, half/full from (1)
- attributes: half, newton on
- pair build: halffull/newton
- stencil: none
- bin: none
-Per MPI rank memory allocation (min/avg/max) = 8.024 | 8.026 | 8.027 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 0 -636.38121 0 -636.38121 -76571.819
- 10 1807.8862 -666.21959 0 -636.54126 -150571.49
- 20 1932.4467 -668.2581 0 -636.53498 -120223.52
- 30 1951.3652 -668.58139 0 -636.54771 -100508.4
- 40 2172.5974 -672.22715 0 -636.5617 -110753.34
- 50 2056.9149 -670.33108 0 -636.56468 -105418.07
- 60 1947.9564 -668.52788 0 -636.55015 -111413.04
- 70 1994.7712 -669.28849 0 -636.54225 -109645.76
- 80 2126.0903 -671.43755 0 -636.53557 -97475.831
- 90 2065.755 -670.4349 0 -636.52338 -95858.837
- 100 2051.4553 -670.20799 0 -636.53122 -107068.9
-Loop time of 0.023721 on 4 procs for 100 steps with 128 atoms
-
-Performance: 364.234 ns/day, 0.066 hours/ns, 4215.667 timesteps/s
-95.5% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.019888 | 0.020242 | 0.020626 | 0.2 | 85.33
-Neigh | 0.00071859 | 0.00076133 | 0.00082922 | 0.0 | 3.21
-Comm | 0.0019681 | 0.0022618 | 0.002651 | 0.5 | 9.53
-Output | 0.00018048 | 0.0002225 | 0.00034213 | 0.0 | 0.94
-Modify | 8.2016e-05 | 8.6308e-05 | 9.203e-05 | 0.0 | 0.36
-Other | | 0.000147 | | | 0.62
-
-Nlocal: 32 ave 36 max 30 min
-Histogram: 1 2 0 0 0 0 0 0 0 1
-Nghost: 293.75 ave 305 max 285 min
-Histogram: 2 0 0 0 0 0 0 1 0 1
-Neighs: 381.5 ave 413 max 334 min
-Histogram: 1 0 0 0 1 0 0 0 0 2
-FullNghs: 763 ave 866 max 678 min
-Histogram: 1 0 1 0 0 1 0 0 0 1
-
-Total # of neighbors = 3052
-Ave neighs/atom = 23.8438
-Neighbor list builds = 10
-Dangerous builds = 10
-Total wall time: 0:00:00
diff --git a/examples/meam/log.27Nov18.meam.shear.g++.1 b/examples/meam/log.27Nov18.meam.shear.g++.1
deleted file mode 100644
index 8eab38bc707ada1464fec0886758f33971b8c52d..0000000000000000000000000000000000000000
--- a/examples/meam/log.27Nov18.meam.shear.g++.1
+++ /dev/null
@@ -1,209 +0,0 @@
-LAMMPS (27 Nov 2018)
- using 1 OpenMP thread(s) per MPI task
-# 3d metal shear simulation
-
-units metal
-boundary s s p
-
-atom_style atomic
-lattice fcc 3.52
-Lattice spacing in x,y,z = 3.52 3.52 3.52
-region box block 0 16.0 0 10.0 0 2.828427
-create_box 3 box
-Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
- 1 by 1 by 1 MPI processor grid
-
-lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0
-Lattice spacing in x,y,z = 3.52 4.97803 4.97803
-create_atoms 1 box
-Created 1912 atoms
- Time spent = 0.0007267 secs
-
-pair_style meam
-WARNING: THE pair_style meam COMMAND IS OBSOLETE AND WILL BE REMOVED VERY SOON. PLEASE USE meam/c (src/MEAM/pair_meam.cpp:51)
-pair_coeff * * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4
-Reading potential file library.meam with DATE: 2012-06-29
-Reading potential file Ni.meam with DATE: 2007-06-11
-
-neighbor 0.3 bin
-neigh_modify delay 5
-
-region lower block INF INF INF 0.9 INF INF
-region upper block INF INF 6.1 INF INF INF
-group lower region lower
-264 atoms in group lower
-group upper region upper
-264 atoms in group upper
-group boundary union lower upper
-528 atoms in group boundary
-group mobile subtract all boundary
-1384 atoms in group mobile
-
-set group lower type 2
- 264 settings made for type
-set group upper type 3
- 264 settings made for type
-
-# void
-
-#region void cylinder z 8 5 2.5 INF INF
-#delete_atoms region void
-
-# temp controllers
-
-compute new3d mobile temp
-compute new2d mobile temp/partial 0 1 1
-
-# equilibrate
-
-velocity mobile create 300.0 5812775 temp new3d
-fix 1 all nve
-fix 2 boundary setforce 0.0 0.0 0.0
-
-fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
-fix_modify 3 temp new3d
-
-thermo 25
-thermo_modify temp new3d
-WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)
-
-timestep 0.001
-run 100
-Neighbor list info ...
- update every 1 steps, delay 5 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 4.3
- ghost atom cutoff = 4.3
- binsize = 2.15, bins = 27 17 5
- 2 neighbor lists, perpetual/occasional/extra = 2 0 0
- (1) pair meam, perpetual
- attributes: full, newton on
- pair build: full/bin/atomonly
- stencil: full/bin/3d
- bin: standard
- (2) pair meam, perpetual, half/full from (1)
- attributes: half, newton on
- pair build: halffull/newton
- stencil: none
- bin: none
-Per MPI rank memory allocation (min/avg/max) = 9.788 | 9.788 | 9.788 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 0 300 -8232.7767 0 -8179.1466 1386.6643 19547.02
- 25 222.78953 -8188.1215 0 -8148.2941 9095.9008 19547.02
- 50 300 -8149.7654 0 -8096.1353 10633.141 19684.382
- 75 304.80657 -8163.4557 0 -8108.9665 7045.457 19759.745
- 100 300 -8173.6884 0 -8120.0584 5952.521 19886.589
-Loop time of 0.894544 on 1 procs for 100 steps with 1912 atoms
-
-Performance: 9.659 ns/day, 2.485 hours/ns, 111.789 timesteps/s
-99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.87012 | 0.87012 | 0.87012 | 0.0 | 97.27
-Neigh | 0.01798 | 0.01798 | 0.01798 | 0.0 | 2.01
-Comm | 0.0016143 | 0.0016143 | 0.0016143 | 0.0 | 0.18
-Output | 0.00011492 | 0.00011492 | 0.00011492 | 0.0 | 0.01
-Modify | 0.0035381 | 0.0035381 | 0.0035381 | 0.0 | 0.40
-Other | | 0.001176 | | | 0.13
-
-Nlocal: 1912 ave 1912 max 1912 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 1672 ave 1672 max 1672 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 23806 ave 23806 max 23806 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs: 47612 ave 47612 max 47612 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 47612
-Ave neighs/atom = 24.9017
-Neighbor list builds = 5
-Dangerous builds = 0
-
-# shear
-
-velocity upper set 1.0 0 0
-velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
-
-unfix 3
-fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
-fix_modify 3 temp new2d
-
-#dump 1 all atom 500 dump.meam.shear
-
-#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
-#dump_modify 2 pad 4
-
-#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
-#dump_modify 3 pad 4
-
-thermo 100
-thermo_modify temp new2d
-WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)
-
-reset_timestep 0
-run 3000
-Per MPI rank memory allocation (min/avg/max) = 9.964 | 9.964 | 9.964 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 0 300.39988 -8173.6884 0 -8137.8874 4992.9811 19894.297
- 100 292.06374 -8177.7096 0 -8142.9021 2568.3762 19871.53
- 200 306.69894 -8177.1357 0 -8140.584 874.24259 20047.24
- 300 295.68229 -8172.9213 0 -8137.6825 -1049.0836 20091.759
- 400 308.99958 -8169.6355 0 -8132.8096 -1785.9335 20121.698
- 500 303.85723 -8163.984 0 -8127.7709 -150.56268 20183.813
- 600 300 -8157.7632 0 -8122.0099 1492.5742 20279.887
- 700 300 -8148.1328 0 -8112.3794 3506.9234 20435.302
- 800 300 -8139.1821 0 -8103.4288 3628.3957 20509.519
- 900 305.03425 -8126.7734 0 -8090.4201 5316.2206 20638.992
- 1000 304.00321 -8112.1616 0 -8075.9311 7441.9638 20767.243
- 1100 304.14041 -8096.5041 0 -8060.2573 9646.6972 20888.167
- 1200 302.78454 -8080.5931 0 -8044.5079 11516.208 20995.917
- 1300 308.67064 -8061.6724 0 -8024.8857 11496.471 21130.013
- 1400 309.82994 -8046.27 0 -8009.3451 12926.819 21247.271
- 1500 300 -8035.0317 0 -7999.2784 15346.797 21370.637
- 1600 300 -8030.6636 0 -7994.9102 14803.43 21496.446
- 1700 300 -8024.4819 0 -7988.7286 13175.257 21611.262
- 1800 300 -8022.8531 0 -7987.0998 10315.63 21743.178
- 1900 300 -8028.4095 0 -7992.6561 6882.0635 21855.551
- 2000 300 -8036.9005 0 -8001.1472 3508.9237 21983.802
- 2100 300 -8037.8224 0 -8002.0691 2724.0594 22112.054
- 2200 306.93248 -8035.3297 0 -7998.7501 4400.6008 22228.091
- 2300 306.24125 -8036.748 0 -8000.2508 6075.0546 22352.678
- 2400 300 -8038.8534 0 -8003.1 8701.8498 22465.051
- 2500 308.34129 -8034.0796 0 -7997.3322 10977.68 22600.632
- 2600 299.70072 -8028.8815 0 -7993.1638 15468.97 22715.447
- 2700 298.78276 -8019.1655 0 -7983.5572 18076.132 22844.921
- 2800 305.57845 -8014.3542 0 -7977.936 17573.035 22962.179
- 2900 300 -8015.7677 0 -7980.0144 13461.463 23087.988
- 3000 300 -8010.5908 0 -7974.8375 9333.4855 23199.139
-Loop time of 29.4592 on 1 procs for 3000 steps with 1912 atoms
-
-Performance: 8.799 ns/day, 2.728 hours/ns, 101.836 timesteps/s
-99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 28.489 | 28.489 | 28.489 | 0.0 | 96.71
-Neigh | 0.77356 | 0.77356 | 0.77356 | 0.0 | 2.63
-Comm | 0.052517 | 0.052517 | 0.052517 | 0.0 | 0.18
-Output | 0.00095224 | 0.00095224 | 0.00095224 | 0.0 | 0.00
-Modify | 0.10813 | 0.10813 | 0.10813 | 0.0 | 0.37
-Other | | 0.03525 | | | 0.12
-
-Nlocal: 1912 ave 1912 max 1912 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 1668 ave 1668 max 1668 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 23391 ave 23391 max 23391 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs: 46782 ave 46782 max 46782 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 46782
-Ave neighs/atom = 24.4676
-Neighbor list builds = 219
-Dangerous builds = 0
-Total wall time: 0:00:30
diff --git a/examples/meam/log.27Nov18.meam.shear.g++.4 b/examples/meam/log.27Nov18.meam.shear.g++.4
deleted file mode 100644
index 708e470925d56ff4eb7d06312ea91f42f692cf75..0000000000000000000000000000000000000000
--- a/examples/meam/log.27Nov18.meam.shear.g++.4
+++ /dev/null
@@ -1,209 +0,0 @@
-LAMMPS (27 Nov 2018)
- using 1 OpenMP thread(s) per MPI task
-# 3d metal shear simulation
-
-units metal
-boundary s s p
-
-atom_style atomic
-lattice fcc 3.52
-Lattice spacing in x,y,z = 3.52 3.52 3.52
-region box block 0 16.0 0 10.0 0 2.828427
-create_box 3 box
-Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
- 2 by 2 by 1 MPI processor grid
-
-lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0
-Lattice spacing in x,y,z = 3.52 4.97803 4.97803
-create_atoms 1 box
-Created 1912 atoms
- Time spent = 0.000408649 secs
-
-pair_style meam
-WARNING: THE pair_style meam COMMAND IS OBSOLETE AND WILL BE REMOVED VERY SOON. PLEASE USE meam/c (src/MEAM/pair_meam.cpp:51)
-pair_coeff * * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4
-Reading potential file library.meam with DATE: 2012-06-29
-Reading potential file Ni.meam with DATE: 2007-06-11
-
-neighbor 0.3 bin
-neigh_modify delay 5
-
-region lower block INF INF INF 0.9 INF INF
-region upper block INF INF 6.1 INF INF INF
-group lower region lower
-264 atoms in group lower
-group upper region upper
-264 atoms in group upper
-group boundary union lower upper
-528 atoms in group boundary
-group mobile subtract all boundary
-1384 atoms in group mobile
-
-set group lower type 2
- 264 settings made for type
-set group upper type 3
- 264 settings made for type
-
-# void
-
-#region void cylinder z 8 5 2.5 INF INF
-#delete_atoms region void
-
-# temp controllers
-
-compute new3d mobile temp
-compute new2d mobile temp/partial 0 1 1
-
-# equilibrate
-
-velocity mobile create 300.0 5812775 temp new3d
-fix 1 all nve
-fix 2 boundary setforce 0.0 0.0 0.0
-
-fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
-fix_modify 3 temp new3d
-
-thermo 25
-thermo_modify temp new3d
-WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)
-
-timestep 0.001
-run 100
-Neighbor list info ...
- update every 1 steps, delay 5 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 4.3
- ghost atom cutoff = 4.3
- binsize = 2.15, bins = 27 17 5
- 2 neighbor lists, perpetual/occasional/extra = 2 0 0
- (1) pair meam, perpetual
- attributes: full, newton on
- pair build: full/bin/atomonly
- stencil: full/bin/3d
- bin: standard
- (2) pair meam, perpetual, half/full from (1)
- attributes: half, newton on
- pair build: halffull/newton
- stencil: none
- bin: none
-Per MPI rank memory allocation (min/avg/max) = 8.954 | 8.957 | 8.959 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 0 300 -8232.7767 0 -8179.1466 1386.6643 19547.02
- 25 221.59546 -8187.6813 0 -8148.0673 9100.4509 19547.02
- 50 300 -8150.0685 0 -8096.4384 10317.407 19685.743
- 75 307.76021 -8164.6669 0 -8109.6496 6289.7138 19757.814
- 100 300 -8176.5141 0 -8122.884 4162.2559 19873.327
-Loop time of 0.263516 on 4 procs for 100 steps with 1912 atoms
-
-Performance: 32.787 ns/day, 0.732 hours/ns, 379.483 timesteps/s
-98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.24401 | 0.2486 | 0.25128 | 0.6 | 94.34
-Neigh | 0.0046518 | 0.0047416 | 0.0048261 | 0.1 | 1.80
-Comm | 0.0054512 | 0.0082117 | 0.012793 | 3.1 | 3.12
-Output | 0.00010562 | 0.00013095 | 0.00019932 | 0.0 | 0.05
-Modify | 0.0010016 | 0.0010275 | 0.0010595 | 0.1 | 0.39
-Other | | 0.0008045 | | | 0.31
-
-Nlocal: 478 ave 492 max 465 min
-Histogram: 2 0 0 0 0 0 0 0 1 1
-Nghost: 809 ave 822 max 795 min
-Histogram: 1 1 0 0 0 0 0 0 0 2
-Neighs: 5916 ave 6133 max 5658 min
-Histogram: 1 0 0 1 0 0 0 0 1 1
-FullNghs: 11832 ave 12277 max 11299 min
-Histogram: 1 0 0 1 0 0 0 0 1 1
-
-Total # of neighbors = 47328
-Ave neighs/atom = 24.7531
-Neighbor list builds = 5
-Dangerous builds = 0
-
-# shear
-
-velocity upper set 1.0 0 0
-velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
-
-unfix 3
-fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
-fix_modify 3 temp new2d
-
-#dump 1 all atom 500 dump.meam.shear
-
-#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
-#dump_modify 2 pad 4
-
-#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
-#dump_modify 3 pad 4
-
-thermo 100
-thermo_modify temp new2d
-WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)
-
-reset_timestep 0
-run 3000
-Per MPI rank memory allocation (min/avg/max) = 8.999 | 9.002 | 9.005 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 0 295.32113 -8176.5141 0 -8141.3183 3169.3113 19886.93
- 100 292.00251 -8176.5358 0 -8141.7356 -825.04802 19918.765
- 200 306.11682 -8176.7719 0 -8140.2895 -1370.6886 19948.877
- 300 300 -8172.6262 0 -8136.8729 -1735.9765 20085.714
- 400 306.88489 -8168.435 0 -8131.8611 -933.02058 20117.012
- 500 308.99003 -8166.2906 0 -8129.4658 -1049.3138 20198.256
- 600 304.23435 -8158.0946 0 -8121.8366 583.93595 20328.848
- 700 296.44479 -8149.7914 0 -8114.4618 1985.4155 20421.046
- 800 307.75738 -8139.1649 0 -8102.487 4319.078 20513.183
- 900 304.61422 -8126.9246 0 -8090.6214 6654.0962 20640.213
- 1000 300 -8113.8464 0 -8078.0931 7760.1237 20768.465
- 1100 300.17873 -8097.7469 0 -8061.9722 8438.1259 20874.731
- 1200 306.01441 -8083.3367 0 -8046.8665 10835.588 20994.432
- 1300 300 -8067.022 0 -8031.2687 11216.061 21126.348
- 1400 300 -8053.223 0 -8017.4696 10570.211 21253.378
- 1500 300 -8043.4848 0 -8007.7314 11360.762 21375.523
- 1600 300 -8034.6201 0 -7998.8667 11371.282 21498.889
- 1700 300 -8028.6797 0 -7992.9263 9596.8454 21613.705
- 1800 300 -8033.0802 0 -7997.3268 8767.8176 21743.178
- 1900 303.23288 -8035.1821 0 -7999.0434 8065.2879 21859.215
- 2000 300 -8025.0795 0 -7989.3262 9321.8098 21980.138
- 2100 300 -8041.3621 0 -8005.6088 6674.2623 22108.39
- 2200 300 -8039.7261 0 -8003.9727 7548.8847 22225.648
- 2300 300 -8052.3497 0 -8016.5964 8936.4935 22352.678
- 2400 300 -8049.395 0 -8013.6416 12633.909 22476.044
- 2500 308.48099 -8039.9448 0 -8003.1807 16242.081 22593.303
- 2600 300 -8032.1953 0 -7996.442 18386.669 22722.776
- 2700 303.49413 -8027.6563 0 -7991.4865 14415.581 22829.042
- 2800 304.13476 -8017.3394 0 -7981.0933 7457.1076 22953.629
- 2900 300 -8010.3658 0 -7974.6124 2815.5155 23074.552
- 3000 309.49253 -7999.74 0 -7962.8553 756.7511 23210.132
-Loop time of 8.57528 on 4 procs for 3000 steps with 1912 atoms
-
-Performance: 30.226 ns/day, 0.794 hours/ns, 349.843 timesteps/s
-98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 8.0046 | 8.0451 | 8.1075 | 1.5 | 93.82
-Neigh | 0.20142 | 0.20699 | 0.21469 | 1.2 | 2.41
-Comm | 0.1972 | 0.2657 | 0.312 | 9.3 | 3.10
-Output | 0.00087762 | 0.0015897 | 0.0037148 | 3.1 | 0.02
-Modify | 0.030267 | 0.031624 | 0.032929 | 0.7 | 0.37
-Other | | 0.02427 | | | 0.28
-
-Nlocal: 478 ave 507 max 447 min
-Histogram: 1 1 0 0 0 0 0 0 1 1
-Nghost: 799.75 ave 842 max 763 min
-Histogram: 2 0 0 0 0 0 0 1 0 1
-Neighs: 5806.5 ave 6097 max 5507 min
-Histogram: 1 0 1 0 0 0 0 1 0 1
-FullNghs: 11613 ave 12159 max 11039 min
-Histogram: 1 0 1 0 0 0 0 1 0 1
-
-Total # of neighbors = 46452
-Ave neighs/atom = 24.295
-Neighbor list builds = 224
-Dangerous builds = 0
-Total wall time: 0:00:08
diff --git a/examples/reax/README b/examples/reax/README
index fe9d33df94cbfb2e93980648f47b957e0a790a89..e839f0ea9926d52d734e8cb20abda4c879532529 100644
--- a/examples/reax/README
+++ b/examples/reax/README
@@ -1,12 +1,8 @@
This directory contains input files for two short ReaxFF simulations
(RDX and TATB crystals) using the ReaxFF parameterization developed
for nitramines. The parameter file ffield.reax is the same as that in
-subdirectory RDX (see below). Input files for both pair_style reax and
-pair_style reax/c are provided.
-
-In addition, each subdirectory contains validated parameter files for
-a particular published version of ReaxFF. In all cases, the examples
-use pair_style reax/c.
+subdirectory RDX (see below). In addition, each subdirectory contains
+validated parameter files for a particular published version of ReaxFF.
Disclaimer: Using these force fields for systems they have not been
explicitly trained against may produce unrealistic results. Please
diff --git a/examples/reax/in.reax.rdx b/examples/reax/in.reax.rdx
deleted file mode 100644
index 768b8e454665fdaeace6737efc9b0fb138c2ad10..0000000000000000000000000000000000000000
--- a/examples/reax/in.reax.rdx
+++ /dev/null
@@ -1,52 +0,0 @@
-# ReaxFF potential for RDX system
-
-units real
-
-atom_style charge
-read_data data.rdx
-
-# reax args: hbcut hbnewflag tripflag precision
-
-pair_style reax 6.0 1 1 1.0e-6
-pair_coeff * * ffield.reax 1 2 3 4
-
-compute reax all pair reax
-
-variable eb equal c_reax[1]
-variable ea equal c_reax[2]
-variable elp equal c_reax[3]
-variable emol equal c_reax[4]
-variable ev equal c_reax[5]
-variable epen equal c_reax[6]
-variable ecoa equal c_reax[7]
-variable ehb equal c_reax[8]
-variable et equal c_reax[9]
-variable eco equal c_reax[10]
-variable ew equal c_reax[11]
-variable ep equal c_reax[12]
-variable efi equal c_reax[13]
-variable eqeq equal c_reax[14]
-
-neighbor 2.5 bin
-neigh_modify every 10 delay 0 check no
-
-fix 1 all nve
-
-thermo 10
-thermo_style custom step temp epair etotal press &
- v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb &
- v_et v_eco v_ew v_ep v_efi v_eqeq
-
-timestep 1.0
-
-#dump 1 all custom 10 dump.reax.rdx id type q xs ys zs
-
-#dump 2 all image 25 image.*.jpg type type &
-# axes yes 0.8 0.02 view 60 -30
-#dump_modify 2 pad 3
-
-#dump 3 all movie 25 movie.mpg type type &
-# axes yes 0.8 0.02 view 60 -30
-#dump_modify 3 pad 3
-
-run 100
diff --git a/examples/reax/in.reax.tatb b/examples/reax/in.reax.tatb
deleted file mode 100644
index a9a4cd9e5e2b553536cfd10264a67a50ca7ee34e..0000000000000000000000000000000000000000
--- a/examples/reax/in.reax.tatb
+++ /dev/null
@@ -1,53 +0,0 @@
-# ReaxFF potential for TATB system
-
-units real
-
-atom_style charge
-read_data data.tatb
-
-# reax args: hbcut hbnewflag tripflag precision
-pair_style reax 6.0 1 1 1.0e-6
-pair_coeff * * ffield.reax 1 2 3 4
-
-compute reax all pair reax
-
-variable eb equal c_reax[1]
-variable ea equal c_reax[2]
-variable elp equal c_reax[3]
-variable emol equal c_reax[4]
-variable ev equal c_reax[5]
-variable epen equal c_reax[6]
-variable ecoa equal c_reax[7]
-variable ehb equal c_reax[8]
-variable et equal c_reax[9]
-variable eco equal c_reax[10]
-variable ew equal c_reax[11]
-variable ep equal c_reax[12]
-variable efi equal c_reax[13]
-variable eqeq equal c_reax[14]
-
-neighbor 2.5 bin
-neigh_modify delay 0 every 5 check no
-
-fix 1 all nve
-
-thermo 5
-thermo_style custom step temp epair etotal press &
- v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa &
- v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
-
-timestep 0.0625
-
-#dump 1 all custom 100 dump.reax.tatb id type q x y z
-
-#dump 2 all image 5 image.*.jpg type type &
-# axes yes 0.8 0.02 view 60 -30
-#dump_modify 2 pad 3
-
-#dump 3 all movie 5 movie.mpg type type &
-# axes yes 0.8 0.02 view 60 -30
-#dump_modify 3 pad 3
-
-fix 2 all reax/bonds 25 bonds.reax.tatb
-
-run 25
diff --git a/examples/reax/log.8March18.reax.rdx.g++.1 b/examples/reax/log.8March18.reax.rdx.g++.1
deleted file mode 100644
index c2edc5d51f33667e51e4c38c778cfe19cbc49d94..0000000000000000000000000000000000000000
--- a/examples/reax/log.8March18.reax.rdx.g++.1
+++ /dev/null
@@ -1,107 +0,0 @@
-LAMMPS (8 Mar 2018)
- using 1 OpenMP thread(s) per MPI task
-# ReaxFF potential for RDX system
-
-units real
-
-atom_style charge
-read_data data.rdx
- orthogonal box = (35 35 35) to (48 48 48)
- 1 by 1 by 1 MPI processor grid
- reading atoms ...
- 21 atoms
-
-# reax args: hbcut hbnewflag tripflag precision
-
-pair_style reax 6.0 1 1 1.0e-6
-WARNING: The pair_style reax command is unsupported. Please switch to pair_style reax/c instead (../pair_reax.cpp:49)
-pair_coeff * * ffield.reax 1 2 3 4
-
-compute reax all pair reax
-
-variable eb equal c_reax[1]
-variable ea equal c_reax[2]
-variable elp equal c_reax[3]
-variable emol equal c_reax[4]
-variable ev equal c_reax[5]
-variable epen equal c_reax[6]
-variable ecoa equal c_reax[7]
-variable ehb equal c_reax[8]
-variable et equal c_reax[9]
-variable eco equal c_reax[10]
-variable ew equal c_reax[11]
-variable ep equal c_reax[12]
-variable efi equal c_reax[13]
-variable eqeq equal c_reax[14]
-
-neighbor 2.5 bin
-neigh_modify every 10 delay 0 check no
-
-fix 1 all nve
-
-thermo 10
-thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
-
-timestep 1.0
-
-#dump 1 all custom 10 dump.reax.rdx id type q xs ys zs
-
-#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
-#dump_modify 2 pad 3
-
-#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
-#dump_modify 3 pad 3
-
-run 100
-Neighbor list info ...
- update every 10 steps, delay 0 steps, check no
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 12.5
- ghost atom cutoff = 12.5
- binsize = 6.25, bins = 3 3 3
- 1 neighbor lists, perpetual/occasional/extra = 1 0 0
- (1) pair reax, perpetual
- attributes: half, newton off
- pair build: half/bin/newtoff
- stencil: half/bin/3d/newtoff
- bin: standard
-Per MPI rank memory allocation (min/avg/max) = 3.278 | 3.278 | 3.278 Mbytes
-Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
- 0 0 -1885.1269 -1885.1269 27233.074 -2958.4712 79.527715 0.31082031 0 97.771125 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79973 0 168.8842
- 10 1281.7558 -1989.1322 -1912.7188 -19609.913 -2733.8828 -15.775275 0.20055725 0 55.02023 3.1070523 -77.710916 0 14.963568 -5.8082203 843.41939 -180.17724 0 107.5115
- 20 516.83079 -1941.677 -1910.8655 -12525.412 -2801.8626 7.410797 0.073134186 0 81.986983 0.2281551 -57.494871 0 30.656735 -10.102557 877.78695 -158.93385 0 88.574159
- 30 467.26411 -1940.978 -1913.1215 -35957.489 -2755.021 -6.9179958 0.049322453 0 78.853173 0.13604393 -51.653635 0 19.862871 -9.7098575 853.79334 -151.232 0 80.86177
- 40 647.45528 -1951.1994 -1912.6006 -5883.713 -2798.3556 17.334814 0.15102862 0 63.235117 0.18070924 -54.598957 0 17.325007 -12.052278 883.0167 -164.21335 0 96.777424
- 50 716.38088 -1949.4735 -1906.7656 5473.1969 -2800.9309 9.2056861 0.15413274 0 85.371466 3.2986127 -78.253597 0 34.861774 -8.553123 882.01431 -193.85254 0 117.21068
- 60 1175.2705 -1975.961 -1905.8958 -1939.4966 -2726.5816 -11.651996 0.24296786 0 48.320654 7.1799691 -75.363638 0 16.520127 -4.8869441 844.75401 -194.23297 0 119.73841
- 70 1156.701 -1975.3497 -1906.3916 24628.304 -2880.5225 25.652501 0.26894311 0 83.724852 7.1049152 -68.70096 0 24.750735 -8.6338267 911.20079 -183.40562 0 113.21047
- 80 840.23677 -1955.4769 -1905.3851 -17731.334 -2755.7299 -8.0167723 0.1386797 0 86.147417 2.2387319 -76.945843 0 23.595869 -7.260968 853.63487 -167.88288 0 94.603961
- 90 365.79122 -1926.4061 -1904.599 898.38479 -2842.1832 47.368107 0.23109002 0 92.288071 0.38031213 -61.361485 0 18.476336 -12.25546 900.24233 -186.48046 0 116.88827
- 100 801.32158 -1953.418 -1905.6462 -2417.6887 -2802.7247 4.6676477 0.18046575 0 76.729987 5.4177322 -77.102566 0 24.997175 -7.7554074 898.67337 -196.89114 0 120.38946
-Loop time of 0.463306 on 1 procs for 100 steps with 21 atoms
-
-Performance: 18.649 ns/day, 1.287 hours/ns, 215.840 timesteps/s
-99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.46143 | 0.46143 | 0.46143 | 0.0 | 99.60
-Neigh | 0.00087953 | 0.00087953 | 0.00087953 | 0.0 | 0.19
-Comm | 0.00042653 | 0.00042653 | 0.00042653 | 0.0 | 0.09
-Output | 0.00034237 | 0.00034237 | 0.00034237 | 0.0 | 0.07
-Modify | 0.00010109 | 0.00010109 | 0.00010109 | 0.0 | 0.02
-Other | | 0.000124 | | | 0.03
-
-Nlocal: 21 ave 21 max 21 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 546 ave 546 max 546 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 1106 ave 1106 max 1106 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 1106
-Ave neighs/atom = 52.6667
-Neighbor list builds = 10
-Dangerous builds not checked
-Total wall time: 0:00:00
diff --git a/examples/reax/log.8March18.reax.rdx.g++.4 b/examples/reax/log.8March18.reax.rdx.g++.4
deleted file mode 100644
index 9526e2566191d08f59bf3fcc6839808e12a8650c..0000000000000000000000000000000000000000
--- a/examples/reax/log.8March18.reax.rdx.g++.4
+++ /dev/null
@@ -1,107 +0,0 @@
-LAMMPS (8 Mar 2018)
- using 1 OpenMP thread(s) per MPI task
-# ReaxFF potential for RDX system
-
-units real
-
-atom_style charge
-read_data data.rdx
- orthogonal box = (35 35 35) to (48 48 48)
- 1 by 2 by 2 MPI processor grid
- reading atoms ...
- 21 atoms
-
-# reax args: hbcut hbnewflag tripflag precision
-
-pair_style reax 6.0 1 1 1.0e-6
-WARNING: The pair_style reax command is unsupported. Please switch to pair_style reax/c instead (../pair_reax.cpp:49)
-pair_coeff * * ffield.reax 1 2 3 4
-
-compute reax all pair reax
-
-variable eb equal c_reax[1]
-variable ea equal c_reax[2]
-variable elp equal c_reax[3]
-variable emol equal c_reax[4]
-variable ev equal c_reax[5]
-variable epen equal c_reax[6]
-variable ecoa equal c_reax[7]
-variable ehb equal c_reax[8]
-variable et equal c_reax[9]
-variable eco equal c_reax[10]
-variable ew equal c_reax[11]
-variable ep equal c_reax[12]
-variable efi equal c_reax[13]
-variable eqeq equal c_reax[14]
-
-neighbor 2.5 bin
-neigh_modify every 10 delay 0 check no
-
-fix 1 all nve
-
-thermo 10
-thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
-
-timestep 1.0
-
-#dump 1 all custom 10 dump.reax.rdx id type q xs ys zs
-
-#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
-#dump_modify 2 pad 3
-
-#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
-#dump_modify 3 pad 3
-
-run 100
-Neighbor list info ...
- update every 10 steps, delay 0 steps, check no
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 12.5
- ghost atom cutoff = 12.5
- binsize = 6.25, bins = 3 3 3
- 1 neighbor lists, perpetual/occasional/extra = 1 0 0
- (1) pair reax, perpetual
- attributes: half, newton off
- pair build: half/bin/newtoff
- stencil: half/bin/3d/newtoff
- bin: standard
-Per MPI rank memory allocation (min/avg/max) = 3.262 | 3.36 | 3.647 Mbytes
-Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
- 0 0 -1885.1268 -1885.1268 27233.074 -2958.4712 79.527715 0.31082031 0 97.771125 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79972 0 168.88428
- 10 1281.7558 -1989.1322 -1912.7187 -19609.913 -2733.8828 -15.775275 0.20055725 0 55.020231 3.1070523 -77.710916 0 14.963568 -5.8082203 843.41939 -180.17724 0 107.51152
- 20 516.83079 -1941.677 -1910.8655 -12525.412 -2801.8626 7.410797 0.073134187 0 81.986983 0.2281551 -57.494871 0 30.656735 -10.102557 877.78695 -158.93385 0 88.574168
- 30 467.26411 -1940.978 -1913.1215 -35957.489 -2755.021 -6.9179959 0.049322449 0 78.853173 0.13604392 -51.653635 0 19.862871 -9.7098575 853.79334 -151.232 0 80.861765
- 40 647.45479 -1951.1995 -1912.6007 -5883.7199 -2798.3556 17.334805 0.15102868 0 63.235116 0.18070946 -54.59897 0 17.32501 -12.052277 883.0166 -164.21339 0 96.777473
- 50 716.37927 -1949.466 -1906.7582 5473.2486 -2800.9309 9.2056758 0.15413278 0 85.37143 3.2986099 -78.253596 0 34.861773 -8.5531243 882.01424 -193.85223 0 117.21791
- 60 1175.2698 -1975.9612 -1905.896 -1939.5206 -2726.5818 -11.651942 0.24296793 0 48.320679 7.1799538 -75.36365 0 16.520134 -4.8869515 844.75405 -194.23289 0 119.7383
- 70 1156.6963 -1975.3494 -1906.3915 24628.423 -2880.5221 25.65242 0.26894312 0 83.724787 7.1049615 -68.700925 0 24.750729 -8.6338123 911.2006 -183.40591 0 113.21091
- 80 840.238 -1955.4788 -1905.387 -17731.371 -2755.7301 -8.0167357 0.13868007 0 86.147246 2.2387405 -76.945868 0 23.595868 -7.2609697 853.6349 -167.88312 0 94.602512
- 90 365.78645 -1926.4072 -1904.6004 898.36945 -2842.1831 47.368307 0.23108998 0 92.288039 0.38031101 -61.361464 0 18.476388 -12.255481 900.24216 -186.48066 0 116.88716
- 100 801.31322 -1953.4165 -1905.6452 -2417.2041 -2802.7247 4.6678077 0.18046498 0 76.730367 5.4176812 -77.102592 0 24.9973 -7.7554425 898.6732 -196.89097 0 120.39043
-Loop time of 0.404551 on 4 procs for 100 steps with 21 atoms
-
-Performance: 21.357 ns/day, 1.124 hours/ns, 247.188 timesteps/s
-97.4% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.2191 | 0.28038 | 0.39839 | 13.2 | 69.31
-Neigh | 5.8651e-05 | 0.00025928 | 0.00062203 | 0.0 | 0.06
-Comm | 0.0046599 | 0.12307 | 0.1845 | 19.9 | 30.42
-Output | 0.00055337 | 0.00062728 | 0.00071192 | 0.0 | 0.16
-Modify | 5.3167e-05 | 7.844e-05 | 0.00010109 | 0.0 | 0.02
-Other | | 0.0001363 | | | 0.03
-
-Nlocal: 5.25 ave 15 max 0 min
-Histogram: 1 0 2 0 0 0 0 0 0 1
-Nghost: 355.5 ave 432 max 282 min
-Histogram: 1 0 0 0 1 1 0 0 0 1
-Neighs: 301.25 ave 827 max 0 min
-Histogram: 1 0 2 0 0 0 0 0 0 1
-
-Total # of neighbors = 1205
-Ave neighs/atom = 57.381
-Neighbor list builds = 10
-Dangerous builds not checked
-Total wall time: 0:00:00
diff --git a/examples/reax/log.8March18.reax.tatb.g++.1 b/examples/reax/log.8March18.reax.tatb.g++.1
deleted file mode 100644
index 53d77cd1da8a10d5c5ecf42a23a819aa8d55a203..0000000000000000000000000000000000000000
--- a/examples/reax/log.8March18.reax.tatb.g++.1
+++ /dev/null
@@ -1,103 +0,0 @@
-LAMMPS (8 Mar 2018)
- using 1 OpenMP thread(s) per MPI task
-# ReaxFF potential for TATB system
-
-units real
-
-atom_style charge
-read_data data.tatb
- triclinic box = (0 0 0) to (13.624 17.1149 15.1826) with tilt (-5.75316 -6.32547 7.42573)
- 1 by 1 by 1 MPI processor grid
- reading atoms ...
- 384 atoms
-
-# reax args: hbcut hbnewflag tripflag precision
-pair_style reax 6.0 1 1 1.0e-6
-WARNING: The pair_style reax command is unsupported. Please switch to pair_style reax/c instead (../pair_reax.cpp:49)
-pair_coeff * * ffield.reax 1 2 3 4
-
-compute reax all pair reax
-
-variable eb equal c_reax[1]
-variable ea equal c_reax[2]
-variable elp equal c_reax[3]
-variable emol equal c_reax[4]
-variable ev equal c_reax[5]
-variable epen equal c_reax[6]
-variable ecoa equal c_reax[7]
-variable ehb equal c_reax[8]
-variable et equal c_reax[9]
-variable eco equal c_reax[10]
-variable ew equal c_reax[11]
-variable ep equal c_reax[12]
-variable efi equal c_reax[13]
-variable eqeq equal c_reax[14]
-
-neighbor 2.5 bin
-neigh_modify delay 0 every 5 check no
-
-fix 1 all nve
-
-thermo 5
-thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
-
-timestep 0.0625
-
-#dump 1 all custom 100 dump.reax.tatb id type q x y z
-
-#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
-#dump_modify 2 pad 3
-
-#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
-#dump_modify 3 pad 3
-
-fix 2 all reax/bonds 25 bonds.reax.tatb
-
-run 25
-Neighbor list info ...
- update every 5 steps, delay 0 steps, check no
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 12.5
- ghost atom cutoff = 12.5
- binsize = 6.25, bins = 5 4 3
- 1 neighbor lists, perpetual/occasional/extra = 1 0 0
- (1) pair reax, perpetual
- attributes: half, newton off
- pair build: half/bin/newtoff
- stencil: half/bin/3d/newtoff
- bin: standard
-Per MPI rank memory allocation (min/avg/max) = 7.764 | 7.764 | 7.764 Mbytes
-Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
- 0 0 -44767.08 -44767.08 7294.6353 -61120.591 486.4378 4.7236377 0 1568.024 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6378 0 6391.0231
- 5 0.63682806 -44767.737 -44767.01 8391.5964 -61118.763 486.82916 4.723415 0 1567.835 20.768662 -278.20804 -1557.6962 252.64683 -655.74117 18859.328 -8738.2728 0 6388.8127
- 10 2.4306958 -44769.409 -44766.634 11717.376 -61113.142 487.89093 4.7227063 0 1567.2936 20.705084 -274.37509 -1560.8546 252.87219 -655.43578 18850.19 -8731.0693 0 6381.7942
- 15 5.0590493 -44772.631 -44766.855 17125.067 -61103.34 489.28007 4.7214008 0 1566.4744 20.590604 -268.28962 -1566.5961 252.97781 -654.93836 18835.335 -8719.3013 0 6370.4551
- 20 8.067859 -44775.936 -44766.725 24620.627 -61088.791 490.42346 4.7193467 0 1565.5541 20.415031 -260.38512 -1574.1001 253.39805 -654.26837 18815.312 -8703.3748 0 6355.1614
- 25 10.975538 -44777.233 -44764.702 34381.173 -61068.889 490.53149 4.7164093 0 1566.5715 20.169755 -251.23109 -1582.8552 253.88696 -653.46042 18790.855 -8683.8691 0 6336.3409
-Loop time of 7.80129 on 1 procs for 25 steps with 384 atoms
-
-Performance: 0.017 ns/day, 1386.896 hours/ns, 3.205 timesteps/s
-99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 7.7384 | 7.7384 | 7.7384 | 0.0 | 99.19
-Neigh | 0.058615 | 0.058615 | 0.058615 | 0.0 | 0.75
-Comm | 0.0022428 | 0.0022428 | 0.0022428 | 0.0 | 0.03
-Output | 0.00033212 | 0.00033212 | 0.00033212 | 0.0 | 0.00
-Modify | 0.0013618 | 0.0013618 | 0.0013618 | 0.0 | 0.02
-Other | | 0.0003309 | | | 0.00
-
-Nlocal: 384 ave 384 max 384 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 7559 ave 7559 max 7559 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 286828 ave 286828 max 286828 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 286828
-Ave neighs/atom = 746.948
-Neighbor list builds = 5
-Dangerous builds not checked
-Total wall time: 0:00:08
diff --git a/examples/reax/log.8March18.reax.tatb.g++.4 b/examples/reax/log.8March18.reax.tatb.g++.4
deleted file mode 100644
index e3acac9d0efde524cae8ef28cd5f3eedac5c8dba..0000000000000000000000000000000000000000
--- a/examples/reax/log.8March18.reax.tatb.g++.4
+++ /dev/null
@@ -1,103 +0,0 @@
-LAMMPS (8 Mar 2018)
- using 1 OpenMP thread(s) per MPI task
-# ReaxFF potential for TATB system
-
-units real
-
-atom_style charge
-read_data data.tatb
- triclinic box = (0 0 0) to (13.624 17.1149 15.1826) with tilt (-5.75316 -6.32547 7.42573)
- 1 by 2 by 2 MPI processor grid
- reading atoms ...
- 384 atoms
-
-# reax args: hbcut hbnewflag tripflag precision
-pair_style reax 6.0 1 1 1.0e-6
-WARNING: The pair_style reax command is unsupported. Please switch to pair_style reax/c instead (../pair_reax.cpp:49)
-pair_coeff * * ffield.reax 1 2 3 4
-
-compute reax all pair reax
-
-variable eb equal c_reax[1]
-variable ea equal c_reax[2]
-variable elp equal c_reax[3]
-variable emol equal c_reax[4]
-variable ev equal c_reax[5]
-variable epen equal c_reax[6]
-variable ecoa equal c_reax[7]
-variable ehb equal c_reax[8]
-variable et equal c_reax[9]
-variable eco equal c_reax[10]
-variable ew equal c_reax[11]
-variable ep equal c_reax[12]
-variable efi equal c_reax[13]
-variable eqeq equal c_reax[14]
-
-neighbor 2.5 bin
-neigh_modify delay 0 every 5 check no
-
-fix 1 all nve
-
-thermo 5
-thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
-
-timestep 0.0625
-
-#dump 1 all custom 100 dump.reax.tatb id type q x y z
-
-#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
-#dump_modify 2 pad 3
-
-#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
-#dump_modify 3 pad 3
-
-fix 2 all reax/bonds 25 bonds.reax.tatb
-
-run 25
-Neighbor list info ...
- update every 5 steps, delay 0 steps, check no
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 12.5
- ghost atom cutoff = 12.5
- binsize = 6.25, bins = 5 4 3
- 1 neighbor lists, perpetual/occasional/extra = 1 0 0
- (1) pair reax, perpetual
- attributes: half, newton off
- pair build: half/bin/newtoff
- stencil: half/bin/3d/newtoff
- bin: standard
-Per MPI rank memory allocation (min/avg/max) = 4.402 | 4.402 | 4.402 Mbytes
-Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
- 0 0 -44767.08 -44767.08 7294.6353 -61120.591 486.4378 4.7236377 0 1568.024 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6378 0 6391.0231
- 5 0.63682727 -44767.816 -44767.089 8391.1708 -61118.763 486.82916 4.723415 0 1567.835 20.768662 -278.20804 -1557.6962 252.64683 -655.74117 18859.328 -8738.3973 0 6388.8581
- 10 2.4306941 -44769.405 -44766.63 11717.306 -61113.142 487.89094 4.7227063 0 1567.2936 20.705084 -274.3751 -1560.8546 252.87219 -655.43578 18850.19 -8731.08 0 6381.8083
- 15 5.0590444 -44772.6 -44766.824 17125.207 -61103.34 489.28008 4.7214008 0 1566.4744 20.590604 -268.28963 -1566.5961 252.97781 -654.93836 18835.335 -8719.2653 0 6370.4505
- 20 8.0678523 -44775.983 -44766.772 24620.114 -61088.791 490.42348 4.7193467 0 1565.5541 20.415031 -260.38513 -1574.1001 253.39804 -654.26837 18815.312 -8703.5228 0 6355.2629
- 25 10.975532 -44777.234 -44764.704 34381.065 -61068.889 490.53151 4.7164093 0 1566.5715 20.169755 -251.23111 -1582.8552 253.88696 -653.46042 18790.855 -8683.898 0 6336.3682
-Loop time of 3.74388 on 4 procs for 25 steps with 384 atoms
-
-Performance: 0.036 ns/day, 665.579 hours/ns, 6.678 timesteps/s
-98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 3.478 | 3.6025 | 3.7215 | 4.8 | 96.22
-Neigh | 0.012731 | 0.01299 | 0.013174 | 0.2 | 0.35
-Comm | 0.0073411 | 0.12653 | 0.25119 | 25.4 | 3.38
-Output | 0.00050354 | 0.00081849 | 0.0011628 | 0.0 | 0.02
-Modify | 0.00049281 | 0.00082356 | 0.001157 | 0.0 | 0.02
-Other | | 0.0002663 | | | 0.01
-
-Nlocal: 96 ave 96 max 96 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-Nghost: 5118 ave 5118 max 5118 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-Neighs: 79754 ave 79754 max 79754 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 319016
-Ave neighs/atom = 830.771
-Neighbor list builds = 5
-Dangerous builds not checked
-Total wall time: 0:00:03
diff --git a/lib/README b/lib/README
index 12c27b2a397d7b0fd9c7f90819774615e5900deb..d89490e2023d47779014f365e1b98678ee77adfa 100644
--- a/lib/README
+++ b/lib/README
@@ -33,8 +33,6 @@ kokkos Kokkos package for GPU and many-core acceleration
from Kokkos development team (Sandia)
linalg set of BLAS and LAPACK routines needed by USER-ATC package
from Axel Kohlmeyer (Temple U)
-meam modified embedded atom method (MEAM) potential, MEAM package
- from Greg Wagner (Sandia)
message client/server communication library via MPI, sockets, files
from Steve Plimpton (Sandia)
molfile hooks to VMD molfile plugins, used by the USER-MOLFILE package
@@ -51,8 +49,6 @@ qmmm quantum mechanics/molecular mechanics coupling interface
from Axel Kohlmeyer (Temple U)
quip interface to QUIP/libAtoms framework, USER-QUIP package
from Albert Bartok-Partay and Gabor Csanyi (U Cambridge)
-reax ReaxFF potential, REAX package
- from Adri van Duin (Penn State) and Aidan Thompson (Sandia)
smd hooks to Eigen library, used by USER-SMD package
from Georg Ganzenmueller (Ernst Mach Institute, Germany)
voronoi hooks to the Voro++ library, used by compute voronoi/atom command
diff --git a/lib/meam/.depend b/lib/meam/.depend
deleted file mode 100644
index 0945fba47a80e18a1cb97f97699615c78d589c47..0000000000000000000000000000000000000000
--- a/lib/meam/.depend
+++ /dev/null
@@ -1,9 +0,0 @@
-# dependencies. needed for parallel make
-$(DIR)meam_data.o: meam_data.F
-$(DIR)meam_cleanup.o: meam_cleanup.F $(DIR)meam_data.o
-$(DIR)meam_dens_final.o: meam_dens_final.F $(DIR)meam_data.o
-$(DIR)meam_dens_init.o: meam_dens_init.F $(DIR)meam_data.o
-$(DIR)meam_force.o: meam_force.F $(DIR)meam_data.o
-$(DIR)meam_setup_done.o: meam_setup_done.F $(DIR)meam_data.o
-$(DIR)meam_setup_global.o: meam_setup_global.F $(DIR)meam_data.o
-$(DIR)meam_setup_param.o: meam_setup_param.F $(DIR)meam_data.o
diff --git a/lib/meam/.gitignore b/lib/meam/.gitignore
deleted file mode 100644
index 63a7748cf4f2c82b741fd13856d3ee73f16a787b..0000000000000000000000000000000000000000
--- a/lib/meam/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-*.mod
diff --git a/lib/meam/Install.py b/lib/meam/Install.py
deleted file mode 120000
index ffe709d44c22d2060ad41538d1f8fc0df2b09b30..0000000000000000000000000000000000000000
--- a/lib/meam/Install.py
+++ /dev/null
@@ -1 +0,0 @@
-../Install.py
\ No newline at end of file
diff --git a/lib/meam/Makefile.g95 b/lib/meam/Makefile.g95
deleted file mode 100644
index 91371441bd66822e3fa16683b976f29bf0afc566..0000000000000000000000000000000000000000
--- a/lib/meam/Makefile.g95
+++ /dev/null
@@ -1,57 +0,0 @@
-# *
-# *_________________________________________________________________________*
-# * MEAM: MODEFIED EMBEDDED ATOM METHOD *
-# * DESCRIPTION: SEE READ-ME *
-# * FILE NAME: Makefile *
-# * AUTHORS: Greg Wagner, Sandia National Laboratories *
-# * CONTACT: gjwagne@sandia.gov *
-# *_________________________________________________________________________*/
-
-SHELL = /bin/sh
-
-# which file will be copied to Makefile.lammps
-
-EXTRAMAKE = Makefile.lammps.gfortran
-
-# ------ FILES ------
-
-SRC = meam_data.F meam_setup_done.F meam_setup_global.F meam_setup_param.F meam_dens_init.F meam_dens_final.F meam_force.F meam_cleanup.F
-
-FILES = $(SRC) Makefile
-
-# ------ DEFINITIONS ------
-
-LIB = libmeam.a
-OBJ = $(SRC:.F=.o) fm_exp.o
-
-# ------ SETTINGS ------
-
-F90 = g95
-F90FLAGS = -O -fPIC
-ARCHIVE = ar
-ARCHFLAG = -rc
-USRLIB =
-SYSLIB =
-
-# ------ MAKE PROCEDURE ------
-
-lib: $(OBJ)
- $(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
- @cp $(EXTRAMAKE) Makefile.lammps
-
-# ------ COMPILE RULES ------
-
-%.o:%.F
- $(F90) $(F90FLAGS) -c $<
-
-%.o:%.c
- $(CC) $(F90FLAGS) -c $<
-
-include .depend
-# ------ CLEAN ------
-
-clean:
- -rm *.o *.mod *~ $(LIB)
-
-tar:
- -tar -cvf ../MEAM.tar $(FILES)
diff --git a/lib/meam/Makefile.gfortran b/lib/meam/Makefile.gfortran
deleted file mode 100644
index 509e4cebc3d4e3bc85cb7c8c6c42c3a53b4841d0..0000000000000000000000000000000000000000
--- a/lib/meam/Makefile.gfortran
+++ /dev/null
@@ -1,61 +0,0 @@
-# *
-# *_________________________________________________________________________*
-# * MEAM: MODEFIED EMBEDDED ATOM METHOD *
-# * DESCRIPTION: SEE READ-ME *
-# * FILE NAME: Makefile *
-# * AUTHORS: Greg Wagner, Sandia National Laboratories *
-# * CONTACT: gjwagne@sandia.gov *
-# *_________________________________________________________________________*/
-
-SHELL = /bin/sh
-
-# which file will be copied to Makefile.lammps
-
-EXTRAMAKE = Makefile.lammps.gfortran
-
-# ------ FILES ------
-
-SRC = meam_data.F meam_setup_done.F meam_setup_global.F meam_setup_param.F meam_dens_init.F meam_dens_final.F meam_force.F meam_cleanup.F
-
-FILES = $(SRC) Makefile
-
-# ------ DEFINITIONS ------
-
-LIB = libmeam.a
-OBJ = $(SRC:.F=.o) fm_exp.o
-
-# ------ SETTINGS ------
-
-F90 = gfortran
-CC = gcc
-F90FLAGS = -O3 -fPIC -ffast-math -ftree-vectorize -fexpensive-optimizations -fno-second-underscore -g
-#F90FLAGS = -O
-ARCHIVE = ar
-ARCHFLAG = -rc
-LINK = g++
-LINKFLAGS = -O
-USRLIB =
-SYSLIB =
-
-# ------ MAKE PROCEDURE ------
-
-lib: $(OBJ)
- $(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
- @cp $(EXTRAMAKE) Makefile.lammps
-
-# ------ COMPILE RULES ------
-
-%.o:%.F
- $(F90) $(F90FLAGS) -c $<
-
-%.o:%.c
- $(CC) $(F90FLAGS) -c $<
-
-include .depend
-# ------ CLEAN ------
-
-clean:
- -rm *.o *.mod *~ $(LIB)
-
-tar:
- -tar -cvf ../MEAM.tar $(FILES)
diff --git a/lib/meam/Makefile.ifort b/lib/meam/Makefile.ifort
deleted file mode 100644
index cd3bca98825c0a9c0f4dd9b13e253cf0ed260320..0000000000000000000000000000000000000000
--- a/lib/meam/Makefile.ifort
+++ /dev/null
@@ -1,57 +0,0 @@
-# *
-# *_________________________________________________________________________*
-# * MEAM: MODEFIED EMBEDDED ATOM METHOD *
-# * DESCRIPTION: SEE READ-ME *
-# * FILE NAME: Makefile *
-# * AUTHORS: Greg Wagner, Sandia National Laboratories *
-# * CONTACT: gjwagne@sandia.gov *
-# *_________________________________________________________________________*/
-
-SHELL = /bin/sh
-
-# which file will be copied to Makefile.lammps
-
-EXTRAMAKE = Makefile.lammps.ifort
-
-# ------ FILES ------
-
-SRC = meam_data.F meam_setup_done.F meam_setup_global.F meam_setup_param.F meam_dens_init.F meam_dens_final.F meam_force.F meam_cleanup.F
-
-FILES = $(SRC) Makefile
-
-# ------ DEFINITIONS ------
-
-LIB = libmeam.a
-OBJ = $(SRC:.F=.o) fm_exp.o
-
-# ------ SETTINGS ------
-
-F90 = ifort
-F90FLAGS = -O -fPIC
-ARCHIVE = ar
-ARCHFLAG = -rc
-USRLIB =
-SYSLIB =
-
-# ------ MAKE PROCEDURE ------
-
-lib: $(OBJ)
- $(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
- @cp $(EXTRAMAKE) Makefile.lammps
-
-# ------ COMPILE RULES ------
-
-%.o:%.F
- $(F90) $(F90FLAGS) -c $<
-
-%.o:%.c
- $(CC) $(F90FLAGS) -c $<
-
-include .depend
-# ------ CLEAN ------
-
-clean:
- -rm *.o *.mod *~ $(LIB)
-
-tar:
- -tar -cvf ../MEAM.tar $(FILES)
diff --git a/lib/meam/Makefile.lammps.empty b/lib/meam/Makefile.lammps.empty
deleted file mode 100644
index 10394b68ad3ae35dda3fde8463195ba72b4cb69f..0000000000000000000000000000000000000000
--- a/lib/meam/Makefile.lammps.empty
+++ /dev/null
@@ -1,5 +0,0 @@
-# Settings that the LAMMPS build will import when this package library is used
-
-meam_SYSINC =
-meam_SYSLIB =
-meam_SYSPATH =
diff --git a/lib/meam/Makefile.lammps.gfortran b/lib/meam/Makefile.lammps.gfortran
deleted file mode 100644
index fa62c997dc371e92ef6acc1ec4fb9c95929a8f32..0000000000000000000000000000000000000000
--- a/lib/meam/Makefile.lammps.gfortran
+++ /dev/null
@@ -1,5 +0,0 @@
-# Settings that the LAMMPS build will import when this package library is used
-
-meam_SYSINC =
-meam_SYSLIB = -lgfortran
-meam_SYSPATH =
diff --git a/lib/meam/Makefile.lammps.glory b/lib/meam/Makefile.lammps.glory
deleted file mode 100644
index 153e699b726be1e5034633839bc62b1f5174c5fd..0000000000000000000000000000000000000000
--- a/lib/meam/Makefile.lammps.glory
+++ /dev/null
@@ -1,5 +0,0 @@
-# Settings that the LAMMPS build will import when this package library is used
-
-meam_SYSINC =
-meam_SYSLIB = -lifcore -lsvml -lompstub -limf
-meam_SYSPATH = -L/opt/intel-11.1.046/lib/intel64
diff --git a/lib/meam/Makefile.lammps.ifort b/lib/meam/Makefile.lammps.ifort
deleted file mode 100644
index bd4d98f92924b60eb9c2ad0d35228af121942938..0000000000000000000000000000000000000000
--- a/lib/meam/Makefile.lammps.ifort
+++ /dev/null
@@ -1,5 +0,0 @@
-# Settings that the LAMMPS build will import when this package library is used
-
-meam_SYSINC =
-meam_SYSLIB = -lifcore -lsvml -lompstub -limf
-meam_SYSPATH = -L/opt/intel/fce/10.0.023/lib
diff --git a/lib/meam/Makefile.mpi b/lib/meam/Makefile.mpi
deleted file mode 100644
index fd3dbde5558b6866dd3b870ebd622bb0fa757705..0000000000000000000000000000000000000000
--- a/lib/meam/Makefile.mpi
+++ /dev/null
@@ -1,61 +0,0 @@
-# *
-# *_________________________________________________________________________*
-# * MEAM: MODEFIED EMBEDDED ATOM METHOD *
-# * DESCRIPTION: SEE READ-ME *
-# * FILE NAME: Makefile *
-# * AUTHORS: Greg Wagner, Sandia National Laboratories *
-# * CONTACT: gjwagne@sandia.gov *
-# *_________________________________________________________________________*/
-
-SHELL = /bin/sh
-
-# which file will be copied to Makefile.lammps
-
-EXTRAMAKE = Makefile.lammps.empty
-
-# ------ FILES ------
-
-SRC = meam_data.F meam_setup_done.F meam_setup_global.F meam_setup_param.F meam_dens_init.F meam_dens_final.F meam_force.F meam_cleanup.F
-
-FILES = $(SRC) Makefile
-
-# ------ DEFINITIONS ------
-
-LIB = libmeam.a
-OBJ = $(SRC:.F=.o) fm_exp.o
-
-# ------ SETTINGS ------
-
-F90 = mpifort
-CC = mpicc
-F90FLAGS = -O3 -fPIC
-#F90FLAGS = -O
-ARCHIVE = ar
-ARCHFLAG = -rc
-LINK = mpicxx
-LINKFLAGS = -O
-USRLIB =
-SYSLIB =
-
-# ------ MAKE PROCEDURE ------
-
-lib: $(OBJ)
- $(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
- @cp $(EXTRAMAKE) Makefile.lammps
-
-# ------ COMPILE RULES ------
-
-%.o:%.F
- $(F90) $(F90FLAGS) -c $<
-
-%.o:%.c
- $(CC) $(F90FLAGS) -c $<
-
-include .depend
-# ------ CLEAN ------
-
-clean:
- -rm *.o *.mod *~ $(LIB)
-
-tar:
- -tar -cvf ../MEAM.tar $(FILES)
diff --git a/lib/meam/Makefile.pgf90 b/lib/meam/Makefile.pgf90
deleted file mode 100644
index 32ce909f4875debee3e2a3a6226fb03cddf8ec17..0000000000000000000000000000000000000000
--- a/lib/meam/Makefile.pgf90
+++ /dev/null
@@ -1,57 +0,0 @@
-# *
-# *_________________________________________________________________________*
-# * MEAM: MODEFIED EMBEDDED ATOM METHOD *
-# * DESCRIPTION: SEE READ-ME *
-# * FILE NAME: Makefile *
-# * AUTHORS: Greg Wagner, Sandia National Laboratories *
-# * CONTACT: gjwagne@sandia.gov *
-# *_________________________________________________________________________*/
-
-SHELL = /bin/sh
-
-# which file will be copied to Makefile.lammps
-
-EXTRAMAKE = Makefile.lammps.pgf90
-
-# ------ FILES ------
-
-SRC = meam_data.F meam_setup_done.F meam_setup_global.F meam_setup_param.F meam_dens_init.F meam_dens_final.F meam_force.F meam_cleanup.F
-
-FILES = $(SRC) Makefile
-
-# ------ DEFINITIONS ------
-
-LIB = libmeam.a
-OBJ = $(SRC:.F=.o) fm_exp.o
-
-# ------ SETTINGS ------
-
-F90 = pgf90
-F90FLAGS = -O -fPIC
-ARCHIVE = ar
-ARCHFLAG = -rc
-USRLIB =
-SYSLIB =
-
-# ------ MAKE PROCEDURE ------
-
-lib: $(OBJ)
- $(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
- @cp $(EXTRAMAKE) Makefile.lammps
-
-# ------ COMPILE RULES ------
-
-%.o:%.F
- $(F90) $(F90FLAGS) -c $<
-
-%.o:%.c
- $(CC) $(F90FLAGS) -c $<
-
-include .depend
-# ------ CLEAN ------
-
-clean:
- -rm *.o *.mod *~ $(LIB)
-
-tar:
- -tar -cvf ../MEAM.tar $(FILES)
diff --git a/lib/meam/Makefile.serial b/lib/meam/Makefile.serial
deleted file mode 120000
index c52fbcb986822e3dfdc79a978a876fb39a762f71..0000000000000000000000000000000000000000
--- a/lib/meam/Makefile.serial
+++ /dev/null
@@ -1 +0,0 @@
-Makefile.gfortran
\ No newline at end of file
diff --git a/lib/meam/Makefile.tbird b/lib/meam/Makefile.tbird
deleted file mode 100644
index 7253d8305b3a833953ec93dc8f066b493c4446b3..0000000000000000000000000000000000000000
--- a/lib/meam/Makefile.tbird
+++ /dev/null
@@ -1,59 +0,0 @@
-# *
-# *_________________________________________________________________________*
-# * MEAM: MODEFIED EMBEDDED ATOM METHOD *
-# * DESCRIPTION: SEE READ-ME *
-# * FILE NAME: Makefile *
-# * AUTHORS: Greg Wagner, Sandia National Laboratories *
-# * CONTACT: gjwagne@sandia.gov *
-# *_________________________________________________________________________*/
-
-SHELL = /bin/sh
-
-# which file will be copied to Makefile.lammps
-
-EXTRAMAKE = Makefile.lammps.glory
-
-# ------ FILES ------
-
-SRC = meam_data.F meam_setup_done.F meam_setup_global.F meam_setup_param.F meam_dens_init.F meam_dens_final.F meam_force.F meam_cleanup.F
-
-FILES = $(SRC) Makefile
-
-# ------ DEFINITIONS ------
-
-LIB = libmeam.a
-OBJ = $(SRC:.F=.o) fm_exp.o
-
-# ------ SETTINGS ------
-
-F90 = mpif90
-F90FLAGS = -O -fPIC
-ARCHIVE = ar
-ARCHFLAG = -rc
-LINK = g++
-LINKFLAGS = -O
-USRLIB =
-SYSLIB =
-
-# ------ MAKE PROCEDURE ------
-
-lib: $(OBJ)
- $(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
- @cp $(EXTRAMAKE) Makefile.lammps
-
-# ------ COMPILE RULES ------
-
-%.o:%.F
- $(F90) $(F90FLAGS) -c $<
-
-%.o:%.c
- $(CC) $(F90FLAGS) -c $<
-
-include .depend
-# ------ CLEAN ------
-
-clean:
- -rm *.o *.mod *~ $(LIB)
-
-tar:
- -tar -cvf ../MEAM.tar $(FILES)
diff --git a/lib/meam/README b/lib/meam/README
deleted file mode 100644
index b3111c131745e4275fc819fd014f3ce40eb194fd..0000000000000000000000000000000000000000
--- a/lib/meam/README
+++ /dev/null
@@ -1,51 +0,0 @@
-MEAM (modified embedded atom method) library
-
-Greg Wagner, Sandia National Labs
-gjwagne at sandia.gov
-Jan 2007
-
-This library is in implementation of the MEAM potential, specifically
-designed to work with LAMMPS.
-
--------------------------------------------------
-
-This directory has source files to build a library that LAMMPS
-links against when using the MEAM package.
-
-This library must be built with a F90 compiler, before LAMMPS is
-built, so LAMMPS can link against it.
-
-You can type "make lib-meam" from the src directory to see help on how
-to build this library via make commands, or you can do the same thing
-by typing "python Install.py" from within this directory, or you can
-do it manually by following the instructions below.
-
-Build the library using one of the provided Makefile.* files or create
-your own, specific to your compiler and system. For example:
-
-make -f Makefile.gfortran
-
-When you are done building this library, two files should
-exist in this directory:
-
-libmeam.a the library LAMMPS will link against
-Makefile.lammps settings the LAMMPS Makefile will import
-
-Makefile.lammps is created by the make command, by copying one of the
-Makefile.lammps.* files. See the EXTRAMAKE setting at the top of the
-Makefile.* files.
-
-IMPORTANT: You must examine the final Makefile.lammps to insure it is
-correct for your system, else the LAMMPS build will likely fail.
-
-Makefile.lammps has settings for 3 variables:
-
-user-meam_SYSINC = leave blank for this package
-user-meam_SYSLIB = auxiliary F90 libs needed to link a F90 lib with
- a C++ program (LAMMPS) via a C++ compiler
-user-meam_SYSPATH = path(s) to where those libraries are
-
-Because you have a F90 compiler on your system, you should have these
-libraries. But you will have to figure out which ones are needed and
-where they are. Examples of common configurations are in the
-Makefile.lammps.* files.
diff --git a/lib/meam/fm_exp.c b/lib/meam/fm_exp.c
deleted file mode 100644
index 26d23b2e245fdfeec182f2bb268f5112f8c08381..0000000000000000000000000000000000000000
--- a/lib/meam/fm_exp.c
+++ /dev/null
@@ -1,133 +0,0 @@
-/*
- Copyright (c) 2012,2013 Axel Kohlmeyer <akohlmey@gmail.com>
- All rights reserved.
-
- Redistribution and use in source and binary forms, with or without
- modification, are permitted provided that the following conditions
- are met:
-
- * Redistributions of source code must retain the above copyright
- notice, this list of conditions and the following disclaimer.
- * Redistributions in binary form must reproduce the above copyright
- notice, this list of conditions and the following disclaimer in the
- documentation and/or other materials provided with the distribution.
- * Neither the name of the <organization> nor the
- names of its contributors may be used to endorse or promote products
- derived from this software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY
-DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
-(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
-LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
-ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
-THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-*/
-
-/* faster versions of 2**x, e**x, and 10**x in single and double precision.
- *
- * Based on the Cephes math library 2.8
- */
-
-#include <math.h>
-#include <stdint.h>
-
-/* internal definitions for the fastermath library */
-
-/* IEEE 754 double precision floating point data manipulation */
-typedef union
-{
- double f;
- uint64_t u;
- struct {int32_t i0,i1;};
-} udi_t;
-#define FM_DOUBLE_BIAS 1023
-#define FM_DOUBLE_EMASK 2146435072
-#define FM_DOUBLE_MBITS 20
-#define FM_DOUBLE_MMASK 1048575
-#define FM_DOUBLE_EZERO 1072693248
-
-/* generate 2**num in floating point by bitshifting */
-#define FM_DOUBLE_INIT_EXP(var,num) \
- var.i0 = 0; \
- var.i1 = (((int) num) + FM_DOUBLE_BIAS) << 20
-
-/* double precision constants */
-#define FM_DOUBLE_LOG2OFE 1.4426950408889634074
-#define FM_DOUBLE_LOGEOF2 6.9314718055994530942e-1
-#define FM_DOUBLE_LOG2OF10 3.32192809488736234789
-#define FM_DOUBLE_LOG10OF2 3.0102999566398119521e-1
-#define FM_DOUBLE_LOG10OFE 4.3429448190325182765e-1
-#define FM_DOUBLE_SQRT2 1.41421356237309504880
-#define FM_DOUBLE_SQRTH 0.70710678118654752440
-
-/* optimizer friendly implementation of exp2(x).
- *
- * strategy:
- *
- * split argument into an integer part and a fraction:
- * ipart = floor(x+0.5);
- * fpart = x - ipart;
- *
- * compute exp2(ipart) from setting the ieee754 exponent
- * compute exp2(fpart) using a pade' approximation for x in [-0.5;0.5[
- *
- * the result becomes: exp2(x) = exp2(ipart) * exp2(fpart)
- */
-
-static const double fm_exp2_q[] = {
-/* 1.00000000000000000000e0, */
- 2.33184211722314911771e2,
- 4.36821166879210612817e3
-};
-static const double fm_exp2_p[] = {
- 2.30933477057345225087e-2,
- 2.02020656693165307700e1,
- 1.51390680115615096133e3
-};
-
-static double fm_exp2(double x)
-{
- double ipart, fpart, px, qx;
- udi_t epart;
-
- ipart = floor(x+0.5);
- fpart = x - ipart;
- FM_DOUBLE_INIT_EXP(epart,ipart);
-
- x = fpart*fpart;
-
- px = fm_exp2_p[0];
- px = px*x + fm_exp2_p[1];
- qx = x + fm_exp2_q[0];
- px = px*x + fm_exp2_p[2];
- qx = qx*x + fm_exp2_q[1];
-
- px = px * fpart;
-
- x = 1.0 + 2.0*(px/(qx-px));
- return epart.f*x;
-}
-
-double fm_exp_(double *x)
-{
-#if defined(__BYTE_ORDER__)
-#if __BYTE_ORDER__ == __ORDER_LITTLE_ENDIAN__
- return fm_exp2(FM_DOUBLE_LOG2OFE * (*x));
-#endif
-#endif
- return exp(*x);
-}
-
-/*
- * Local Variables:
- * mode: c
- * compile-command: "make -C .."
- * c-basic-offset: 4
- * fill-column: 76
- * indent-tabs-mode: nil
- * End:
- */
diff --git a/lib/meam/meam_cleanup.F b/lib/meam/meam_cleanup.F
deleted file mode 100644
index dce0c6469edb4e1f3d5390956a49766e291836bd..0000000000000000000000000000000000000000
--- a/lib/meam/meam_cleanup.F
+++ /dev/null
@@ -1,26 +0,0 @@
-c Declaration in pair_meam.h:
-c
-c void meam_cleanup()
-c
-c Call from PairMEAM destructor
-c
-c meam_cleanup()
-c
-
- subroutine meam_cleanup
- use meam_data
- implicit none
-
- integer dealloc_error
-
- deallocate(phir,STAT=dealloc_error)
- deallocate(phirar,STAT=dealloc_error)
- deallocate(phirar1,STAT=dealloc_error)
- deallocate(phirar2,STAT=dealloc_error)
- deallocate(phirar3,STAT=dealloc_error)
- deallocate(phirar4,STAT=dealloc_error)
- deallocate(phirar5,STAT=dealloc_error)
- deallocate(phirar6,STAT=dealloc_error)
-
- return
- end
diff --git a/lib/meam/meam_data.F b/lib/meam/meam_data.F
deleted file mode 100644
index 719963bd5979eac903b23e9945fa7fd1ec81d1f9..0000000000000000000000000000000000000000
--- a/lib/meam/meam_data.F
+++ /dev/null
@@ -1,87 +0,0 @@
-
- module meam_data
-
- integer, parameter :: maxelt = 5
- real*8 , external :: fm_exp
-
-c cutforce = force cutoff
-c cutforcesq = force cutoff squared
-
- real*8 cutforce,cutforcesq
-
-c Ec_meam = cohesive energy
-c re_meam = nearest-neighbor distance
-c Omega_meam = atomic volume
-c B_meam = bulk modulus
-c Z_meam = number of first neighbors for reference structure
-c ielt_meam = atomic number of element
-c A_meam = adjustable parameter
-c alpha_meam = sqrt(9*Omega*B/Ec)
-c rho0_meam = density scaling parameter
-c delta_meam = heat of formation for alloys
-c beta[0-3]_meam = electron density constants
-c t[0-3]_meam = coefficients on densities in Gamma computation
-c rho_ref_meam = background density for reference structure
-c ibar_meam(i) = selection parameter for Gamma function for elt i,
-c lattce_meam(i,j) = lattce configuration for elt i or alloy (i,j)
-c neltypes = maximum number of element type defined
-c eltind = index number of pair (similar to Voigt notation; ij = ji)
-c phir = pair potential function array
-c phirar[1-6] = spline coeffs
-c attrac_meam = attraction parameter in Rose energy
-c repuls_meam = repulsion parameter in Rose energy
-c nn2_meam = 1 if second nearest neighbors are to be computed, else 0
-c zbl_meam = 1 if zbl potential for small r to be use, else 0
-c emb_lin_neg = 1 if linear embedding function for rhob to be used, else 0
-c bkgd_dyn = 1 if reference densities follows Dynamo, else 0
-c Cmin_meam, Cmax_meam = min and max values in screening cutoff
-c rc_meam = cutoff distance for meam
-c delr_meam = cutoff region for meam
-c ebound_meam = factor giving maximum boundary of sceen fcn ellipse
-c augt1 = flag for whether t1 coefficient should be augmented
-c ialloy = flag for newer alloy formulation (as in dynamo code)
-c mix_ref_t = flag to recover "old" way of computing t in reference config
-c erose_form = selection parameter for form of E_rose function
-c gsmooth_factor = factor determining length of G smoothing region
-c vind[23]D = Voight notation index maps for 2 and 3D
-c v2D,v3D = array of factors to apply for Voight notation
-
-c nr,dr = pair function discretization parameters
-c nrar,rdrar = spline coeff array parameters
-
- real*8 Ec_meam(maxelt,maxelt),re_meam(maxelt,maxelt)
- real*8 Omega_meam(maxelt),Z_meam(maxelt)
- real*8 A_meam(maxelt),alpha_meam(maxelt,maxelt),rho0_meam(maxelt)
- real*8 delta_meam(maxelt,maxelt)
- real*8 beta0_meam(maxelt),beta1_meam(maxelt)
- real*8 beta2_meam(maxelt),beta3_meam(maxelt)
- real*8 t0_meam(maxelt),t1_meam(maxelt)
- real*8 t2_meam(maxelt),t3_meam(maxelt)
- real*8 rho_ref_meam(maxelt)
- integer ibar_meam(maxelt),ielt_meam(maxelt)
- character*3 lattce_meam(maxelt,maxelt)
- integer nn2_meam(maxelt,maxelt)
- integer zbl_meam(maxelt,maxelt)
- integer eltind(maxelt,maxelt)
- integer neltypes
-
- real*8, allocatable :: phir(:,:)
-
- real*8, allocatable :: phirar(:,:),phirar1(:,:),phirar2(:,:),
- $ phirar3(:,:),phirar4(:,:),phirar5(:,:),phirar6(:,:)
-
- real*8 attrac_meam(maxelt,maxelt),repuls_meam(maxelt,maxelt)
-
- real*8 Cmin_meam(maxelt,maxelt,maxelt)
- real*8 Cmax_meam(maxelt,maxelt,maxelt)
- real*8 rc_meam,delr_meam,ebound_meam(maxelt,maxelt)
- integer augt1, ialloy, mix_ref_t, erose_form
- integer emb_lin_neg, bkgd_dyn
- real*8 gsmooth_factor
- integer vind2D(3,3),vind3D(3,3,3)
- integer v2D(6),v3D(10)
-
- integer nr,nrar
- real*8 dr,rdrar
-
- end module
diff --git a/lib/meam/meam_dens_final.F b/lib/meam/meam_dens_final.F
deleted file mode 100644
index 098b00f296a7b525a1f01e7a322167a157605fbd..0000000000000000000000000000000000000000
--- a/lib/meam/meam_dens_final.F
+++ /dev/null
@@ -1,296 +0,0 @@
-c Extern "C" declaration has the form:
-c
-c void meam_dens_final_(int *, int *, int *, int *, int *, double *, double *,
-c int *, int *, int *,
-c double *, double *, double *, double *, double *, double *,
-c double *, double *, double *, double *, double *, double *,
-c double *, double *, double *, double *, double *, int *);
-c
-c Call from pair_meam.cpp has the form:
-c
-c meam_dens_final_(&nlocal,&nmax,&eflag_either,&eflag_global,&eflag_atom,
-c &eng_vdwl,eatom,ntype,type,fmap,
-c &arho1[0][0],&arho2[0][0],arho2b,&arho3[0][0],
-c &arho3b[0][0],&t_ave[0][0],&tsq_ave[0][0],gamma,dgamma1,
-c dgamma2,dgamma3,rho,rho0,rho1,rho2,rho3,frhop,&errorflag);
-c
-
- subroutine meam_dens_final(nlocal, nmax,
- $ eflag_either, eflag_global, eflag_atom, eng_vdwl, eatom,
- $ ntype, type, fmap,
- $ Arho1, Arho2, Arho2b, Arho3, Arho3b, t_ave, tsq_ave,
- $ Gamma, dGamma1, dGamma2, dGamma3,
- $ rho, rho0, rho1, rho2, rho3, fp, errorflag)
-
- use meam_data
- implicit none
-
- integer nlocal, nmax, eflag_either, eflag_global, eflag_atom
- integer ntype, type, fmap
- real*8 eng_vdwl, eatom, Arho1, Arho2
- real*8 Arho2b, Arho3, Arho3b
- real*8 t_ave, tsq_ave
- real*8 Gamma, dGamma1, dGamma2, dGamma3
- real*8 rho, rho0, rho1, rho2, rho3
- real*8 fp
- integer errorflag
-
- dimension eatom(nmax)
- dimension type(nmax), fmap(ntype)
- dimension Arho1(3,nmax), Arho2(6,nmax), Arho2b(nmax)
- dimension Arho3(10,nmax), Arho3b(3,nmax), t_ave(3,nmax)
- dimension tsq_ave(3,nmax)
- dimension Gamma(nmax), dGamma1(nmax), dGamma2(nmax)
- dimension dGamma3(nmax), rho(nmax), rho0(nmax)
- dimension rho1(nmax), rho2(nmax), rho3(nmax)
- dimension fp(nmax)
-
- integer i, elti
- integer m
- real*8 rhob, G, dG, Gbar, dGbar, gam, shp(3), shpi(3), Z
- real*8 B, denom, rho_bkgd
-
-c Complete the calculation of density
-
- do i = 1,nlocal
-
- elti = fmap(type(i))
- if (elti.gt.0) then
- rho1(i) = 0.d0
- rho2(i) = -1.d0/3.d0*Arho2b(i)*Arho2b(i)
- rho3(i) = 0.d0
- do m = 1,3
- rho1(i) = rho1(i) + Arho1(m,i)*Arho1(m,i)
- rho3(i) = rho3(i) - 3.d0/5.d0*Arho3b(m,i)*Arho3b(m,i)
- enddo
- do m = 1,6
- rho2(i) = rho2(i) + v2D(m)*Arho2(m,i)*Arho2(m,i)
- enddo
- do m = 1,10
- rho3(i) = rho3(i) + v3D(m)*Arho3(m,i)*Arho3(m,i)
- enddo
-
- if( rho0(i) .gt. 0.0 ) then
- if (ialloy.eq.1) then
- if (tsq_ave(1,i) .ne. 0.0d0) then
- t_ave(1,i) = t_ave(1,i)/tsq_ave(1,i)
- else
- t_ave(1,i) = 0.0d0
- endif
- if (tsq_ave(2,i) .ne. 0.0d0) then
- t_ave(2,i) = t_ave(2,i)/tsq_ave(2,i)
- else
- t_ave(2,i) = 0.0d0
- endif
- if (tsq_ave(3,i) .ne. 0.0d0) then
- t_ave(3,i) = t_ave(3,i)/tsq_ave(3,i)
- else
- t_ave(3,i) = 0.0d0
- endif
- else if (ialloy.eq.2) then
- t_ave(1,i) = t1_meam(elti)
- t_ave(2,i) = t2_meam(elti)
- t_ave(3,i) = t3_meam(elti)
- else
- t_ave(1,i) = t_ave(1,i)/rho0(i)
- t_ave(2,i) = t_ave(2,i)/rho0(i)
- t_ave(3,i) = t_ave(3,i)/rho0(i)
- endif
- endif
-
- Gamma(i) = t_ave(1,i)*rho1(i)
- $ + t_ave(2,i)*rho2(i) + t_ave(3,i)*rho3(i)
-
- if( rho0(i) .gt. 0.0 ) then
- Gamma(i) = Gamma(i)/(rho0(i)*rho0(i))
- end if
-
- Z = Z_meam(elti)
-
- call G_gam(Gamma(i),ibar_meam(elti),
- $ gsmooth_factor,G,errorflag)
- if (errorflag.ne.0) return
- call get_shpfcn(shp,lattce_meam(elti,elti))
- if (ibar_meam(elti).le.0) then
- Gbar = 1.d0
- dGbar = 0.d0
- else
- if (mix_ref_t.eq.1) then
- gam = (t_ave(1,i)*shp(1)+t_ave(2,i)*shp(2)
- $ +t_ave(3,i)*shp(3))/(Z*Z)
- else
- gam = (t1_meam(elti)*shp(1)+t2_meam(elti)*shp(2)
- $ +t3_meam(elti)*shp(3))/(Z*Z)
- endif
- call G_gam(gam,ibar_meam(elti),gsmooth_factor,
- $ Gbar,errorflag)
- endif
- rho(i) = rho0(i) * G
-
- if (mix_ref_t.eq.1) then
- if (ibar_meam(elti).le.0) then
- Gbar = 1.d0
- dGbar = 0.d0
- else
- gam = (t_ave(1,i)*shp(1)+t_ave(2,i)*shp(2)
- $ +t_ave(3,i)*shp(3))/(Z*Z)
- call dG_gam(gam,ibar_meam(elti),gsmooth_factor,
- $ Gbar,dGbar)
- endif
- rho_bkgd = rho0_meam(elti)*Z*Gbar
- else
- if (bkgd_dyn.eq.1) then
- rho_bkgd = rho0_meam(elti)*Z
- else
- rho_bkgd = rho_ref_meam(elti)
- endif
- endif
- rhob = rho(i)/rho_bkgd
- denom = 1.d0/rho_bkgd
-
- call dG_gam(Gamma(i),ibar_meam(elti),gsmooth_factor,G,dG)
-
- dGamma1(i) = (G - 2*dG*Gamma(i))*denom
-
- if( rho0(i) .ne. 0.d0 ) then
- dGamma2(i) = (dG/rho0(i))*denom
- else
- dGamma2(i) = 0.d0
- end if
-
-c dGamma3 is nonzero only if we are using the "mixed" rule for
-c computing t in the reference system (which is not correct, but
-c included for backward compatibility
- if (mix_ref_t.eq.1) then
- dGamma3(i) = rho0(i)*G*dGbar/(Gbar*Z*Z)*denom
- else
- dGamma3(i) = 0.0
- endif
-
- B = A_meam(elti)*Ec_meam(elti,elti)
-
- if( rhob .ne. 0.d0 ) then
- if (emb_lin_neg.eq.1 .and. rhob.le.0) then
- fp(i) = -B
- else
- fp(i) = B*(log(rhob)+1.d0)
- endif
- if (eflag_either.ne.0) then
- if (eflag_global.ne.0) then
- if (emb_lin_neg.eq.1 .and. rhob.le.0) then
- eng_vdwl = eng_vdwl - B*rhob
- else
- eng_vdwl = eng_vdwl + B*rhob*log(rhob)
- endif
- endif
- if (eflag_atom.ne.0) then
- if (emb_lin_neg.eq.1 .and. rhob.le.0) then
- eatom(i) = eatom(i) - B*rhob
- else
- eatom(i) = eatom(i) + B*rhob*log(rhob)
- endif
- endif
- endif
- else
- if (emb_lin_neg.eq.1) then
- fp(i) = -B
- else
- fp(i) = B
- endif
- endif
- endif
- enddo
-
- return
- end
-
-cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
-
- subroutine G_gam(Gamma,ibar,gsmooth_factor,G,errorflag)
-c Compute G(Gamma) based on selection flag ibar:
-c 0 => G = sqrt(1+Gamma)
-c 1 => G = exp(Gamma/2)
-c 2 => not implemented
-c 3 => G = 2/(1+exp(-Gamma))
-c 4 => G = sqrt(1+Gamma)
-c -5 => G = +-sqrt(abs(1+Gamma))
- use meam_data , only: fm_exp
- implicit none
- real*8 Gamma,G
- real*8 gsmooth_factor, gsmooth_switchpoint
- integer ibar, errorflag
- if (ibar.eq.0.or.ibar.eq.4) then
- gsmooth_switchpoint = -gsmooth_factor / (gsmooth_factor+1)
- if (Gamma.lt.gsmooth_switchpoint) then
-c e.g. gsmooth_factor is 99, then:
-c gsmooth_switchpoint = -0.99
-c G = 0.01*(-0.99/Gamma)**99
- G = 1/(gsmooth_factor+1)
- $ *(gsmooth_switchpoint/Gamma)**gsmooth_factor
- G = sqrt(G)
- else
- G = sqrt(1.d0+Gamma)
- endif
- else if (ibar.eq.1) then
- G = fm_exp(Gamma/2.d0)
- else if (ibar.eq.3) then
- G = 2.d0/(1.d0+exp(-Gamma))
- else if (ibar.eq.-5) then
- if ((1.d0+Gamma).ge.0) then
- G = sqrt(1.d0+Gamma)
- else
- G = -sqrt(-1.d0-Gamma)
- endif
- else
- errorflag = 1
- endif
- return
- end
-
-cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
-
- subroutine dG_gam(Gamma,ibar,gsmooth_factor,G,dG)
-c Compute G(Gamma) and dG(gamma) based on selection flag ibar:
-c 0 => G = sqrt(1+Gamma)
-c 1 => G = fm_exp(Gamma/2)
-c 2 => not implemented
-c 3 => G = 2/(1+fm_exp(-Gamma))
-c 4 => G = sqrt(1+Gamma)
-c -5 => G = +-sqrt(abs(1+Gamma))
- use meam_data , only: fm_exp
- real*8 Gamma,G,dG
- real*8 gsmooth_factor, gsmooth_switchpoint
- integer ibar
- if (ibar.eq.0.or.ibar.eq.4) then
- gsmooth_switchpoint = -gsmooth_factor / (gsmooth_factor+1)
- if (Gamma.lt.gsmooth_switchpoint) then
-c e.g. gsmooth_factor is 99, then:
-c gsmooth_switchpoint = -0.99
-c G = 0.01*(-0.99/Gamma)**99
- G = 1/(gsmooth_factor+1)
- $ *(gsmooth_switchpoint/Gamma)**gsmooth_factor
- G = sqrt(G)
- dG = -gsmooth_factor*G/(2.0*Gamma)
- else
- G = sqrt(1.d0+Gamma)
- dG = 1.d0/(2.d0*G)
- endif
- else if (ibar.eq.1) then
- G = fm_exp(Gamma/2.d0)
- dG = G/2.d0
- else if (ibar.eq.3) then
- G = 2.d0/(1.d0+fm_exp(-Gamma))
- dG = G*(2.d0-G)/2
- else if (ibar.eq.-5) then
- if ((1.d0+Gamma).ge.0) then
- G = sqrt(1.d0+Gamma)
- dG = 1.d0/(2.d0*G)
- else
- G = -sqrt(-1.d0-Gamma)
- dG = -1.d0/(2.d0*G)
- endif
- endif
- return
- end
-
-cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
diff --git a/lib/meam/meam_dens_init.F b/lib/meam/meam_dens_init.F
deleted file mode 100644
index 2ca2558135faeb5259059476e3171498f16739af..0000000000000000000000000000000000000000
--- a/lib/meam/meam_dens_init.F
+++ /dev/null
@@ -1,564 +0,0 @@
-c Extern "C" declaration has the form:
-c
-c void meam_dens_init_(int *, int *, int *, double *, int *, int *, int *, double *,
-c int *, int *, int *, int *,
-c double *, double *, double *, double *, double *, double *,
-c double *, double *, double *, double *, double *, int *);
-c
-c
-c Call from pair_meam.cpp has the form:
-c
-c meam_dens_init_(&i,&nmax,ntype,type,fmap,&x[0][0],
-c &numneigh[i],firstneigh[i],&numneigh_full[i],firstneigh_full[i],
-c &scrfcn[offset],&dscrfcn[offset],&fcpair[offset],
-c rho0,&arho1[0][0],&arho2[0][0],arho2b,
-c &arho3[0][0],&arho3b[0][0],&t_ave[0][0],&tsq_ave[0][0],&errorflag);
-c
-
- subroutine meam_dens_init(i, nmax,
- $ ntype, type, fmap, x,
- $ numneigh, firstneigh,
- $ numneigh_full, firstneigh_full,
- $ scrfcn, dscrfcn, fcpair, rho0, arho1, arho2, arho2b,
- $ arho3, arho3b, t_ave, tsq_ave, errorflag)
-
- use meam_data
- implicit none
-
- integer i, nmax, ntype, type, fmap
- real*8 x
- integer numneigh, firstneigh, numneigh_full, firstneigh_full
- real*8 scrfcn, dscrfcn, fcpair
- real*8 rho0, arho1, arho2
- real*8 arho2b, arho3, arho3b, t_ave, tsq_ave
- integer errorflag
- integer j,jn
-
- dimension x(3,nmax)
- dimension type(nmax), fmap(ntype)
- dimension firstneigh(numneigh), firstneigh_full(numneigh_full)
- dimension scrfcn(numneigh), dscrfcn(numneigh), fcpair(numneigh)
- dimension rho0(nmax), arho1(3,nmax), arho2(6,nmax)
- dimension arho2b(nmax), arho3(10,nmax), arho3b(3,nmax)
- dimension t_ave(3,nmax), tsq_ave(3,nmax)
-
- errorflag = 0
-
-c Compute screening function and derivatives
- call getscreen(i, nmax, scrfcn, dscrfcn, fcpair, x,
- $ numneigh, firstneigh,
- $ numneigh_full, firstneigh_full,
- $ ntype, type, fmap)
-
-c Calculate intermediate density terms to be communicated
- call calc_rho1(i, nmax, ntype, type, fmap, x,
- $ numneigh, firstneigh,
- $ scrfcn, fcpair, rho0, arho1, arho2, arho2b,
- $ arho3, arho3b, t_ave, tsq_ave)
-
- return
- end
-
-cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
-
- subroutine getscreen(i, nmax, scrfcn, dscrfcn, fcpair, x,
- $ numneigh, firstneigh,
- $ numneigh_full, firstneigh_full,
- $ ntype, type, fmap)
-
- use meam_data
- implicit none
-
- integer i, nmax
- real*8 scrfcn, dscrfcn, fcpair, x
- integer numneigh, firstneigh, numneigh_full, firstneigh_full
- integer ntype, type, fmap
-
- dimension scrfcn(numneigh), dscrfcn(numneigh)
- dimension fcpair(numneigh), x(3,nmax)
- dimension firstneigh(numneigh), firstneigh_full(numneigh_full)
- dimension type(nmax), fmap(ntype)
-
- integer jn,j,kn,k
- integer elti,eltj,eltk
- real*8 xitmp,yitmp,zitmp,delxij,delyij,delzij,rij2,rij
- real*8 xjtmp,yjtmp,zjtmp,delxik,delyik,delzik,rik2,rik
- real*8 xktmp,yktmp,zktmp,delxjk,delyjk,delzjk,rjk2,rjk
- real*8 xik,xjk,sij,fcij,sfcij,dfcij,sikj,dfikj,cikj
- real*8 Cmin,Cmax,delc,ebound,rbound,a,coef1,coef2
- real*8 coef1a,coef1b,coef2a,coef2b
- real*8 dcikj
- real*8 dC1a,dC1b,dC2a,dC2b
- real*8 rnorm,fc,dfc,drinv
-
- drinv = 1.d0/delr_meam
- elti = fmap(type(i))
-
- if (elti.gt.0) then
-
- xitmp = x(1,i)
- yitmp = x(2,i)
- zitmp = x(3,i)
-
- do jn = 1,numneigh
- j = firstneigh(jn)
-
- eltj = fmap(type(j))
- if (eltj.gt.0) then
-
-c First compute screening function itself, sij
- xjtmp = x(1,j)
- yjtmp = x(2,j)
- zjtmp = x(3,j)
- delxij = xjtmp - xitmp
- delyij = yjtmp - yitmp
- delzij = zjtmp - zitmp
- rij2 = delxij*delxij + delyij*delyij + delzij*delzij
- rij = sqrt(rij2)
- if (rij.gt.rc_meam) then
- fcij = 0.0
- dfcij = 0.d0
- sij = 0.d0
- else
- rnorm = (rc_meam-rij)*drinv
- call screen(i, j, nmax, x, rij2, sij,
- $ numneigh_full, firstneigh_full, ntype, type, fmap)
- call dfcut(rnorm,fc,dfc)
- fcij = fc
- dfcij = dfc*drinv
- endif
-
-c Now compute derivatives
- dscrfcn(jn) = 0.d0
- sfcij = sij*fcij
- if (sfcij.eq.0.d0.or.sfcij.eq.1.d0) goto 100
- rbound = ebound_meam(elti,eltj) * rij2
- do kn = 1,numneigh_full
- k = firstneigh_full(kn)
- if (k.eq.j) goto 10
- eltk = fmap(type(k))
- if (eltk.eq.0) goto 10
- xktmp = x(1,k)
- yktmp = x(2,k)
- zktmp = x(3,k)
- delxjk = xktmp - xjtmp
- delyjk = yktmp - yjtmp
- delzjk = zktmp - zjtmp
- rjk2 = delxjk*delxjk + delyjk*delyjk + delzjk*delzjk
- if (rjk2.gt.rbound) goto 10
- delxik = xktmp - xitmp
- delyik = yktmp - yitmp
- delzik = zktmp - zitmp
- rik2 = delxik*delxik + delyik*delyik + delzik*delzik
- if (rik2.gt.rbound) goto 10
- xik = rik2/rij2
- xjk = rjk2/rij2
- a = 1 - (xik-xjk)*(xik-xjk)
-c if a < 0, then ellipse equation doesn't describe this case and
-c atom k can't possibly screen i-j
- if (a.le.0.d0) goto 10
- cikj = (2.d0*(xik+xjk) + a - 2.d0)/a
- Cmax = Cmax_meam(elti,eltj,eltk)
- Cmin = Cmin_meam(elti,eltj,eltk)
- if (cikj.ge.Cmax) then
- goto 10
-c Note that cikj may be slightly negative (within numerical
-c tolerance) if atoms are colinear, so don't reject that case here
-c (other negative cikj cases were handled by the test on "a" above)
-c Note that we never have 0<cikj<Cmin here, else sij=0 (rejected above)
- else
- delc = Cmax - Cmin
- cikj = (cikj-Cmin)/delc
- call dfcut(cikj,sikj,dfikj)
- coef1 = dfikj/(delc*sikj)
- call dCfunc(rij2,rik2,rjk2,dCikj)
- dscrfcn(jn) = dscrfcn(jn) + coef1*dCikj
- endif
- 10 continue
- enddo
- coef1 = sfcij
- coef2 = sij*dfcij/rij
- dscrfcn(jn) = dscrfcn(jn)*coef1 - coef2
- 100 continue
-
- scrfcn(jn) = sij
- fcpair(jn) = fcij
-
- endif
-
- enddo
-
- endif
-
- return
- end
-
-
-cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
-
- subroutine calc_rho1(i, nmax, ntype, type, fmap, x,
- $ numneigh, firstneigh,
- $ scrfcn, fcpair, rho0, arho1, arho2, arho2b,
- $ arho3, arho3b, t_ave, tsq_ave)
-
- use meam_data
- implicit none
-
- integer i, nmax, ntype, type, fmap
- real*8 x
- integer numneigh, firstneigh
- real*8 scrfcn, fcpair, rho0, arho1, arho2
- real*8 arho2b, arho3, arho3b, t_ave, tsq_ave
-
- dimension type(nmax), fmap(ntype), x(3,nmax)
- dimension firstneigh(numneigh)
- dimension scrfcn(numneigh), fcpair(numneigh)
- dimension rho0(nmax), arho1(3,nmax), arho2(6,nmax)
- dimension arho2b(nmax), arho3(10,nmax), arho3b(3,nmax)
- dimension t_ave(3,nmax), tsq_ave(3,nmax)
-
- integer jn,j,m,n,p,elti,eltj
- integer nv2,nv3
- real*8 xtmp,ytmp,ztmp,delij(3),rij2,rij,sij
- real*8 ai,aj,rhoa0j,rhoa1j,rhoa2j,rhoa3j,A1j,A2j,A3j
- real*8 G,Gbar,gam,shp(3)
- real*8 ro0i,ro0j
- real*8 rhoa0i,rhoa1i,rhoa2i,rhoa3i,A1i,A2i,A3i
-
- elti = fmap(type(i))
- xtmp = x(1,i)
- ytmp = x(2,i)
- ztmp = x(3,i)
- do jn = 1,numneigh
- if (scrfcn(jn).ne.0.d0) then
- j = firstneigh(jn)
- sij = scrfcn(jn)*fcpair(jn)
- delij(1) = x(1,j) - xtmp
- delij(2) = x(2,j) - ytmp
- delij(3) = x(3,j) - ztmp
- rij2 = delij(1)*delij(1) + delij(2)*delij(2)
- $ + delij(3)*delij(3)
- if (rij2.lt.cutforcesq) then
- eltj = fmap(type(j))
- rij = sqrt(rij2)
- ai = rij/re_meam(elti,elti) - 1.d0
- aj = rij/re_meam(eltj,eltj) - 1.d0
- ro0i = rho0_meam(elti)
- ro0j = rho0_meam(eltj)
- rhoa0j = ro0j*fm_exp(-beta0_meam(eltj)*aj)*sij
- rhoa1j = ro0j*fm_exp(-beta1_meam(eltj)*aj)*sij
- rhoa2j = ro0j*fm_exp(-beta2_meam(eltj)*aj)*sij
- rhoa3j = ro0j*fm_exp(-beta3_meam(eltj)*aj)*sij
- rhoa0i = ro0i*fm_exp(-beta0_meam(elti)*ai)*sij
- rhoa1i = ro0i*fm_exp(-beta1_meam(elti)*ai)*sij
- rhoa2i = ro0i*fm_exp(-beta2_meam(elti)*ai)*sij
- rhoa3i = ro0i*fm_exp(-beta3_meam(elti)*ai)*sij
- if (ialloy.eq.1) then
- rhoa1j = rhoa1j * t1_meam(eltj)
- rhoa2j = rhoa2j * t2_meam(eltj)
- rhoa3j = rhoa3j * t3_meam(eltj)
- rhoa1i = rhoa1i * t1_meam(elti)
- rhoa2i = rhoa2i * t2_meam(elti)
- rhoa3i = rhoa3i * t3_meam(elti)
- endif
- rho0(i) = rho0(i) + rhoa0j
- rho0(j) = rho0(j) + rhoa0i
-c For ialloy = 2, use single-element value (not average)
- if (ialloy.ne.2) then
- t_ave(1,i) = t_ave(1,i) + t1_meam(eltj)*rhoa0j
- t_ave(2,i) = t_ave(2,i) + t2_meam(eltj)*rhoa0j
- t_ave(3,i) = t_ave(3,i) + t3_meam(eltj)*rhoa0j
- t_ave(1,j) = t_ave(1,j) + t1_meam(elti)*rhoa0i
- t_ave(2,j) = t_ave(2,j) + t2_meam(elti)*rhoa0i
- t_ave(3,j) = t_ave(3,j) + t3_meam(elti)*rhoa0i
- endif
- if (ialloy.eq.1) then
- tsq_ave(1,i) = tsq_ave(1,i) +
- $ t1_meam(eltj)*t1_meam(eltj)*rhoa0j
- tsq_ave(2,i) = tsq_ave(2,i) +
- $ t2_meam(eltj)*t2_meam(eltj)*rhoa0j
- tsq_ave(3,i) = tsq_ave(3,i) +
- $ t3_meam(eltj)*t3_meam(eltj)*rhoa0j
- tsq_ave(1,j) = tsq_ave(1,j) +
- $ t1_meam(elti)*t1_meam(elti)*rhoa0i
- tsq_ave(2,j) = tsq_ave(2,j) +
- $ t2_meam(elti)*t2_meam(elti)*rhoa0i
- tsq_ave(3,j) = tsq_ave(3,j) +
- $ t3_meam(elti)*t3_meam(elti)*rhoa0i
- endif
- Arho2b(i) = Arho2b(i) + rhoa2j
- Arho2b(j) = Arho2b(j) + rhoa2i
-
- A1j = rhoa1j/rij
- A2j = rhoa2j/rij2
- A3j = rhoa3j/(rij2*rij)
- A1i = rhoa1i/rij
- A2i = rhoa2i/rij2
- A3i = rhoa3i/(rij2*rij)
- nv2 = 1
- nv3 = 1
- do m = 1,3
- Arho1(m,i) = Arho1(m,i) + A1j*delij(m)
- Arho1(m,j) = Arho1(m,j) - A1i*delij(m)
- Arho3b(m,i) = Arho3b(m,i) + rhoa3j*delij(m)/rij
- Arho3b(m,j) = Arho3b(m,j) - rhoa3i*delij(m)/rij
- do n = m,3
- Arho2(nv2,i) = Arho2(nv2,i) + A2j*delij(m)*delij(n)
- Arho2(nv2,j) = Arho2(nv2,j) + A2i*delij(m)*delij(n)
- nv2 = nv2+1
- do p = n,3
- Arho3(nv3,i) = Arho3(nv3,i)
- $ + A3j*delij(m)*delij(n)*delij(p)
- Arho3(nv3,j) = Arho3(nv3,j)
- $ - A3i*delij(m)*delij(n)*delij(p)
- nv3 = nv3+1
- enddo
- enddo
- enddo
- endif
- endif
- enddo
-
- return
- end
-
-cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
-
- subroutine screen(i, j, nmax, x, rijsq, sij,
- $ numneigh_full, firstneigh_full, ntype, type, fmap)
-c Screening function
-c Inputs: i = atom 1 id (integer)
-c j = atom 2 id (integer)
-c rijsq = squared distance between i and j
-c Outputs: sij = screening function
- use meam_data
- implicit none
-
- integer i,j,nmax,k,nk,m
- real*8 x,rijsq,sij
- integer numneigh_full, firstneigh_full
- integer ntype, type, fmap
-
- dimension x(3,nmax), firstneigh_full(numneigh_full)
- dimension type(nmax), fmap(ntype)
-
- integer elti,eltj,eltk
- real*8 delxik,delyik,delzik
- real*8 delxjk,delyjk,delzjk
- real*8 riksq,rjksq,xik,xjk,cikj,a,delc,sikj,fcij,rij
- real*8 Cmax,Cmin,rbound
-
- sij = 1.d0
- elti = fmap(type(i))
- eltj = fmap(type(j))
-
-c if rjksq > ebound*rijsq, atom k is definitely outside the ellipse
- rbound = ebound_meam(elti,eltj)*rijsq
-
- do nk = 1,numneigh_full
- k = firstneigh_full(nk)
- eltk = fmap(type(k))
- if (k.eq.j) goto 10
- delxjk = x(1,k) - x(1,j)
- delyjk = x(2,k) - x(2,j)
- delzjk = x(3,k) - x(3,j)
- rjksq = delxjk*delxjk + delyjk*delyjk + delzjk*delzjk
- if (rjksq.gt.rbound) goto 10
- delxik = x(1,k) - x(1,i)
- delyik = x(2,k) - x(2,i)
- delzik = x(3,k) - x(3,i)
- riksq = delxik*delxik + delyik*delyik + delzik*delzik
- if (riksq.gt.rbound) goto 10
- xik = riksq/rijsq
- xjk = rjksq/rijsq
- a = 1 - (xik-xjk)*(xik-xjk)
-c if a < 0, then ellipse equation doesn't describe this case and
-c atom k can't possibly screen i-j
- if (a.le.0.d0) goto 10
- cikj = (2.d0*(xik+xjk) + a - 2.d0)/a
- Cmax = Cmax_meam(elti,eltj,eltk)
- Cmin = Cmin_meam(elti,eltj,eltk)
- if (cikj.ge.Cmax) then
- goto 10
-c note that cikj may be slightly negative (within numerical
-c tolerance) if atoms are colinear, so don't reject that case here
-c (other negative cikj cases were handled by the test on "a" above)
- else if (cikj.le.Cmin) then
- sij = 0.d0
- goto 20
- else
- delc = Cmax - Cmin
- cikj = (cikj-Cmin)/delc
- call fcut(cikj,sikj)
- endif
- sij = sij * sikj
- 10 continue
- enddo
-
- 20 continue
-
- return
- end
-
-cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
-
- subroutine dsij(i,j,k,jn,nmax,numneigh,rij2,dsij1,dsij2,
- $ ntype,type,fmap,x,scrfcn,fcpair)
-c Inputs: i,j,k = id's of 3 atom triplet
-c jn = id of i-j pair
-c rij2 = squared distance between i and j
-c Outputs: dsij1 = deriv. of sij w.r.t. rik
-c dsij2 = deriv. of sij w.r.t. rjk
- use meam_data
- implicit none
- integer i,j,k,jn,nmax,numneigh
- integer elti,eltj,eltk
- real*8 rij2,rik2,rjk2,dsij1,dsij2
- integer ntype, type, fmap
- real*8 x, scrfcn, fcpair
-
- dimension type(nmax), fmap(ntype)
- dimension x(3,nmax), scrfcn(numneigh), fcpair(numneigh)
-
- real*8 dxik,dyik,dzik
- real*8 dxjk,dyjk,dzjk
- real*8 rbound,delc,sij,xik,xjk,cikj,sikj,dfc,a
- real*8 Cmax,Cmin,dCikj1,dCikj2
-
- sij = scrfcn(jn)*fcpair(jn)
- elti = fmap(type(i))
- eltj = fmap(type(j))
- eltk = fmap(type(k))
- Cmax = Cmax_meam(elti,eltj,eltk)
- Cmin = Cmin_meam(elti,eltj,eltk)
-
- dsij1 = 0.d0
- dsij2 = 0.d0
- if ((sij.ne.0.d0).and.(sij.ne.1.d0)) then
- rbound = rij2*ebound_meam(elti,eltj)
- delc = Cmax-Cmin
- dxjk = x(1,k) - x(1,j)
- dyjk = x(2,k) - x(2,j)
- dzjk = x(3,k) - x(3,j)
- rjk2 = dxjk*dxjk + dyjk*dyjk + dzjk*dzjk
- if (rjk2.le.rbound) then
- dxik = x(1,k) - x(1,i)
- dyik = x(2,k) - x(2,i)
- dzik = x(3,k) - x(3,i)
- rik2 = dxik*dxik + dyik*dyik + dzik*dzik
- if (rik2.le.rbound) then
- xik = rik2/rij2
- xjk = rjk2/rij2
- a = 1 - (xik-xjk)*(xik-xjk)
- if (a.ne.0.d0) then
- cikj = (2.d0*(xik+xjk) + a - 2.d0)/a
- if (cikj.ge.Cmin.and.cikj.le.Cmax) then
- cikj = (cikj-Cmin)/delc
- call dfcut(cikj,sikj,dfc)
- call dCfunc2(rij2,rik2,rjk2,dCikj1,dCikj2)
- a = sij/delc*dfc/sikj
- dsij1 = a*dCikj1
- dsij2 = a*dCikj2
- endif
- endif
- endif
- endif
- endif
-
- return
- end
-
-
-cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
-
- subroutine fcut(xi,fc)
-c cutoff function
- implicit none
- real*8 xi,fc
- real*8 a
- if (xi.ge.1.d0) then
- fc = 1.d0
- else if (xi.le.0.d0) then
- fc = 0.d0
- else
- a = 1.d0-xi
- a = a*a
- a = a*a
- a = 1.d0-a
- fc = a*a
-c fc = xi
- endif
- return
- end
-
-cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
-
- subroutine dfcut(xi,fc,dfc)
-c cutoff function and its derivative
- implicit none
- real*8 xi,fc,dfc,a,a3,a4
- if (xi.ge.1.d0) then
- fc = 1.d0
- dfc = 0.d0
- else if (xi.le.0.d0) then
- fc = 0.d0
- dfc = 0.d0
- else
- a = 1.d0-xi
- a3 = a*a*a
- a4 = a*a3
- fc = (1.d0-a4)**2
- dfc = 8*(1.d0-a4)*a3
-c fc = xi
-c dfc = 1.d0
- endif
- return
- end
-
-cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
-
- subroutine dCfunc(rij2,rik2,rjk2,dCikj)
-c Inputs: rij,rij2,rik2,rjk2
-c Outputs: dCikj = derivative of Cikj w.r.t. rij
- implicit none
- real*8 rij2,rik2,rjk2,dCikj
- real*8 rij4,a,b,denom
-
- rij4 = rij2*rij2
- a = rik2-rjk2
- b = rik2+rjk2
- denom = rij4 - a*a
- denom = denom*denom
- dCikj = -4*(-2*rij2*a*a + rij4*b + a*a*b)/denom
- return
- end
-
-cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
-
- subroutine dCfunc2(rij2,rik2,rjk2,dCikj1,dCikj2)
-c Inputs: rij,rij2,rik2,rjk2
-c Outputs: dCikj1 = derivative of Cikj w.r.t. rik
-c dCikj2 = derivative of Cikj w.r.t. rjk
- implicit none
- real*8 rij2,rik2,rjk2,dCikj1,dCikj2
- real*8 rij4,rik4,rjk4,a,b,denom
-
- rij4 = rij2*rij2
- rik4 = rik2*rik2
- rjk4 = rjk2*rjk2
- a = rik2-rjk2
- b = rik2+rjk2
- denom = rij4 - a*a
- denom = denom*denom
- dCikj1 = 4*rij2*(rij4 + rik4 + 2*rik2*rjk2 - 3*rjk4 - 2*rij2*a)/
- $ denom
- dCikj2 = 4*rij2*(rij4 - 3*rik4 + 2*rik2*rjk2 + rjk4 + 2*rij2*a)/
- $ denom
- return
- end
-
-cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
-
-
-
-
diff --git a/lib/meam/meam_force.F b/lib/meam/meam_force.F
deleted file mode 100644
index 1297eb217097015d0205f7fafa8c0c3e657b5345..0000000000000000000000000000000000000000
--- a/lib/meam/meam_force.F
+++ /dev/null
@@ -1,608 +0,0 @@
-c Extern "C" declaration has the form:
-c
-c void meam_force_(int *, int *, int *, double *, int *, int *, int *, double *,
-c int *, int *, int *, int *, double *, double *,
-c double *, double *, double *, double *, double *, double *,
-c double *, double *, double *, double *, double *, double *,
-c double *, double *, double *, double *, double *, double *, int *);
-c
-c Call from pair_meam.cpp has the form:
-c
-c meam_force_(&i,&nmax,&eflag_either,&eflag_global,&eflag_atom,&vflag_atom,
-c &eng_vdwl,eatom,&ntype,type,fmap,&x[0][0],
-c &numneigh[i],firstneigh[i],&numneigh_full[i],firstneigh_full[i],
-c &scrfcn[offset],&dscrfcn[offset],&fcpair[offset],
-c dgamma1,dgamma2,dgamma3,rho0,rho1,rho2,rho3,frhop,
-c &arho1[0][0],&arho2[0][0],arho2b,&arho3[0][0],&arho3b[0][0],
-c &t_ave[0][0],&tsq_ave[0][0],&f[0][0],&vatom[0][0],&errorflag);
-c
-
- subroutine meam_force(i, nmax,
- $ eflag_either, eflag_global, eflag_atom, vflag_atom,
- $ eng_vdwl, eatom, ntype, type, fmap, x,
- $ numneigh, firstneigh, numneigh_full, firstneigh_full,
- $ scrfcn, dscrfcn, fcpair,
- $ dGamma1, dGamma2, dGamma3, rho0, rho1, rho2, rho3, fp,
- $ Arho1, Arho2, Arho2b, Arho3, Arho3b, t_ave, tsq_ave, f,
- $ vatom, errorflag)
-
- use meam_data
- implicit none
-
- integer eflag_either, eflag_global, eflag_atom, vflag_atom
- integer nmax, ntype, type, fmap
- real*8 eng_vdwl, eatom, x
- integer numneigh, firstneigh, numneigh_full, firstneigh_full
- real*8 scrfcn, dscrfcn, fcpair
- real*8 dGamma1, dGamma2, dGamma3
- real*8 rho0, rho1, rho2, rho3, fp
- real*8 Arho1, Arho2, Arho2b
- real*8 Arho3, Arho3b
- real*8 t_ave, tsq_ave, f, vatom
- integer errorflag
-
- dimension eatom(nmax)
- dimension type(nmax), fmap(ntype)
- dimension x(3,nmax)
- dimension firstneigh(numneigh), firstneigh_full(numneigh_full)
- dimension scrfcn(numneigh), dscrfcn(numneigh), fcpair(numneigh)
- dimension dGamma1(nmax), dGamma2(nmax), dGamma3(nmax)
- dimension rho0(nmax), rho1(nmax), rho2(nmax), rho3(nmax), fp(nmax)
- dimension Arho1(3,nmax), Arho2(6,nmax), Arho2b(nmax)
- dimension Arho3(10,nmax), Arho3b(3,nmax)
- dimension t_ave(3,nmax), tsq_ave(3,nmax), f(3,nmax), vatom(6,nmax)
-
- integer i,j,jn,k,kn,kk,m,n,p,q
- integer nv2,nv3,elti,eltj,eltk,ind
- real*8 xitmp,yitmp,zitmp,delij(3),delref(3),rij2,rij,rij3
- real*8 delik(3),deljk(3),v(6),fi(3),fj(3)
- real*8 Eu,astar,astarp,third,sixth
- real*8 pp,phiforce,dUdrij,dUdsij,dUdrijm(3),force,forcem
- real*8 B,r,recip,phi,phip,rhop,a
- real*8 sij,fcij,dfcij,ds(3)
- real*8 a0,a1,a1i,a1j,a2,a2i,a2j
- real*8 a3i,a3j,a3i1,a3i2,a3j1,a3j2
- real*8 G,dG,Gbar,dGbar,gam,shpi(3),shpj(3),Z,denom
- real*8 ai,aj,ro0i,ro0j,invrei,invrej
- real*8 b0,rhoa0j,drhoa0j,rhoa0i,drhoa0i
- real*8 b1,rhoa1j,drhoa1j,rhoa1i,drhoa1i
- real*8 b2,rhoa2j,drhoa2j,rhoa2i,drhoa2i
- real*8 a3,a3a,b3,rhoa3j,drhoa3j,rhoa3i,drhoa3i
- real*8 drho0dr1,drho0dr2,drho0ds1,drho0ds2
- real*8 drho1dr1,drho1dr2,drho1ds1,drho1ds2
- real*8 drho1drm1(3),drho1drm2(3)
- real*8 drho2dr1,drho2dr2,drho2ds1,drho2ds2
- real*8 drho2drm1(3),drho2drm2(3)
- real*8 drho3dr1,drho3dr2,drho3ds1,drho3ds2
- real*8 drho3drm1(3),drho3drm2(3)
- real*8 dt1dr1,dt1dr2,dt1ds1,dt1ds2
- real*8 dt2dr1,dt2dr2,dt2ds1,dt2ds2
- real*8 dt3dr1,dt3dr2,dt3ds1,dt3ds2
- real*8 drhodr1,drhodr2,drhods1,drhods2,drhodrm1(3),drhodrm2(3)
- real*8 arg,arg1,arg2
- real*8 arg1i1,arg1j1,arg1i2,arg1j2,arg2i2,arg2j2
- real*8 arg1i3,arg1j3,arg2i3,arg2j3,arg3i3,arg3j3
- real*8 dsij1,dsij2,force1,force2
- real*8 t1i,t2i,t3i,t1j,t2j,t3j
-
- errorflag = 0
- third = 1.0/3.0
- sixth = 1.0/6.0
-
-c Compute forces atom i
-
- elti = fmap(type(i))
-
- if (elti.gt.0) then
- xitmp = x(1,i)
- yitmp = x(2,i)
- zitmp = x(3,i)
-
-c Treat each pair
- do jn = 1,numneigh
-
- j = firstneigh(jn)
- eltj = fmap(type(j))
-
- if (scrfcn(jn).ne.0.d0.and.eltj.gt.0) then
-
- sij = scrfcn(jn)*fcpair(jn)
- delij(1) = x(1,j) - xitmp
- delij(2) = x(2,j) - yitmp
- delij(3) = x(3,j) - zitmp
- rij2 = delij(1)*delij(1) + delij(2)*delij(2)
- $ + delij(3)*delij(3)
- if (rij2.lt.cutforcesq) then
- rij = sqrt(rij2)
- r = rij
-
-c Compute phi and phip
- ind = eltind(elti,eltj)
- pp = rij*rdrar + 1.0D0
- kk = pp
- kk = min(kk,nrar-1)
- pp = pp - kk
- pp = min(pp,1.0D0)
- phi = ((phirar3(kk,ind)*pp + phirar2(kk,ind))*pp
- $ + phirar1(kk,ind))*pp + phirar(kk,ind)
- phip = (phirar6(kk,ind)*pp + phirar5(kk,ind))*pp
- $ + phirar4(kk,ind)
- recip = 1.0d0/r
-
- if (eflag_either.ne.0) then
- if (eflag_global.ne.0) eng_vdwl = eng_vdwl + phi*sij
- if (eflag_atom.ne.0) then
- eatom(i) = eatom(i) + 0.5*phi*sij
- eatom(j) = eatom(j) + 0.5*phi*sij
- endif
- endif
-
-c write(1,*) "force_meamf: phi: ",phi
-c write(1,*) "force_meamf: phip: ",phip
-
-c Compute pair densities and derivatives
- invrei = 1.d0/re_meam(elti,elti)
- ai = rij*invrei - 1.d0
- ro0i = rho0_meam(elti)
- rhoa0i = ro0i*fm_exp(-beta0_meam(elti)*ai)
- drhoa0i = -beta0_meam(elti)*invrei*rhoa0i
- rhoa1i = ro0i*fm_exp(-beta1_meam(elti)*ai)
- drhoa1i = -beta1_meam(elti)*invrei*rhoa1i
- rhoa2i = ro0i*fm_exp(-beta2_meam(elti)*ai)
- drhoa2i = -beta2_meam(elti)*invrei*rhoa2i
- rhoa3i = ro0i*fm_exp(-beta3_meam(elti)*ai)
- drhoa3i = -beta3_meam(elti)*invrei*rhoa3i
-
- if (elti.ne.eltj) then
- invrej = 1.d0/re_meam(eltj,eltj)
- aj = rij*invrej - 1.d0
- ro0j = rho0_meam(eltj)
- rhoa0j = ro0j*fm_exp(-beta0_meam(eltj)*aj)
- drhoa0j = -beta0_meam(eltj)*invrej*rhoa0j
- rhoa1j = ro0j*fm_exp(-beta1_meam(eltj)*aj)
- drhoa1j = -beta1_meam(eltj)*invrej*rhoa1j
- rhoa2j = ro0j*fm_exp(-beta2_meam(eltj)*aj)
- drhoa2j = -beta2_meam(eltj)*invrej*rhoa2j
- rhoa3j = ro0j*fm_exp(-beta3_meam(eltj)*aj)
- drhoa3j = -beta3_meam(eltj)*invrej*rhoa3j
- else
- rhoa0j = rhoa0i
- drhoa0j = drhoa0i
- rhoa1j = rhoa1i
- drhoa1j = drhoa1i
- rhoa2j = rhoa2i
- drhoa2j = drhoa2i
- rhoa3j = rhoa3i
- drhoa3j = drhoa3i
- endif
-
- if (ialloy.eq.1) then
- rhoa1j = rhoa1j * t1_meam(eltj)
- rhoa2j = rhoa2j * t2_meam(eltj)
- rhoa3j = rhoa3j * t3_meam(eltj)
- rhoa1i = rhoa1i * t1_meam(elti)
- rhoa2i = rhoa2i * t2_meam(elti)
- rhoa3i = rhoa3i * t3_meam(elti)
- drhoa1j = drhoa1j * t1_meam(eltj)
- drhoa2j = drhoa2j * t2_meam(eltj)
- drhoa3j = drhoa3j * t3_meam(eltj)
- drhoa1i = drhoa1i * t1_meam(elti)
- drhoa2i = drhoa2i * t2_meam(elti)
- drhoa3i = drhoa3i * t3_meam(elti)
- endif
-
- nv2 = 1
- nv3 = 1
- arg1i1 = 0.d0
- arg1j1 = 0.d0
- arg1i2 = 0.d0
- arg1j2 = 0.d0
- arg1i3 = 0.d0
- arg1j3 = 0.d0
- arg3i3 = 0.d0
- arg3j3 = 0.d0
- do n = 1,3
- do p = n,3
- do q = p,3
- arg = delij(n)*delij(p)*delij(q)*v3D(nv3)
- arg1i3 = arg1i3 + Arho3(nv3,i)*arg
- arg1j3 = arg1j3 - Arho3(nv3,j)*arg
- nv3 = nv3+1
- enddo
- arg = delij(n)*delij(p)*v2D(nv2)
- arg1i2 = arg1i2 + Arho2(nv2,i)*arg
- arg1j2 = arg1j2 + Arho2(nv2,j)*arg
- nv2 = nv2+1
- enddo
- arg1i1 = arg1i1 + Arho1(n,i)*delij(n)
- arg1j1 = arg1j1 - Arho1(n,j)*delij(n)
- arg3i3 = arg3i3 + Arho3b(n,i)*delij(n)
- arg3j3 = arg3j3 - Arho3b(n,j)*delij(n)
- enddo
-
-c rho0 terms
- drho0dr1 = drhoa0j * sij
- drho0dr2 = drhoa0i * sij
-
-c rho1 terms
- a1 = 2*sij/rij
- drho1dr1 = a1*(drhoa1j-rhoa1j/rij)*arg1i1
- drho1dr2 = a1*(drhoa1i-rhoa1i/rij)*arg1j1
- a1 = 2.d0*sij/rij
- do m = 1,3
- drho1drm1(m) = a1*rhoa1j*Arho1(m,i)
- drho1drm2(m) = -a1*rhoa1i*Arho1(m,j)
- enddo
-
-c rho2 terms
- a2 = 2*sij/rij2
- drho2dr1 = a2*(drhoa2j - 2*rhoa2j/rij)*arg1i2
- $ - 2.d0/3.d0*Arho2b(i)*drhoa2j*sij
- drho2dr2 = a2*(drhoa2i - 2*rhoa2i/rij)*arg1j2
- $ - 2.d0/3.d0*Arho2b(j)*drhoa2i*sij
- a2 = 4*sij/rij2
- do m = 1,3
- drho2drm1(m) = 0.d0
- drho2drm2(m) = 0.d0
- do n = 1,3
- drho2drm1(m) = drho2drm1(m)
- $ + Arho2(vind2D(m,n),i)*delij(n)
- drho2drm2(m) = drho2drm2(m)
- $ - Arho2(vind2D(m,n),j)*delij(n)
- enddo
- drho2drm1(m) = a2*rhoa2j*drho2drm1(m)
- drho2drm2(m) = -a2*rhoa2i*drho2drm2(m)
- enddo
-
-c rho3 terms
- rij3 = rij*rij2
- a3 = 2*sij/rij3
- a3a = 6.d0/5.d0*sij/rij
- drho3dr1 = a3*(drhoa3j - 3*rhoa3j/rij)*arg1i3
- $ - a3a*(drhoa3j - rhoa3j/rij)*arg3i3
- drho3dr2 = a3*(drhoa3i - 3*rhoa3i/rij)*arg1j3
- $ - a3a*(drhoa3i - rhoa3i/rij)*arg3j3
- a3 = 6*sij/rij3
- a3a = 6*sij/(5*rij)
- do m = 1,3
- drho3drm1(m) = 0.d0
- drho3drm2(m) = 0.d0
- nv2 = 1
- do n = 1,3
- do p = n,3
- arg = delij(n)*delij(p)*v2D(nv2)
- drho3drm1(m) = drho3drm1(m)
- $ + Arho3(vind3D(m,n,p),i)*arg
- drho3drm2(m) = drho3drm2(m)
- $ + Arho3(vind3D(m,n,p),j)*arg
- nv2 = nv2 + 1
- enddo
- enddo
- drho3drm1(m) = (a3*drho3drm1(m) - a3a*Arho3b(m,i))
- $ *rhoa3j
- drho3drm2(m) = (-a3*drho3drm2(m) + a3a*Arho3b(m,j))
- $ *rhoa3i
- enddo
-
-c Compute derivatives of weighting functions t wrt rij
- t1i = t_ave(1,i)
- t2i = t_ave(2,i)
- t3i = t_ave(3,i)
- t1j = t_ave(1,j)
- t2j = t_ave(2,j)
- t3j = t_ave(3,j)
-
- if (ialloy.eq.1) then
-
- a1i = 0.d0
- a1j = 0.d0
- a2i = 0.d0
- a2j = 0.d0
- a3i = 0.d0
- a3j = 0.d0
- if ( tsq_ave(1,i) .ne. 0.d0 ) then
- a1i = drhoa0j*sij/tsq_ave(1,i)
- endif
- if ( tsq_ave(1,j) .ne. 0.d0 ) then
- a1j = drhoa0i*sij/tsq_ave(1,j)
- endif
- if ( tsq_ave(2,i) .ne. 0.d0 ) then
- a2i = drhoa0j*sij/tsq_ave(2,i)
- endif
- if ( tsq_ave(2,j) .ne. 0.d0 ) then
- a2j = drhoa0i*sij/tsq_ave(2,j)
- endif
- if ( tsq_ave(3,i) .ne. 0.d0 ) then
- a3i = drhoa0j*sij/tsq_ave(3,i)
- endif
- if ( tsq_ave(3,j) .ne. 0.d0 ) then
- a3j = drhoa0i*sij/tsq_ave(3,j)
- endif
-
- dt1dr1 = a1i*(t1_meam(eltj)-t1i*t1_meam(eltj)**2)
- dt1dr2 = a1j*(t1_meam(elti)-t1j*t1_meam(elti)**2)
- dt2dr1 = a2i*(t2_meam(eltj)-t2i*t2_meam(eltj)**2)
- dt2dr2 = a2j*(t2_meam(elti)-t2j*t2_meam(elti)**2)
- dt3dr1 = a3i*(t3_meam(eltj)-t3i*t3_meam(eltj)**2)
- dt3dr2 = a3j*(t3_meam(elti)-t3j*t3_meam(elti)**2)
-
- else if (ialloy.eq.2) then
-
- dt1dr1 = 0.d0
- dt1dr2 = 0.d0
- dt2dr1 = 0.d0
- dt2dr2 = 0.d0
- dt3dr1 = 0.d0
- dt3dr2 = 0.d0
-
- else
-
- ai = 0.d0
- if( rho0(i) .ne. 0.d0 ) then
- ai = drhoa0j*sij/rho0(i)
- end if
- aj = 0.d0
- if( rho0(j) .ne. 0.d0 ) then
- aj = drhoa0i*sij/rho0(j)
- end if
-
- dt1dr1 = ai*(t1_meam(eltj)-t1i)
- dt1dr2 = aj*(t1_meam(elti)-t1j)
- dt2dr1 = ai*(t2_meam(eltj)-t2i)
- dt2dr2 = aj*(t2_meam(elti)-t2j)
- dt3dr1 = ai*(t3_meam(eltj)-t3i)
- dt3dr2 = aj*(t3_meam(elti)-t3j)
-
- endif
-
-c Compute derivatives of total density wrt rij, sij and rij(3)
- call get_shpfcn(shpi,lattce_meam(elti,elti))
- call get_shpfcn(shpj,lattce_meam(eltj,eltj))
- drhodr1 = dGamma1(i)*drho0dr1
- $ + dGamma2(i)*
- $ (dt1dr1*rho1(i)+t1i*drho1dr1
- $ + dt2dr1*rho2(i)+t2i*drho2dr1
- $ + dt3dr1*rho3(i)+t3i*drho3dr1)
- $ - dGamma3(i)*
- $ (shpi(1)*dt1dr1+shpi(2)*dt2dr1+shpi(3)*dt3dr1)
- drhodr2 = dGamma1(j)*drho0dr2
- $ + dGamma2(j)*
- $ (dt1dr2*rho1(j)+t1j*drho1dr2
- $ + dt2dr2*rho2(j)+t2j*drho2dr2
- $ + dt3dr2*rho3(j)+t3j*drho3dr2)
- $ - dGamma3(j)*
- $ (shpj(1)*dt1dr2+shpj(2)*dt2dr2+shpj(3)*dt3dr2)
- do m = 1,3
- drhodrm1(m) = 0.d0
- drhodrm2(m) = 0.d0
- drhodrm1(m) = dGamma2(i)*
- $ (t1i*drho1drm1(m)
- $ + t2i*drho2drm1(m)
- $ + t3i*drho3drm1(m))
- drhodrm2(m) = dGamma2(j)*
- $ (t1j*drho1drm2(m)
- $ + t2j*drho2drm2(m)
- $ + t3j*drho3drm2(m))
- enddo
-
-c Compute derivatives wrt sij, but only if necessary
- if (dscrfcn(jn).ne.0.d0) then
- drho0ds1 = rhoa0j
- drho0ds2 = rhoa0i
- a1 = 2.d0/rij
- drho1ds1 = a1*rhoa1j*arg1i1
- drho1ds2 = a1*rhoa1i*arg1j1
- a2 = 2.d0/rij2
- drho2ds1 = a2*rhoa2j*arg1i2
- $ - 2.d0/3.d0*Arho2b(i)*rhoa2j
- drho2ds2 = a2*rhoa2i*arg1j2
- $ - 2.d0/3.d0*Arho2b(j)*rhoa2i
- a3 = 2.d0/rij3
- a3a = 6.d0/(5.d0*rij)
- drho3ds1 = a3*rhoa3j*arg1i3 - a3a*rhoa3j*arg3i3
- drho3ds2 = a3*rhoa3i*arg1j3 - a3a*rhoa3i*arg3j3
-
- if (ialloy.eq.1) then
-
- a1i = 0.d0
- a1j = 0.d0
- a2i = 0.d0
- a2j = 0.d0
- a3i = 0.d0
- a3j = 0.d0
- if ( tsq_ave(1,i) .ne. 0.d0 ) then
- a1i = rhoa0j/tsq_ave(1,i)
- endif
- if ( tsq_ave(1,j) .ne. 0.d0 ) then
- a1j = rhoa0i/tsq_ave(1,j)
- endif
- if ( tsq_ave(2,i) .ne. 0.d0 ) then
- a2i = rhoa0j/tsq_ave(2,i)
- endif
- if ( tsq_ave(2,j) .ne. 0.d0 ) then
- a2j = rhoa0i/tsq_ave(2,j)
- endif
- if ( tsq_ave(3,i) .ne. 0.d0 ) then
- a3i = rhoa0j/tsq_ave(3,i)
- endif
- if ( tsq_ave(3,j) .ne. 0.d0 ) then
- a3j = rhoa0i/tsq_ave(3,j)
- endif
-
- dt1ds1 = a1i*(t1_meam(eltj)-t1i*t1_meam(eltj)**2)
- dt1ds2 = a1j*(t1_meam(elti)-t1j*t1_meam(elti)**2)
- dt2ds1 = a2i*(t2_meam(eltj)-t2i*t2_meam(eltj)**2)
- dt2ds2 = a2j*(t2_meam(elti)-t2j*t2_meam(elti)**2)
- dt3ds1 = a3i*(t3_meam(eltj)-t3i*t3_meam(eltj)**2)
- dt3ds2 = a3j*(t3_meam(elti)-t3j*t3_meam(elti)**2)
-
- else if (ialloy.eq.2) then
-
- dt1ds1 = 0.d0
- dt1ds2 = 0.d0
- dt2ds1 = 0.d0
- dt2ds2 = 0.d0
- dt3ds1 = 0.d0
- dt3ds2 = 0.d0
-
- else
-
- ai = 0.d0
- if( rho0(i) .ne. 0.d0 ) then
- ai = rhoa0j/rho0(i)
- end if
- aj = 0.d0
- if( rho0(j) .ne. 0.d0 ) then
- aj = rhoa0i/rho0(j)
- end if
-
- dt1ds1 = ai*(t1_meam(eltj)-t1i)
- dt1ds2 = aj*(t1_meam(elti)-t1j)
- dt2ds1 = ai*(t2_meam(eltj)-t2i)
- dt2ds2 = aj*(t2_meam(elti)-t2j)
- dt3ds1 = ai*(t3_meam(eltj)-t3i)
- dt3ds2 = aj*(t3_meam(elti)-t3j)
-
- endif
-
- drhods1 = dGamma1(i)*drho0ds1
- $ + dGamma2(i)*
- $ (dt1ds1*rho1(i)+t1i*drho1ds1
- $ + dt2ds1*rho2(i)+t2i*drho2ds1
- $ + dt3ds1*rho3(i)+t3i*drho3ds1)
- $ - dGamma3(i)*
- $ (shpi(1)*dt1ds1+shpi(2)*dt2ds1+shpi(3)*dt3ds1)
- drhods2 = dGamma1(j)*drho0ds2
- $ + dGamma2(j)*
- $ (dt1ds2*rho1(j)+t1j*drho1ds2
- $ + dt2ds2*rho2(j)+t2j*drho2ds2
- $ + dt3ds2*rho3(j)+t3j*drho3ds2)
- $ - dGamma3(j)*
- $ (shpj(1)*dt1ds2+shpj(2)*dt2ds2+shpj(3)*dt3ds2)
- endif
-
-c Compute derivatives of energy wrt rij, sij and rij(3)
- dUdrij = phip*sij
- $ + fp(i)*drhodr1 + fp(j)*drhodr2
- dUdsij = 0.d0
- if (dscrfcn(jn).ne.0.d0) then
- dUdsij = phi
- $ + fp(i)*drhods1 + fp(j)*drhods2
- endif
- do m = 1,3
- dUdrijm(m) = fp(i)*drhodrm1(m) + fp(j)*drhodrm2(m)
- enddo
-
-c Add the part of the force due to dUdrij and dUdsij
-
- force = dUdrij*recip + dUdsij*dscrfcn(jn)
- do m = 1,3
- forcem = delij(m)*force + dUdrijm(m)
- f(m,i) = f(m,i) + forcem
- f(m,j) = f(m,j) - forcem
- enddo
-
-c Tabulate per-atom virial as symmetrized stress tensor
-
- if (vflag_atom.ne.0) then
- fi(1) = delij(1)*force + dUdrijm(1)
- fi(2) = delij(2)*force + dUdrijm(2)
- fi(3) = delij(3)*force + dUdrijm(3)
- v(1) = -0.5 * (delij(1) * fi(1))
- v(2) = -0.5 * (delij(2) * fi(2))
- v(3) = -0.5 * (delij(3) * fi(3))
- v(4) = -0.25 * (delij(1)*fi(2) + delij(2)*fi(1))
- v(5) = -0.25 * (delij(1)*fi(3) + delij(3)*fi(1))
- v(6) = -0.25 * (delij(2)*fi(3) + delij(3)*fi(2))
-
- vatom(1,i) = vatom(1,i) + v(1)
- vatom(2,i) = vatom(2,i) + v(2)
- vatom(3,i) = vatom(3,i) + v(3)
- vatom(4,i) = vatom(4,i) + v(4)
- vatom(5,i) = vatom(5,i) + v(5)
- vatom(6,i) = vatom(6,i) + v(6)
- vatom(1,j) = vatom(1,j) + v(1)
- vatom(2,j) = vatom(2,j) + v(2)
- vatom(3,j) = vatom(3,j) + v(3)
- vatom(4,j) = vatom(4,j) + v(4)
- vatom(5,j) = vatom(5,j) + v(5)
- vatom(6,j) = vatom(6,j) + v(6)
- endif
-
-c Now compute forces on other atoms k due to change in sij
-
- if (sij.eq.0.d0.or.sij.eq.1.d0) goto 100
- do kn = 1,numneigh_full
- k = firstneigh_full(kn)
- eltk = fmap(type(k))
- if (k.ne.j.and.eltk.gt.0) then
- call dsij(i,j,k,jn,nmax,numneigh,rij2,dsij1,dsij2,
- $ ntype,type,fmap,x,scrfcn,fcpair)
- if (dsij1.ne.0.d0.or.dsij2.ne.0.d0) then
- force1 = dUdsij*dsij1
- force2 = dUdsij*dsij2
- do m = 1,3
- delik(m) = x(m,k) - x(m,i)
- deljk(m) = x(m,k) - x(m,j)
- enddo
- do m = 1,3
- f(m,i) = f(m,i) + force1*delik(m)
- f(m,j) = f(m,j) + force2*deljk(m)
- f(m,k) = f(m,k) - force1*delik(m)
- $ - force2*deljk(m)
- enddo
-
-c Tabulate per-atom virial as symmetrized stress tensor
-
- if (vflag_atom.ne.0) then
- fi(1) = force1*delik(1)
- fi(2) = force1*delik(2)
- fi(3) = force1*delik(3)
- fj(1) = force2*deljk(1)
- fj(2) = force2*deljk(2)
- fj(3) = force2*deljk(3)
- v(1) = -third * (delik(1)*fi(1) + deljk(1)*fj(1))
- v(2) = -third * (delik(2)*fi(2) + deljk(2)*fj(2))
- v(3) = -third * (delik(3)*fi(3) + deljk(3)*fj(3))
- v(4) = -sixth * (delik(1)*fi(2) + deljk(1)*fj(2) +
- $ delik(2)*fi(1) + deljk(2)*fj(1))
- v(5) = -sixth * (delik(1)*fi(3) + deljk(1)*fj(3) +
- $ delik(3)*fi(1) + deljk(3)*fj(1))
- v(6) = -sixth * (delik(2)*fi(3) + deljk(2)*fj(3) +
- $ delik(3)*fi(2) + deljk(3)*fj(2))
-
- vatom(1,i) = vatom(1,i) + v(1)
- vatom(2,i) = vatom(2,i) + v(2)
- vatom(3,i) = vatom(3,i) + v(3)
- vatom(4,i) = vatom(4,i) + v(4)
- vatom(5,i) = vatom(5,i) + v(5)
- vatom(6,i) = vatom(6,i) + v(6)
- vatom(1,j) = vatom(1,j) + v(1)
- vatom(2,j) = vatom(2,j) + v(2)
- vatom(3,j) = vatom(3,j) + v(3)
- vatom(4,j) = vatom(4,j) + v(4)
- vatom(5,j) = vatom(5,j) + v(5)
- vatom(6,j) = vatom(6,j) + v(6)
- vatom(1,k) = vatom(1,k) + v(1)
- vatom(2,k) = vatom(2,k) + v(2)
- vatom(3,k) = vatom(3,k) + v(3)
- vatom(4,k) = vatom(4,k) + v(4)
- vatom(5,k) = vatom(5,k) + v(5)
- vatom(6,k) = vatom(6,k) + v(6)
- endif
-
- endif
- endif
-c end of k loop
- enddo
- endif
- 100 continue
- endif
-c end of j loop
- enddo
-
-c else if elti=0, this is not a meam atom
- endif
-
- return
- end
diff --git a/lib/meam/meam_setup_done.F b/lib/meam/meam_setup_done.F
deleted file mode 100644
index c94bce8b445602ca6a8d8d3b0b56028d425f67e4..0000000000000000000000000000000000000000
--- a/lib/meam/meam_setup_done.F
+++ /dev/null
@@ -1,1041 +0,0 @@
-c Declaration in pair_meam.h:
-c
-c void meam_setup_done(double *)
-c
-c Call from pair_meam.cpp:
-c
-c meam_setup_done(&cutmax)
-c
-
- subroutine meam_setup_done(cutmax)
- use meam_data
- implicit none
-
- real*8 cutmax
-
- integer nv2, nv3, m, n, p
-
-c Force cutoff
- cutforce = rc_meam
- cutforcesq = cutforce*cutforce
-
-c Pass cutoff back to calling program
- cutmax = cutforce
-
-c Augment t1 term
- t1_meam(:) = t1_meam(:) + augt1 * 3.d0/5.d0 * t3_meam(:)
-
-c Compute off-diagonal alloy parameters
- call alloyparams
-
-c indices and factors for Voight notation
- nv2 = 1
- nv3 = 1
- do m = 1,3
- do n = m,3
- vind2D(m,n) = nv2
- vind2D(n,m) = nv2
- nv2 = nv2+1
- do p = n,3
- vind3D(m,n,p) = nv3
- vind3D(m,p,n) = nv3
- vind3D(n,m,p) = nv3
- vind3D(n,p,m) = nv3
- vind3D(p,m,n) = nv3
- vind3D(p,n,m) = nv3
- nv3 = nv3+1
- enddo
- enddo
- enddo
-
- v2D(1) = 1
- v2D(2) = 2
- v2D(3) = 2
- v2D(4) = 1
- v2D(5) = 2
- v2D(6) = 1
-
- v3D(1) = 1
- v3D(2) = 3
- v3D(3) = 3
- v3D(4) = 3
- v3D(5) = 6
- v3D(6) = 3
- v3D(7) = 1
- v3D(8) = 3
- v3D(9) = 3
- v3D(10) = 1
-
- nv2 = 1
- do m = 1,neltypes
- do n = m,neltypes
- eltind(m,n) = nv2
- eltind(n,m) = nv2
- nv2 = nv2+1
- enddo
- enddo
-
-c Compute background densities for reference structure
- call compute_reference_density
-
-c Compute pair potentials and setup arrays for interpolation
- nr = 1000
- dr = 1.1*rc_meam/nr
- call compute_pair_meam
-
- return
- end
-
-cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
-c Fill off-diagonal alloy parameters
- subroutine alloyparams
- use meam_data
- implicit none
- integer i,j,k
- real*8 eb
-
-c Loop over pairs
- do i = 1,neltypes
- do j = 1,neltypes
-c Treat off-diagonal pairs
-c If i>j, set all equal to i<j case (which has aready been set,
-c here or in the input file)
- if (i.gt.j) then
- re_meam(i,j) = re_meam(j,i)
- Ec_meam(i,j) = Ec_meam(j,i)
- alpha_meam(i,j) = alpha_meam(j,i)
- lattce_meam(i,j) = lattce_meam(j,i)
- nn2_meam(i,j) = nn2_meam(j,i)
-c If i<j and term is unset, use default values (e.g. mean of i-i and j-j)
- else if (j.gt.i) then
- if (Ec_meam(i,j).eq.0.d0) then
- if (lattce_meam(i,j).eq.'l12') then
- Ec_meam(i,j) = (3*Ec_meam(i,i)+Ec_meam(j,j))/4.d0
- $ - delta_meam(i,j)
- else if (lattce_meam(i,j).eq.'c11') then
- if (lattce_meam(i,i).eq.'dia') then
- Ec_meam(i,j) = (2*Ec_meam(i,i)+Ec_meam(j,j))/3.d0
- $ - delta_meam(i,j)
- else
- Ec_meam(i,j) = (Ec_meam(i,i)+2*Ec_meam(j,j))/3.d0
- $ - delta_meam(i,j)
- endif
- else
- Ec_meam(i,j) = (Ec_meam(i,i)+Ec_meam(j,j))/2.d0
- $ - delta_meam(i,j)
- endif
- endif
- if (alpha_meam(i,j).eq.0.d0) then
- alpha_meam(i,j) = (alpha_meam(i,i)+alpha_meam(j,j))/2.d0
- endif
- if (re_meam(i,j).eq.0.d0) then
- re_meam(i,j) = (re_meam(i,i)+re_meam(j,j))/2.d0
- endif
- endif
- enddo
- enddo
-
-c Cmin(i,k,j) is symmetric in i-j, but not k. For all triplets
-c where i>j, set equal to the i<j element. Likewise for Cmax.
- do i = 2,neltypes
- do j = 1,i-1
- do k = 1,neltypes
- Cmin_meam(i,j,k) = Cmin_meam(j,i,k)
- Cmax_meam(i,j,k) = Cmax_meam(j,i,k)
- enddo
- enddo
- enddo
-
-c ebound gives the squared distance such that, for rik2 or rjk2>ebound,
-c atom k definitely lies outside the screening function ellipse (so
-c there is no need to calculate its effects). Here, compute it for all
-c triplets (i,j,k) so that ebound(i,j) is the maximized over k
- do i = 1,neltypes
- do j = 1,neltypes
- do k = 1,neltypes
- eb = (Cmax_meam(i,j,k)*Cmax_meam(i,j,k))
- $ /(4.d0*(Cmax_meam(i,j,k)-1.d0))
- ebound_meam(i,j) = max(ebound_meam(i,j),eb)
- enddo
- enddo
- enddo
-
- return
- end
-
-c-----------------------------------------------------------------------
-c compute MEAM pair potential for each pair of element types
-c
-
- subroutine compute_pair_meam
- use meam_data
- implicit none
-
- real*8 r, temp
- integer j,a,b,nv2
- real*8 astar,frac,phizbl
- integer n,nmax,Z1,Z2
- real*8 arat,rarat,scrn,scrn2
- real*8 phiaa,phibb,phitmp
- real*8 C,s111,s112,s221,S11,S22
-
- real*8, external :: phi_meam
- real*8, external :: zbl
- real*8, external :: compute_phi
-
-c check for previously allocated arrays and free them
- if(allocated(phir)) deallocate(phir)
- if(allocated(phirar)) deallocate(phirar)
- if(allocated(phirar1)) deallocate(phirar1)
- if(allocated(phirar2)) deallocate(phirar2)
- if(allocated(phirar3)) deallocate(phirar3)
- if(allocated(phirar4)) deallocate(phirar4)
- if(allocated(phirar5)) deallocate(phirar5)
- if(allocated(phirar6)) deallocate(phirar6)
-
-c allocate memory for array that defines the potential
- allocate(phir(nr,(neltypes*(neltypes+1))/2))
-
-c allocate coeff memory
-
- allocate(phirar(nr,(neltypes*(neltypes+1))/2))
- allocate(phirar1(nr,(neltypes*(neltypes+1))/2))
- allocate(phirar2(nr,(neltypes*(neltypes+1))/2))
- allocate(phirar3(nr,(neltypes*(neltypes+1))/2))
- allocate(phirar4(nr,(neltypes*(neltypes+1))/2))
- allocate(phirar5(nr,(neltypes*(neltypes+1))/2))
- allocate(phirar6(nr,(neltypes*(neltypes+1))/2))
-
-c loop over pairs of element types
- nv2 = 0
- do a = 1,neltypes
- do b = a,neltypes
- nv2 = nv2 + 1
-
-c loop over r values and compute
- do j = 1,nr
-
- r = (j-1)*dr
-
- phir(j,nv2) = phi_meam(r,a,b)
-
-c if using second-nearest neighbor, solve recursive problem
-c (see Lee and Baskes, PRB 62(13):8564 eqn.(21))
- if (nn2_meam(a,b).eq.1) then
- call get_Zij(Z1,lattce_meam(a,b))
- call get_Zij2(Z2,arat,scrn,lattce_meam(a,b),
- $ Cmin_meam(a,a,b),Cmax_meam(a,a,b))
-
-c The B1, B2, and L12 cases with NN2 have a trick to them; we need to
-c compute the contributions from second nearest neighbors, like a-a
-c pairs, but need to include NN2 contributions to those pairs as
-c well.
- if (lattce_meam(a,b).eq.'b1'.or.
- $ lattce_meam(a,b).eq.'b2'.or.
- $ lattce_meam(a,b).eq.'l12'.or.
- $ lattce_meam(a,b).eq.'dia') then
- rarat = r*arat
-
-c phi_aa
- phiaa = phi_meam(rarat,a,a)
- call get_Zij(Z1,lattce_meam(a,a))
- call get_Zij2(Z2,arat,scrn,lattce_meam(a,a),
- $ Cmin_meam(a,a,a),Cmax_meam(a,a,a))
- nmax = 10
- if (scrn.gt.0.0) then
- do n = 1,nmax
- phiaa = phiaa +
- $ (-Z2*scrn/Z1)**n * phi_meam(rarat*arat**n,a,a)
- enddo
- endif
-
-c phi_bb
- phibb = phi_meam(rarat,b,b)
- call get_Zij(Z1,lattce_meam(b,b))
- call get_Zij2(Z2,arat,scrn,lattce_meam(b,b),
- $ Cmin_meam(b,b,b),Cmax_meam(b,b,b))
- nmax = 10
- if (scrn.gt.0.0) then
- do n = 1,nmax
- phibb = phibb +
- $ (-Z2*scrn/Z1)**n * phi_meam(rarat*arat**n,b,b)
- enddo
- endif
-
- if (lattce_meam(a,b).eq.'b1'.
- $ or.lattce_meam(a,b).eq.'b2'.
- $ or.lattce_meam(a,b).eq.'dia') then
-c Add contributions to the B1 or B2 potential
- call get_Zij(Z1,lattce_meam(a,b))
- call get_Zij2(Z2,arat,scrn,lattce_meam(a,b),
- $ Cmin_meam(a,a,b),Cmax_meam(a,a,b))
- phir(j,nv2) = phir(j,nv2) -
- $ Z2*scrn/(2*Z1) * phiaa
- call get_Zij2(Z2,arat,scrn2,lattce_meam(a,b),
- $ Cmin_meam(b,b,a),Cmax_meam(b,b,a))
- phir(j,nv2) = phir(j,nv2) -
- $ Z2*scrn2/(2*Z1) * phibb
-
- else if (lattce_meam(a,b).eq.'l12') then
-c The L12 case has one last trick; we have to be careful to compute
-c the correct screening between 2nd-neighbor pairs. 1-1
-c second-neighbor pairs are screened by 2 type 1 atoms and two type
-c 2 atoms. 2-2 second-neighbor pairs are screened by 4 type 1
-c atoms.
- C = 1.d0
- call get_sijk(C,a,a,a,s111)
- call get_sijk(C,a,a,b,s112)
- call get_sijk(C,b,b,a,s221)
- S11 = s111 * s111 * s112 * s112
- S22 = s221**4
- phir(j,nv2) = phir(j,nv2) -
- $ 0.75*S11*phiaa - 0.25*S22*phibb
-
- endif
-
- else
- nmax = 10
- do n = 1,nmax
- phir(j,nv2) = phir(j,nv2) +
- $ (-Z2*scrn/Z1)**n * phi_meam(r*arat**n,a,b)
- enddo
- endif
-
- endif
-
-c For Zbl potential:
-c if astar <= -3
-c potential is zbl potential
-c else if -3 < astar < -1
-c potential is linear combination with zbl potential
-c endif
- if (zbl_meam(a,b).eq.1) then
- astar = alpha_meam(a,b) * (r/re_meam(a,b) - 1.d0)
- if (astar.le.-3.d0) then
- phir(j,nv2) = zbl(r,ielt_meam(a),ielt_meam(b))
- else if (astar.gt.-3.d0.and.astar.lt.-1.d0) then
- call fcut(1-(astar+1.d0)/(-3.d0+1.d0),frac)
- phizbl = zbl(r,ielt_meam(a),ielt_meam(b))
- phir(j,nv2) = frac*phir(j,nv2) + (1-frac)*phizbl
- endif
- endif
-
- enddo
-
-c call interpolation
- call interpolate_meam(nv2)
-
- enddo
- enddo
-
- return
- end
-
-
-c----------------------------------------------------------------------c
-c Compute MEAM pair potential for distance r, element types a and b
-c
- real*8 recursive function phi_meam(r,a,b)result(phi_m)
- use meam_data
- implicit none
-
-
- integer a,b
- real*8 r
- real*8 a1,a2,a12
- real*8 t11av,t21av,t31av,t12av,t22av,t32av
- real*8 G1,G2,s1(3),s2(3),s12(3),rho0_1,rho0_2
- real*8 Gam1,Gam2,Z1,Z2
- real*8 rhobar1,rhobar2,F1,F2
- real*8 rhoa01,rhoa11,rhoa21,rhoa31
- real*8 rhoa02,rhoa12,rhoa22,rhoa32
- real*8 rho01,rho11,rho21,rho31
- real*8 rho02,rho12,rho22,rho32
- real*8 scalfac,phiaa,phibb
- real*8 Eu
- real*8 arat,scrn,scrn2
- integer Z12, errorflag
- integer n,nmax,Z1nn,Z2nn
- character*3 latta,lattb
- real*8 rho_bkgd1, rho_bkgd2
-
- real*8, external :: erose
-
-c Equation numbers below refer to:
-c I. Huang et.al., Modelling simul. Mater. Sci. Eng. 3:615
-
-c get number of neighbors in the reference structure
-c Nref(i,j) = # of i's neighbors of type j
- call get_Zij(Z12,lattce_meam(a,b))
-
- call get_densref(r,a,b,rho01,rho11,rho21,rho31,
- $ rho02,rho12,rho22,rho32)
-
-c if densities are too small, numerical problems may result; just return zero
- if (rho01.le.1e-14.and.rho02.le.1e-14) then
- phi_m = 0.0
- return
- endif
-
-c calculate average weighting factors for the reference structure
- if (lattce_meam(a,b).eq.'c11') then
- if (ialloy.eq.2) then
- t11av = t1_meam(a)
- t12av = t1_meam(b)
- t21av = t2_meam(a)
- t22av = t2_meam(b)
- t31av = t3_meam(a)
- t32av = t3_meam(b)
- else
- scalfac = 1.0/(rho01+rho02)
- t11av = scalfac*(t1_meam(a)*rho01 + t1_meam(b)*rho02)
- t12av = t11av
- t21av = scalfac*(t2_meam(a)*rho01 + t2_meam(b)*rho02)
- t22av = t21av
- t31av = scalfac*(t3_meam(a)*rho01 + t3_meam(b)*rho02)
- t32av = t31av
- endif
- else
-c average weighting factors for the reference structure, eqn. I.8
- call get_tavref(t11av,t21av,t31av,t12av,t22av,t32av,
- $ t1_meam(a),t2_meam(a),t3_meam(a),
- $ t1_meam(b),t2_meam(b),t3_meam(b),
- $ r,a,b,lattce_meam(a,b))
- endif
-
-c for c11b structure, calculate background electron densities
- if (lattce_meam(a,b).eq.'c11') then
- latta = lattce_meam(a,a)
- if (latta.eq.'dia') then
- rhobar1 = ((Z12/2)*(rho02+rho01))**2 +
- $ t11av*(rho12-rho11)**2 +
- $ t21av/6.0*(rho22+rho21)**2 +
- $ 121.0/40.*t31av*(rho32-rho31)**2
- rhobar1 = sqrt(rhobar1)
- rhobar2 = (Z12*rho01)**2 + 2.0/3.0*t21av*rho21**2
- rhobar2 = sqrt(rhobar2)
- else
- rhobar2 = ((Z12/2)*(rho01+rho02))**2 +
- $ t12av*(rho11-rho12)**2 +
- $ t22av/6.0*(rho21+rho22)**2 +
- $ 121.0/40.*t32av*(rho31-rho32)**2
- rhobar2 = sqrt(rhobar2)
- rhobar1 = (Z12*rho02)**2 + 2.0/3.0*t22av*rho22**2
- rhobar1 = sqrt(rhobar1)
- endif
- else
-c for other structures, use formalism developed in Huang's paper
-c
-c composition-dependent scaling, equation I.7
-c If using mixing rule for t, apply to reference structure; else
-c use precomputed values
- if (mix_ref_t.eq.1) then
- Z1 = Z_meam(a)
- Z2 = Z_meam(b)
- if (ibar_meam(a).le.0) then
- G1 = 1.d0
- else
- call get_shpfcn(s1,lattce_meam(a,a))
- Gam1 = (s1(1)*t11av+s1(2)*t21av+s1(3)*t31av)/(Z1*Z1)
- call G_gam(Gam1,ibar_meam(a),gsmooth_factor,G1,errorflag)
- endif
- if (ibar_meam(b).le.0) then
- G2 = 1.d0
- else
- call get_shpfcn(s2,lattce_meam(b,b))
- Gam2 = (s2(1)*t12av+s2(2)*t22av+s2(3)*t32av)/(Z2*Z2)
- call G_gam(Gam2,ibar_meam(b),gsmooth_factor,G2,errorflag)
- endif
- rho0_1 = rho0_meam(a)*Z1*G1
- rho0_2 = rho0_meam(b)*Z2*G2
- endif
- Gam1 = (t11av*rho11+t21av*rho21+t31av*rho31)
- if (rho01 < 1.0d-14) then
- Gam1 = 0.0d0
- else
- Gam1 = Gam1/(rho01*rho01)
- endif
- Gam2 = (t12av*rho12+t22av*rho22+t32av*rho32)
- if (rho02 < 1.0d-14) then
- Gam2 = 0.0d0
- else
- Gam2 = Gam2/(rho02*rho02)
- endif
- call G_gam(Gam1,ibar_meam(a),gsmooth_factor,G1,errorflag)
- call G_gam(Gam2,ibar_meam(b),gsmooth_factor,G2,errorflag)
- if (mix_ref_t.eq.1) then
- rho_bkgd1 = rho0_1
- rho_bkgd2 = rho0_2
- else
- if (bkgd_dyn.eq.1) then
- rho_bkgd1 = rho0_meam(a)*Z_meam(a)
- rho_bkgd2 = rho0_meam(b)*Z_meam(b)
- else
- rho_bkgd1 = rho_ref_meam(a)
- rho_bkgd2 = rho_ref_meam(b)
- endif
- endif
- rhobar1 = rho01/rho_bkgd1*G1
- rhobar2 = rho02/rho_bkgd2*G2
-
- endif
-
-c compute embedding functions, eqn I.5
- if (rhobar1.eq.0.d0) then
- F1 = 0.d0
- else
- if (emb_lin_neg.eq.1 .and. rhobar1.le.0) then
- F1 = -A_meam(a)*Ec_meam(a,a)*rhobar1
- else
- F1 = A_meam(a)*Ec_meam(a,a)*rhobar1*log(rhobar1)
- endif
- endif
- if (rhobar2.eq.0.d0) then
- F2 = 0.d0
- else
- if (emb_lin_neg.eq.1 .and. rhobar2.le.0) then
- F2 = -A_meam(b)*Ec_meam(b,b)*rhobar2
- else
- F2 = A_meam(b)*Ec_meam(b,b)*rhobar2*log(rhobar2)
- endif
- endif
-
-c compute Rose function, I.16
- Eu = erose(r,re_meam(a,b),alpha_meam(a,b),
- $ Ec_meam(a,b),repuls_meam(a,b),attrac_meam(a,b),erose_form)
-
-c calculate the pair energy
- if (lattce_meam(a,b).eq.'c11') then
- latta = lattce_meam(a,a)
- if (latta.eq.'dia') then
- phiaa = phi_meam(r,a,a)
- phi_m = (3*Eu - F2 - 2*F1 - 5*phiaa)/Z12
- else
- phibb = phi_meam(r,b,b)
- phi_m = (3*Eu - F1 - 2*F2 - 5*phibb)/Z12
- endif
- else if (lattce_meam(a,b).eq.'l12') then
- phiaa = phi_meam(r,a,a)
-c account for second neighbor a-a potential here...
- call get_Zij(Z1nn,lattce_meam(a,a))
- call get_Zij2(Z2nn,arat,scrn,lattce_meam(a,a),
- $ Cmin_meam(a,a,a),Cmax_meam(a,a,a))
- nmax = 10
- if (scrn.gt.0.0) then
- do n = 1,nmax
- phiaa = phiaa +
- $ (-Z2nn*scrn/Z1nn)**n * phi_meam(r*arat**n,a,a)
- enddo
- endif
- phi_m = Eu/3. - F1/4. - F2/12. - phiaa
- else
-c
-c potential is computed from Rose function and embedding energy
- phi_m = (2*Eu - F1 - F2)/Z12
-c
- endif
-
-c if r = 0, just return 0
- if (r.eq.0.d0) then
- phi_m = 0.d0
- endif
-
- return
- end
-
-c----------------------------------------------------------------------c
-c Compute background density for reference structure of each element
- subroutine compute_reference_density
- use meam_data
- implicit none
-
- integer a,Z,Z2,errorflag
- real*8 gam,Gbar,shp(3)
- real*8 rho0,rho0_2nn,arat,scrn
-
-c loop over element types
- do a = 1,neltypes
-
- Z = Z_meam(a)
- if (ibar_meam(a).le.0) then
- Gbar = 1.d0
- else
- call get_shpfcn(shp,lattce_meam(a,a))
- gam = (t1_meam(a)*shp(1)+t2_meam(a)*shp(2)
- $ +t3_meam(a)*shp(3))/(Z*Z)
- call G_gam(gam,ibar_meam(a),gsmooth_factor,
- $ Gbar,errorflag)
- endif
-
-c The zeroth order density in the reference structure, with
-c equilibrium spacing, is just the number of first neighbors times
-c the rho0_meam coefficient...
- rho0 = rho0_meam(a)*Z
-
-c ...unless we have unscreened second neighbors, in which case we
-c add on the contribution from those (accounting for partial
-c screening)
- if (nn2_meam(a,a).eq.1) then
- call get_Zij2(Z2,arat,scrn,lattce_meam(a,a),
- $ Cmin_meam(a,a,a),Cmax_meam(a,a,a))
- rho0_2nn = rho0_meam(a)*fm_exp(-beta0_meam(a)*(arat-1))
- rho0 = rho0 + Z2*rho0_2nn*scrn
- endif
-
- rho_ref_meam(a) = rho0*Gbar
-
- enddo
-
- return
- end
-
-c----------------------------------------------------------------------c
-c Shape factors for various configurations
- subroutine get_shpfcn(s,latt)
- implicit none
- real*8 s(3)
- character*3 latt
- if (latt.eq.'fcc'.or.latt.eq.'bcc'.
- $ or.latt.eq.'b1'.or.latt.eq.'b2') then
- s(1) = 0.d0
- s(2) = 0.d0
- s(3) = 0.d0
- else if (latt.eq.'hcp') then
- s(1) = 0.d0
- s(2) = 0.d0
- s(3) = 1.d0/3.d0
- else if (latt.eq.'dia') then
- s(1) = 0.d0
- s(2) = 0.d0
- s(3) = 32.d0/9.d0
- else if (latt.eq.'dim') then
- s(1) = 1.d0
- s(2) = 2.d0/3.d0
-c s(3) = 1.d0
- s(3) = 0.4d0
- else
- s(1) = 0.0
-c call error('Lattice not defined in get_shpfcn.')
- endif
- return
- end
-c------------------------------------------------------------------------------c
-c Average weighting factors for the reference structure
- subroutine get_tavref(t11av,t21av,t31av,t12av,t22av,t32av,
- $ t11,t21,t31,t12,t22,t32,
- $ r,a,b,latt)
- use meam_data
- implicit none
- real*8 t11av,t21av,t31av,t12av,t22av,t32av
- real*8 t11,t21,t31,t12,t22,t32,r
- integer a,b
- character*3 latt
- real*8 rhoa01,rhoa02,a1,a2,rho01,rho02
-
-c For ialloy = 2, no averaging is done
- if (ialloy.eq.2) then
- t11av = t11
- t21av = t21
- t31av = t31
- t12av = t12
- t22av = t22
- t32av = t32
- else
- if (latt.eq.'fcc'.or.latt.eq.'bcc'.or.latt.eq.'dia'
- $ .or.latt.eq.'hcp'.or.latt.eq.'b1'
- $ .or.latt.eq.'dim'.or.latt.eq.'b2') then
-c all neighbors are of the opposite type
- t11av = t12
- t21av = t22
- t31av = t32
- t12av = t11
- t22av = t21
- t32av = t31
- else
- a1 = r/re_meam(a,a) - 1.d0
- a2 = r/re_meam(b,b) - 1.d0
- rhoa01 = rho0_meam(a)*fm_exp(-beta0_meam(a)*a1)
- rhoa02 = rho0_meam(b)*fm_exp(-beta0_meam(b)*a2)
- if (latt.eq.'l12') then
- rho01 = 8*rhoa01 + 4*rhoa02
- t11av = (8*t11*rhoa01 + 4*t12*rhoa02)/rho01
- t12av = t11
- t21av = (8*t21*rhoa01 + 4*t22*rhoa02)/rho01
- t22av = t21
- t31av = (8*t31*rhoa01 + 4*t32*rhoa02)/rho01
- t32av = t31
- else
-c call error('Lattice not defined in get_tavref.')
- endif
- endif
- endif
- return
- end
-c------------------------------------------------------------------------------c
-c Number of neighbors for the reference structure
- subroutine get_Zij(Zij,latt)
- implicit none
- integer Zij
- character*3 latt
- if (latt.eq.'fcc') then
- Zij = 12
- else if (latt.eq.'bcc') then
- Zij = 8
- else if (latt.eq.'hcp') then
- Zij = 12
- else if (latt.eq.'b1') then
- Zij = 6
- else if (latt.eq.'dia') then
- Zij = 4
- else if (latt.eq.'dim') then
- Zij = 1
- else if (latt.eq.'c11') then
- Zij = 10
- else if (latt.eq.'l12') then
- Zij = 12
- else if (latt.eq.'b2') then
- Zij = 8
- else
-c call error('Lattice not defined in get_Zij.')
- endif
- return
- end
-
-c------------------------------------------------------------------------------c
-c Zij2 = number of second neighbors, a = distance ratio R1/R2, and S = second
-c neighbor screening function for lattice type "latt"
-
- subroutine get_Zij2(Zij2,a,S,latt,cmin,cmax)
- implicit none
- integer Zij2
- real*8 a,S,cmin,cmax
- character*3 latt
- real*8 rratio,C,x,sijk
- integer numscr
-
- if (latt.eq.'bcc') then
- Zij2 = 6
- a = 2.d0/sqrt(3.d0)
- numscr = 4
- else if (latt.eq.'fcc') then
- Zij2 = 6
- a = sqrt(2.d0)
- numscr = 4
- else if (latt.eq.'dia') then
- Zij2 = 12
- a = sqrt(8.d0/3.d0)
- numscr = 1
- if (cmin.lt.0.500001) then
-c call error('can not do 2NN MEAM for dia')
- endif
- else if (latt.eq.'hcp') then
- Zij2 = 6
- a = sqrt(2.d0)
- numscr = 4
- else if (latt.eq.'b1') then
- Zij2 = 12
- a = sqrt(2.d0)
- numscr = 2
- else if (latt.eq.'l12') then
- Zij2 = 6
- a = sqrt(2.d0)
- numscr = 4
- else if (latt.eq.'b2') then
- Zij2 = 6
- a = 2.d0/sqrt(3.d0)
- numscr = 4
- else if (latt.eq.'dim') then
-c this really shouldn't be allowed; make sure screening is zero
- Zij2 = 0
- a = 1
- S = 0
- return
- else
-c call error('Lattice not defined in get_Zij2.')
- endif
-
-c Compute screening for each first neighbor
- C = 4.d0/(a*a) - 1.d0
- x = (C-cmin)/(cmax-cmin)
- call fcut(x,sijk)
-c There are numscr first neighbors screening the second neighbors
- S = sijk**numscr
-
- return
- end
-
-
-c------------------------------------------------------------------------------c
- subroutine get_sijk(C,i,j,k,sijk)
- use meam_data
- implicit none
- real*8 C,sijk
- integer i,j,k
- real*8 x
- x = (C-Cmin_meam(i,j,k))/(Cmax_meam(i,j,k)-Cmin_meam(i,j,k))
- call fcut(x,sijk)
- return
- end
-
-c------------------------------------------------------------------------------c
-c Calculate density functions, assuming reference configuration
- subroutine get_densref(r,a,b,rho01,rho11,rho21,rho31,
- $ rho02,rho12,rho22,rho32)
- use meam_data
- implicit none
- real*8 r,rho01,rho11,rho21,rho31,rho02,rho12,rho22,rho32
- real*8 a1,a2
- real*8 rhoa01,rhoa11,rhoa21,rhoa31,rhoa02,rhoa12,rhoa22,rhoa32
- real*8 s(3)
- character*3 lat
- integer a,b
- integer Zij1nn,Zij2nn
- real*8 rhoa01nn,rhoa02nn
- real*8 arat,scrn,denom
- real*8 C,s111,s112,s221,S11,S22
-
- a1 = r/re_meam(a,a) - 1.d0
- a2 = r/re_meam(b,b) - 1.d0
-
- rhoa01 = rho0_meam(a)*fm_exp(-beta0_meam(a)*a1)
- rhoa11 = rho0_meam(a)*fm_exp(-beta1_meam(a)*a1)
- rhoa21 = rho0_meam(a)*fm_exp(-beta2_meam(a)*a1)
- rhoa31 = rho0_meam(a)*fm_exp(-beta3_meam(a)*a1)
- rhoa02 = rho0_meam(b)*fm_exp(-beta0_meam(b)*a2)
- rhoa12 = rho0_meam(b)*fm_exp(-beta1_meam(b)*a2)
- rhoa22 = rho0_meam(b)*fm_exp(-beta2_meam(b)*a2)
- rhoa32 = rho0_meam(b)*fm_exp(-beta3_meam(b)*a2)
-
- lat = lattce_meam(a,b)
-
- rho11 = 0.d0
- rho21 = 0.d0
- rho31 = 0.d0
- rho12 = 0.d0
- rho22 = 0.d0
- rho32 = 0.d0
-
- call get_Zij(Zij1nn,lat)
-
- if (lat.eq.'fcc') then
- rho01 = 12.d0*rhoa02
- rho02 = 12.d0*rhoa01
- else if (lat.eq.'bcc') then
- rho01 = 8.d0*rhoa02
- rho02 = 8.d0*rhoa01
- else if (lat.eq.'b1') then
- rho01 = 6*rhoa02
- rho02 = 6*rhoa01
- else if (lat.eq.'dia') then
- rho01 = 4*rhoa02
- rho02 = 4*rhoa01
- rho31 = 32.d0/9.d0*rhoa32*rhoa32
- rho32 = 32.d0/9.d0*rhoa31*rhoa31
- else if (lat.eq.'hcp') then
- rho01 = 12*rhoa02
- rho02 = 12*rhoa01
- rho31 = 1.d0/3.d0*rhoa32*rhoa32
- rho32 = 1.d0/3.d0*rhoa31*rhoa31
- else if (lat.eq.'dim') then
- call get_shpfcn(s,'dim')
- rho01 = rhoa02
- rho02 = rhoa01
- rho11 = s(1)*rhoa12*rhoa12
- rho12 = s(1)*rhoa11*rhoa11
- rho21 = s(2)*rhoa22*rhoa22
- rho22 = s(2)*rhoa21*rhoa21
- rho31 = s(3)*rhoa32*rhoa32
- rho32 = s(3)*rhoa31*rhoa31
- else if (lat.eq.'c11') then
- rho01 = rhoa01
- rho02 = rhoa02
- rho11 = rhoa11
- rho12 = rhoa12
- rho21 = rhoa21
- rho22 = rhoa22
- rho31 = rhoa31
- rho32 = rhoa32
- else if (lat.eq.'l12') then
- rho01 = 8*rhoa01 + 4*rhoa02
- rho02 = 12*rhoa01
- if (ialloy.eq.1) then
- rho21 = 8./3.*(rhoa21*t2_meam(a)-rhoa22*t2_meam(b))**2
- denom = 8*rhoa01*t2_meam(a)**2 + 4*rhoa02*t2_meam(b)**2
- if (denom.gt.0.) then
- rho21 = rho21/denom * rho01
- endif
- else
- rho21 = 8./3.*(rhoa21-rhoa22)*(rhoa21-rhoa22)
- endif
- else if (lat.eq.'b2') then
- rho01 = 8.d0*rhoa02
- rho02 = 8.d0*rhoa01
- else
-c call error('Lattice not defined in get_densref.')
- endif
-
- if (nn2_meam(a,b).eq.1) then
-
- call get_Zij2(Zij2nn,arat,scrn,lat,
- $ Cmin_meam(a,a,b),Cmax_meam(a,a,b))
-
- a1 = arat*r/re_meam(a,a) - 1.d0
- a2 = arat*r/re_meam(b,b) - 1.d0
-
- rhoa01nn = rho0_meam(a)*fm_exp(-beta0_meam(a)*a1)
- rhoa02nn = rho0_meam(b)*fm_exp(-beta0_meam(b)*a2)
-
- if (lat.eq.'l12') then
-c As usual, L12 thinks it's special; we need to be careful computing
-c the screening functions
- C = 1.d0
- call get_sijk(C,a,a,a,s111)
- call get_sijk(C,a,a,b,s112)
- call get_sijk(C,b,b,a,s221)
- S11 = s111 * s111 * s112 * s112
- S22 = s221**4
- rho01 = rho01 + 6*S11*rhoa01nn
- rho02 = rho02 + 6*S22*rhoa02nn
-
- else
-c For other cases, assume that second neighbor is of same type,
-c first neighbor may be of different type
-
- rho01 = rho01 + Zij2nn*scrn*rhoa01nn
-
-c Assume Zij2nn and arat don't depend on order, but scrn might
- call get_Zij2(Zij2nn,arat,scrn,lat,
- $ Cmin_meam(b,b,a),Cmax_meam(b,b,a))
- rho02 = rho02 + Zij2nn*scrn*rhoa02nn
-
- endif
-
- endif
-
- return
- end
-
-c---------------------------------------------------------------------
-c Compute ZBL potential
-c
- real*8 function zbl(r,z1,z2)
- use meam_data , only : fm_exp
- implicit none
- integer i,z1,z2
- real*8 r,c,d,a,azero,cc,x
- dimension c(4),d(4)
- data c /0.028171,0.28022,0.50986,0.18175/
- data d /0.20162,0.40290,0.94229,3.1998/
- data azero /0.4685/
- data cc /14.3997/
-c azero = (9pi^2/128)^1/3 (0.529) Angstroms
- a = azero/(z1**0.23+z2**0.23)
- zbl = 0.0
- x = r/a
- do i=1,4
- zbl = zbl + c(i)*fm_exp(-d(i)*x)
- enddo
- if (r.gt.0.d0) zbl = zbl*z1*z2/r*cc
- return
- end
-
-c---------------------------------------------------------------------
-c Compute Rose energy function, I.16
-c
- real*8 function erose(r,re,alpha,Ec,repuls,attrac,form)
- use meam_data , only : fm_exp
- implicit none
- real*8 r,re,alpha,Ec,repuls,attrac,astar,a3
- integer form
-
- erose = 0.d0
-
- if (r.gt.0.d0) then
- astar = alpha * (r/re - 1.d0)
- a3 = 0.d0
- if (astar.ge.0) then
- a3 = attrac
- else if (astar.lt.0) then
- a3 = repuls
- endif
- if (form.eq.1) then
- erose = -Ec*(1+astar+(-attrac+repuls/r)*
- $ (astar**3))*fm_exp(-astar)
- else if (form.eq.2) then
- erose = -Ec * (1 +astar + a3*(astar**3))*fm_exp(-astar)
- else
- erose = -Ec * (1+ astar + a3*(astar**3)/(r/re))*fm_exp(-astar)
- endif
- endif
-
- return
- end
-
-c -----------------------------------------------------------------------
-
- subroutine interpolate_meam(ind)
- use meam_data
- implicit none
-
- integer j,ind
- real*8 drar
-
-c map to coefficient space
-
- nrar = nr
- drar = dr
- rdrar = 1.0D0/drar
-
-c phir interp
- do j = 1,nrar
- phirar(j,ind) = phir(j,ind)
- enddo
-
- phirar1(1,ind) = phirar(2,ind)-phirar(1,ind)
- phirar1(2,ind) = 0.5D0*(phirar(3,ind)-phirar(1,ind))
- phirar1(nrar-1,ind) = 0.5D0*(phirar(nrar,ind)
- $ -phirar(nrar-2,ind))
- phirar1(nrar,ind) = 0.0D0
- do j = 3,nrar-2
- phirar1(j,ind) = ((phirar(j-2,ind)-phirar(j+2,ind)) +
- $ 8.0D0*(phirar(j+1,ind)-phirar(j-1,ind)))/12.
- enddo
-
- do j = 1,nrar-1
- phirar2(j,ind) = 3.0D0*(phirar(j+1,ind)-phirar(j,ind)) -
- $ 2.0D0*phirar1(j,ind) - phirar1(j+1,ind)
- phirar3(j,ind) = phirar1(j,ind) + phirar1(j+1,ind) -
- $ 2.0D0*(phirar(j+1,ind)-phirar(j,ind))
- enddo
- phirar2(nrar,ind) = 0.0D0
- phirar3(nrar,ind) = 0.0D0
-
- do j = 1,nrar
- phirar4(j,ind) = phirar1(j,ind)/drar
- phirar5(j,ind) = 2.0D0*phirar2(j,ind)/drar
- phirar6(j,ind) = 3.0D0*phirar3(j,ind)/drar
- enddo
-
- end
-
-c---------------------------------------------------------------------
-c Compute Rose energy function, I.16
-c
- real*8 function compute_phi(rij, elti, eltj)
- use meam_data
- implicit none
-
- real*8 rij, pp
- integer elti, eltj, ind, kk
-
- ind = eltind(elti, eltj)
- pp = rij*rdrar + 1.0D0
- kk = pp
- kk = min(kk,nrar-1)
- pp = pp - kk
- pp = min(pp,1.0D0)
- compute_phi = ((phirar3(kk,ind)*pp + phirar2(kk,ind))*pp
- $ + phirar1(kk,ind))*pp + phirar(kk,ind)
-
- return
- end
diff --git a/lib/meam/meam_setup_global.F b/lib/meam/meam_setup_global.F
deleted file mode 100644
index d11dec5a4a6178c212ac27bb8e0d745c6ca25ecb..0000000000000000000000000000000000000000
--- a/lib/meam/meam_setup_global.F
+++ /dev/null
@@ -1,111 +0,0 @@
-c
-c declaration in pair_meam.h:
-c
-c void meam_setup_global(int *, int *, double *, int *, double *, double *,
-c double *, double *, double *, double *, double *,
-c double *, double *, double *, double *, double *,
-c double *, double *, int *);
-c
-c call in pair_meam.cpp:
-c
-c meam_setup_global(&nelements,lat,z,ielement,atwt,alpha,b0,b1,b2,b3,
-c alat,esub,asub,t0,t1,t2,t3,rozero,ibar);
-c
-c
-
- subroutine meam_setup_global(nelt, lat, z, ielement, atwt, alpha,
- $ b0, b1, b2, b3, alat, esub, asub,
- $ t0, t1, t2, t3, rozero, ibar)
-
- use meam_data
- implicit none
-
- integer nelt, lat, ielement, ibar
- real*8 z, atwt, alpha, b0, b1, b2, b3
- real*8 alat, esub, asub, t0, t1, t2, t3
- real*8 rozero
-
- dimension lat(nelt), ielement(nelt), ibar(nelt)
- dimension z(nelt), atwt(nelt), alpha(nelt)
- dimension b0(nelt), b1(nelt), b2(nelt), b3(nelt)
- dimension alat(nelt), esub(nelt), asub(nelt)
- dimension t0(nelt), t1(nelt), t2(nelt), t3(nelt), rozero(nelt)
-
- integer i
- real*8 tmplat(maxelt)
-
- neltypes = nelt
-
- do i = 1,nelt
-
- if (lat(i).eq.0) then
- lattce_meam(i,i) = 'fcc'
- else if (lat(i).eq.1) then
- lattce_meam(i,i) = 'bcc'
- else if (lat(i).eq.2) then
- lattce_meam(i,i) = 'hcp'
- else if (lat(i).eq.3) then
- lattce_meam(i,i) = 'dim'
- else if (lat(i).eq.4) then
- lattce_meam(i,i) = 'dia'
- else
-c unknown
- endif
-
- Z_meam(i) = z(i)
- ielt_meam(i) = ielement(i)
- alpha_meam(i,i) = alpha(i)
- beta0_meam(i) = b0(i)
- beta1_meam(i) = b1(i)
- beta2_meam(i) = b2(i)
- beta3_meam(i) = b3(i)
- tmplat(i) = alat(i)
- Ec_meam(i,i) = esub(i)
- A_meam(i) = asub(i)
- t0_meam(i) = t0(i)
- t1_meam(i) = t1(i)
- t2_meam(i) = t2(i)
- t3_meam(i) = t3(i)
- rho0_meam(i) = rozero(i)
- ibar_meam(i) = ibar(i)
-
- if (lattce_meam(i,i).eq.'fcc') then
- re_meam(i,i) = tmplat(i)/sqrt(2.d0)
- elseif (lattce_meam(i,i).eq.'bcc') then
- re_meam(i,i) = tmplat(i)*sqrt(3.d0)/2.d0
- elseif (lattce_meam(i,i).eq.'hcp') then
- re_meam(i,i) = tmplat(i)
- elseif (lattce_meam(i,i).eq.'dim') then
- re_meam(i,i) = tmplat(i)
- elseif (lattce_meam(i,i).eq.'dia') then
- re_meam(i,i) = tmplat(i)*sqrt(3.d0)/4.d0
- else
-c error
- endif
-
- enddo
-
-
-c Set some defaults
- rc_meam = 4.0
- delr_meam = 0.1
- attrac_meam(:,:) = 0.0
- repuls_meam(:,:) = 0.0
- Cmax_meam(:,:,:) = 2.8
- Cmin_meam(:,:,:) = 2.0
- ebound_meam(:,:) = (2.8d0**2)/(4.d0*(2.8d0-1.d0))
- delta_meam(:,:) = 0.0
- nn2_meam(:,:) = 0
- zbl_meam(:,:) = 1
- gsmooth_factor = 99.0
- augt1 = 1
- ialloy = 0
- mix_ref_t = 0
- emb_lin_neg = 0
- bkgd_dyn = 0
- erose_form = 0
-
- return
- end
-
-
diff --git a/lib/meam/meam_setup_param.F b/lib/meam/meam_setup_param.F
deleted file mode 100644
index cfe7430285983698124fb2f06e9628746feaaf9b..0000000000000000000000000000000000000000
--- a/lib/meam/meam_setup_param.F
+++ /dev/null
@@ -1,204 +0,0 @@
-c
-c do a sanity check on index parameters
- subroutine meam_checkindex(num,lim,nidx,idx,ierr)
- implicit none
- integer i,num,lim,nidx,idx(3),ierr
-
- ierr = 0
- if (nidx.lt.num) then
- ierr = 2
- return
- endif
-
- do i=1,num
- if ((idx(i).lt.1).or.(idx(i).gt.lim)) then
- ierr = 3
- return
- endif
- enddo
- end
-
-c
-c Declaration in pair_meam.h:
-c
-c void meam_setup_param(int *, double *, int *, int *, int *);
-c
-c Call in pair_meam.cpp
-c
-c meam_setup_param(&which,&value,&nindex,index,&errorflag);
-c
-c
-c
-c The "which" argument corresponds to the index of the "keyword" array
-c in pair_meam.cpp:
-c
-c 0 = Ec_meam
-c 1 = alpha_meam
-c 2 = rho0_meam
-c 3 = delta_meam
-c 4 = lattce_meam
-c 5 = attrac_meam
-c 6 = repuls_meam
-c 7 = nn2_meam
-c 8 = Cmin_meam
-c 9 = Cmax_meam
-c 10 = rc_meam
-c 11 = delr_meam
-c 12 = augt1
-c 13 = gsmooth_factor
-c 14 = re_meam
-c 15 = ialloy
-c 16 = mixture_ref_t
-c 17 = erose_form
-c 18 = zbl_meam
-c 19 = emb_lin_neg
-c 20 = bkgd_dyn
-
- subroutine meam_setup_param(which, value, nindex,
- $ index, errorflag)
-
- use meam_data
- implicit none
-
- integer which, nindex, index(3), errorflag
- real*8 value
- integer i1, i2
-
- errorflag = 0
-
-c 0 = Ec_meam
- if (which.eq.0) then
- call meam_checkindex(2,maxelt,nindex,index,errorflag)
- if (errorflag.ne.0) return
- Ec_meam(index(1),index(2)) = value
-
-c 1 = alpha_meam
- else if (which.eq.1) then
- call meam_checkindex(2,maxelt,nindex,index,errorflag)
- if (errorflag.ne.0) return
- alpha_meam(index(1),index(2)) = value
-
-c 2 = rho0_meam
- else if (which.eq.2) then
- call meam_checkindex(1,maxelt,nindex,index,errorflag)
- if (errorflag.ne.0) return
- rho0_meam(index(1)) = value
-
-c 3 = delta_meam
- else if (which.eq.3) then
- call meam_checkindex(2,maxelt,nindex,index,errorflag)
- if (errorflag.ne.0) return
- delta_meam(index(1),index(2)) = value
-
-c 4 = lattce_meam
- else if (which.eq.4) then
- call meam_checkindex(2,maxelt,nindex,index,errorflag)
- if (errorflag.ne.0) return
- if (value.eq.0) then
- lattce_meam(index(1),index(2)) = "fcc"
- else if (value.eq.1) then
- lattce_meam(index(1),index(2)) = "bcc"
- else if (value.eq.2) then
- lattce_meam(index(1),index(2)) = "hcp"
- else if (value.eq.3) then
- lattce_meam(index(1),index(2)) = "dim"
- else if (value.eq.4) then
- lattce_meam(index(1),index(2)) = "dia"
- else if (value.eq.5) then
- lattce_meam(index(1),index(2)) = 'b1'
- else if (value.eq.6) then
- lattce_meam(index(1),index(2)) = 'c11'
- else if (value.eq.7) then
- lattce_meam(index(1),index(2)) = 'l12'
- else if (value.eq.8) then
- lattce_meam(index(1),index(2)) = 'b2'
- endif
-
-c 5 = attrac_meam
- else if (which.eq.5) then
- call meam_checkindex(2,maxelt,nindex,index,errorflag)
- if (errorflag.ne.0) return
- attrac_meam(index(1),index(2)) = value
-
-c 6 = repuls_meam
- else if (which.eq.6) then
- call meam_checkindex(2,maxelt,nindex,index,errorflag)
- if (errorflag.ne.0) return
- repuls_meam(index(1),index(2)) = value
-
-c 7 = nn2_meam
- else if (which.eq.7) then
- call meam_checkindex(2,maxelt,nindex,index,errorflag)
- if (errorflag.ne.0) return
- i1 = min(index(1),index(2))
- i2 = max(index(1),index(2))
- nn2_meam(i1,i2) = value
-
-c 8 = Cmin_meam
- else if (which.eq.8) then
- call meam_checkindex(3,maxelt,nindex,index,errorflag)
- if (errorflag.ne.0) return
- Cmin_meam(index(1),index(2),index(3)) = value
-
-c 9 = Cmax_meam
- else if (which.eq.9) then
- call meam_checkindex(3,maxelt,nindex,index,errorflag)
- if (errorflag.ne.0) return
- Cmax_meam(index(1),index(2),index(3)) = value
-
-c 10 = rc_meam
- else if (which.eq.10) then
- rc_meam = value
-
-c 11 = delr_meam
- else if (which.eq.11) then
- delr_meam = value
-
-c 12 = augt1
- else if (which.eq.12) then
- augt1 = value
-
-c 13 = gsmooth
- else if (which.eq.13) then
- gsmooth_factor = value
-
-c 14 = re_meam
- else if (which.eq.14) then
- call meam_checkindex(2,maxelt,nindex,index,errorflag)
- if (errorflag.ne.0) return
- re_meam(index(1),index(2)) = value
-
-c 15 = ialloy
- else if (which.eq.15) then
- ialloy = value
-
-c 16 = mixture_ref_t
- else if (which.eq.16) then
- mix_ref_t = value
-
-c 17 = erose_form
- else if (which.eq.17) then
- erose_form = value
-
-c 18 = zbl_meam
- else if (which.eq.18) then
- call meam_checkindex(2,maxelt,nindex,index,errorflag)
- if (errorflag.ne.0) return
- i1 = min(index(1),index(2))
- i2 = max(index(1),index(2))
- zbl_meam(i1,i2) = value
-
-c 19 = emb_lin_neg
- else if (which.eq.19) then
- emb_lin_neg = value
-
-c 20 = bkgd_dyn
- else if (which.eq.20) then
- bkgd_dyn = value
-
- else
- errorflag = 1
- endif
-
- return
- end
diff --git a/lib/reax/Install.py b/lib/reax/Install.py
deleted file mode 120000
index ffe709d44c22d2060ad41538d1f8fc0df2b09b30..0000000000000000000000000000000000000000
--- a/lib/reax/Install.py
+++ /dev/null
@@ -1 +0,0 @@
-../Install.py
\ No newline at end of file
diff --git a/lib/reax/Makefile.g95 b/lib/reax/Makefile.g95
deleted file mode 100644
index 55c40daa00ba87d00e1a70d58ac206406d4ba8bc..0000000000000000000000000000000000000000
--- a/lib/reax/Makefile.g95
+++ /dev/null
@@ -1,51 +0,0 @@
-# *
-# *_________________________________________________________________________*
-# * Fortran Library for Reactive Force Field *
-# * DESCRIPTION: SEE READ-ME *
-# * FILE NAME: Makefile *
-# * CONTRIBUTING AUTHORS: Hansohl Cho(MIT), Aidan Thompson(SNL) *
-# * and Greg Wagner(SNL) *
-# * CONTACT: hansohl@mit.edu, athompson@sandia.gov, gjwagne@sandia.gov *
-# *_________________________________________________________________________*/
-
-SHELL = /bin/sh
-
-# which file will be copied to Makefile.lammps
-
-EXTRAMAKE = Makefile.lammps.gfortran
-
-# ------ FILES ------
-
-SRC = reax_connect.F reax_inout.F reax_lammps.F reax_poten.F reax_reac.F reax_charges.F
-
-HEADERFILES = reax_defs.h *.blk
-
-# ------ DEFINITIONS ------
-
-LIB = libreax.a
-OBJ = $(SRC:.F=.o)
-
-# ------ SETTINGS ------
-
-F90 = g95
-F90FLAGS = -O -fPIC
-ARCHIVE = ar
-ARCHFLAG = -rc
-USRLIB =
-SYSLIB =
-
-# ------ MAKE PROCEDURE ------
-
-lib: $(OBJ)
- $(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
- @cp $(EXTRAMAKE) Makefile.lammps
-
-# ------ COMPILE RULES ------
-
-%.o:%.F $(HEADERFILES)
- $(F90) $(F90FLAGS) -c $<
-
-# ------ CLEAN ------
-
-clean:
- -rm *.o $(LIB)
diff --git a/lib/reax/Makefile.gfortran b/lib/reax/Makefile.gfortran
deleted file mode 100644
index ab423016887a444548529d84c6a32d03fdb5c880..0000000000000000000000000000000000000000
--- a/lib/reax/Makefile.gfortran
+++ /dev/null
@@ -1,51 +0,0 @@
-# *
-# *_________________________________________________________________________*
-# * Fortran Library for Reactive Force Field *
-# * DESCRIPTION: SEE READ-ME *
-# * FILE NAME: Makefile *
-# * CONTRIBUTING AUTHORS: Hansohl Cho(MIT), Aidan Thompson(SNL) *
-# * and Greg Wagner(SNL) *
-# * CONTACT: hansohl@mit.edu, athompson@sandia.gov, gjwagne@sandia.gov *
-# *_________________________________________________________________________*/
-
-SHELL = /bin/sh
-
-# which file will be copied to Makefile.lammps
-
-EXTRAMAKE = Makefile.lammps.gfortran
-
-# ------ FILES ------
-
-SRC = reax_connect.F reax_inout.F reax_lammps.F reax_poten.F reax_reac.F reax_charges.F
-
-HEADERFILES = reax_defs.h *.blk
-
-# ------ DEFINITIONS ------
-
-LIB = libreax.a
-OBJ = $(SRC:.F=.o)
-
-# ------ SETTINGS ------
-
-F90 = gfortran
-F90FLAGS = -O3 -fPIC -fno-second-underscore
-ARCHIVE = ar
-ARCHFLAG = -rc
-USRLIB =
-SYSLIB =
-
-# ------ MAKE PROCEDURE ------
-
-lib: $(OBJ)
- $(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
- @cp $(EXTRAMAKE) Makefile.lammps
-
-# ------ COMPILE RULES ------
-
-%.o:%.F $(HEADERFILES)
- $(F90) $(F90FLAGS) -c $<
-
-# ------ CLEAN ------
-
-clean:
- -rm *.o $(LIB)
diff --git a/lib/reax/Makefile.ifort b/lib/reax/Makefile.ifort
deleted file mode 100644
index 1760cb9c6a5259695fc1a3c0715a45ee1ce7f9c6..0000000000000000000000000000000000000000
--- a/lib/reax/Makefile.ifort
+++ /dev/null
@@ -1,51 +0,0 @@
-# *
-# *_________________________________________________________________________*
-# * Fortran Library for Reactive Force Field *
-# * DESCRIPTION: SEE READ-ME *
-# * FILE NAME: Makefile *
-# * CONTRIBUTING AUTHORS: Hansohl Cho(MIT), Aidan Thompson(SNL) *
-# * and Greg Wagner(SNL) *
-# * CONTACT: hansohl@mit.edu, athompson@sandia.gov, gjwagne@sandia.gov *
-# *_________________________________________________________________________*/
-
-SHELL = /bin/sh
-
-# which file will be copied to Makefile.lammps
-
-EXTRAMAKE = Makefile.lammps.ifort
-
-# ------ FILES ------
-
-SRC = reax_connect.F reax_inout.F reax_lammps.F reax_poten.F reax_reac.F reax_charges.F
-
-HEADERFILES = reax_defs.h *.blk
-
-# ------ DEFINITIONS ------
-
-LIB = libreax.a
-OBJ = $(SRC:.F=.o)
-
-# ------ SETTINGS ------
-
-F90 = ifort
-F90FLAGS = -O -fPIC
-ARCHIVE = ar
-ARCHFLAG = -rc
-USRLIB =
-SYSLIB =
-
-# ------ MAKE PROCEDURE ------
-
-lib: $(OBJ)
- $(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
- @cp $(EXTRAMAKE) Makefile.lammps
-
-# ------ COMPILE RULES ------
-
-%.o:%.F $(HEADERFILES)
- $(F90) $(F90FLAGS) -c $<
-
-# ------ CLEAN ------
-
-clean:
- -rm *.o $(LIB)
diff --git a/lib/reax/Makefile.lammps.empty b/lib/reax/Makefile.lammps.empty
deleted file mode 100644
index 758755f3c8064d8b40d3d1af1310bd093a366004..0000000000000000000000000000000000000000
--- a/lib/reax/Makefile.lammps.empty
+++ /dev/null
@@ -1,5 +0,0 @@
-# Settings that the LAMMPS build will import when this package library is used
-
-reax_SYSINC =
-reax_SYSLIB =
-reax_SYSPATH =
diff --git a/lib/reax/Makefile.lammps.gfortran b/lib/reax/Makefile.lammps.gfortran
deleted file mode 100644
index f5da63bc38e61c43efec29ead418f107ccd35b18..0000000000000000000000000000000000000000
--- a/lib/reax/Makefile.lammps.gfortran
+++ /dev/null
@@ -1,5 +0,0 @@
-# Settings that the LAMMPS build will import when this package library is used
-
-reax_SYSINC =
-reax_SYSLIB = -lgfortran
-reax_SYSPATH =
diff --git a/lib/reax/Makefile.lammps.ifort b/lib/reax/Makefile.lammps.ifort
deleted file mode 100644
index 69ac12606dd2d50b29639222764d82c1012a0d0f..0000000000000000000000000000000000000000
--- a/lib/reax/Makefile.lammps.ifort
+++ /dev/null
@@ -1,6 +0,0 @@
-# Settings that the LAMMPS build will import when this package library is used
-
-reax_SYSINC =
-reax_SYSLIB = -lifcore
-reax_SYSPATH =
-
diff --git a/lib/reax/Makefile.mpi b/lib/reax/Makefile.mpi
deleted file mode 100644
index 142f7e9bc6ffc01a1e18fe12548af8e1b4638564..0000000000000000000000000000000000000000
--- a/lib/reax/Makefile.mpi
+++ /dev/null
@@ -1,51 +0,0 @@
-# *
-# *_________________________________________________________________________*
-# * Fortran Library for Reactive Force Field *
-# * DESCRIPTION: SEE READ-ME *
-# * FILE NAME: Makefile *
-# * CONTRIBUTING AUTHORS: Hansohl Cho(MIT), Aidan Thompson(SNL) *
-# * and Greg Wagner(SNL) *
-# * CONTACT: hansohl@mit.edu, athompson@sandia.gov, gjwagne@sandia.gov *
-# *_________________________________________________________________________*/
-
-SHELL = /bin/sh
-
-# which file will be copied to Makefile.lammps
-
-EXTRAMAKE = Makefile.lammps.empty
-
-# ------ FILES ------
-
-SRC = reax_connect.F reax_inout.F reax_lammps.F reax_poten.F reax_reac.F reax_charges.F
-
-HEADERFILES = reax_defs.h *.blk
-
-# ------ DEFINITIONS ------
-
-LIB = libreax.a
-OBJ = $(SRC:.F=.o)
-
-# ------ SETTINGS ------
-
-F90 = mpifort
-F90FLAGS = -O3 -fPIC
-ARCHIVE = ar
-ARCHFLAG = -rc
-USRLIB =
-SYSLIB =
-
-# ------ MAKE PROCEDURE ------
-
-lib: $(OBJ)
- $(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
- @cp $(EXTRAMAKE) Makefile.lammps
-
-# ------ COMPILE RULES ------
-
-%.o:%.F $(HEADERFILES)
- $(F90) $(F90FLAGS) -c $<
-
-# ------ CLEAN ------
-
-clean:
- -rm *.o $(LIB)
diff --git a/lib/reax/Makefile.pgf90 b/lib/reax/Makefile.pgf90
deleted file mode 100644
index dfc17eca11bdec707e4391769699dff4223e5e41..0000000000000000000000000000000000000000
--- a/lib/reax/Makefile.pgf90
+++ /dev/null
@@ -1,51 +0,0 @@
-# *
-# *_________________________________________________________________________*
-# * Fortran Library for Reactive Force Field *
-# * DESCRIPTION: SEE READ-ME *
-# * FILE NAME: Makefile *
-# * CONTRIBUTING AUTHORS: Hansohl Cho(MIT), Aidan Thompson(SNL) *
-# * and Greg Wagner(SNL) *
-# * CONTACT: hansohl@mit.edu, athompson@sandia.gov, gjwagne@sandia.gov *
-# *_________________________________________________________________________*/
-
-SHELL = /bin/sh
-
-# which file will be copied to Makefile.lammps
-
-EXTRAMAKE = Makefile.lammps.pgf90
-
-# ------ FILES ------
-
-SRC = reax_connect.F reax_inout.F reax_lammps.F reax_poten.F reax_reac.F reax_charges.F
-
-HEADERFILES = reax_defs.h *.blk
-
-# ------ DEFINITIONS ------
-
-LIB = libreax.a
-OBJ = $(SRC:.F=.o)
-
-# ------ SETTINGS ------
-
-F90 = pgf90
-F90FLAGS = -O -fPIC
-ARCHIVE = ar
-ARCHFLAG = -rc
-USRLIB =
-SYSLIB =
-
-# ------ MAKE PROCEDURE ------
-
-lib: $(OBJ)
- $(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
- @cp $(EXTRAMAKE) Makefile.lammps
-
-# ------ COMPILE RULES ------
-
-%.o:%.F $(HEADERFILES)
- $(F90) $(F90FLAGS) -c $<
-
-# ------ CLEAN ------
-
-clean:
- -rm *.o $(LIB)
diff --git a/lib/reax/Makefile.redsky b/lib/reax/Makefile.redsky
deleted file mode 100644
index f51a15d1f10956457a96c3c66dfa8a77a8871587..0000000000000000000000000000000000000000
--- a/lib/reax/Makefile.redsky
+++ /dev/null
@@ -1,51 +0,0 @@
-# *
-# *_________________________________________________________________________*
-# * Fortran Library for Reactive Force Field *
-# * DESCRIPTION: SEE READ-ME *
-# * FILE NAME: Makefile *
-# * CONTRIBUTING AUTHORS: Hansohl Cho(MIT), Aidan Thompson(SNL) *
-# * and Greg Wagner(SNL) *
-# * CONTACT: hansohl@mit.edu, athompson@sandia.gov, gjwagne@sandia.gov *
-# *_________________________________________________________________________*/
-
-SHELL = /bin/sh
-
-# which file will be copied to Makefile.lammps
-
-EXTRAMAKE = Makefile.lammps.ifort
-
-# ------ FILES ------
-
-SRC = reax_connect.F reax_inout.F reax_lammps.F reax_poten.F reax_reac.F reax_charges.F
-
-HEADERFILES = reax_defs.h *.blk
-
-# ------ DEFINITIONS ------
-
-LIB = libreax.a
-OBJ = $(SRC:.F=.o)
-
-# ------ SETTINGS ------
-
-F90 = mpif90
-F90FLAGS = -O -fPIC
-ARCHIVE = ar
-ARCHFLAG = -rc
-USRLIB =
-SYSLIB =
-
-# ------ MAKE PROCEDURE ------
-
-lib: $(OBJ)
- $(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
- @cp $(EXTRAMAKE) Makefile.lammps
-
-# ------ COMPILE RULES ------
-
-%.o:%.F $(HEADERFILES)
- $(F90) $(F90FLAGS) -c $<
-
-# ------ CLEAN ------
-
-clean:
- -rm *.o $(LIB)
diff --git a/lib/reax/Makefile.serial b/lib/reax/Makefile.serial
deleted file mode 120000
index c52fbcb986822e3dfdc79a978a876fb39a762f71..0000000000000000000000000000000000000000
--- a/lib/reax/Makefile.serial
+++ /dev/null
@@ -1 +0,0 @@
-Makefile.gfortran
\ No newline at end of file
diff --git a/lib/reax/Makefile.tbird b/lib/reax/Makefile.tbird
deleted file mode 100644
index f51a15d1f10956457a96c3c66dfa8a77a8871587..0000000000000000000000000000000000000000
--- a/lib/reax/Makefile.tbird
+++ /dev/null
@@ -1,51 +0,0 @@
-# *
-# *_________________________________________________________________________*
-# * Fortran Library for Reactive Force Field *
-# * DESCRIPTION: SEE READ-ME *
-# * FILE NAME: Makefile *
-# * CONTRIBUTING AUTHORS: Hansohl Cho(MIT), Aidan Thompson(SNL) *
-# * and Greg Wagner(SNL) *
-# * CONTACT: hansohl@mit.edu, athompson@sandia.gov, gjwagne@sandia.gov *
-# *_________________________________________________________________________*/
-
-SHELL = /bin/sh
-
-# which file will be copied to Makefile.lammps
-
-EXTRAMAKE = Makefile.lammps.ifort
-
-# ------ FILES ------
-
-SRC = reax_connect.F reax_inout.F reax_lammps.F reax_poten.F reax_reac.F reax_charges.F
-
-HEADERFILES = reax_defs.h *.blk
-
-# ------ DEFINITIONS ------
-
-LIB = libreax.a
-OBJ = $(SRC:.F=.o)
-
-# ------ SETTINGS ------
-
-F90 = mpif90
-F90FLAGS = -O -fPIC
-ARCHIVE = ar
-ARCHFLAG = -rc
-USRLIB =
-SYSLIB =
-
-# ------ MAKE PROCEDURE ------
-
-lib: $(OBJ)
- $(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
- @cp $(EXTRAMAKE) Makefile.lammps
-
-# ------ COMPILE RULES ------
-
-%.o:%.F $(HEADERFILES)
- $(F90) $(F90FLAGS) -c $<
-
-# ------ CLEAN ------
-
-clean:
- -rm *.o $(LIB)
diff --git a/lib/reax/README b/lib/reax/README
deleted file mode 100644
index f21a47061827aab3c4c26fc8b3ccfbb5133b8fe4..0000000000000000000000000000000000000000
--- a/lib/reax/README
+++ /dev/null
@@ -1,78 +0,0 @@
-ReaxFF library
-
-Aidan Thompson, Sandia National Labs
-athomps at sandia.gov
-Jan 2008
-
-This library is an implementation of the ReaxFF potential,
-specifically designed to work with LAMMPS. It is derived from Adri van
-Duin's original serial code, with intervening incarnations in CMDF and
-GRASP.
-
--------------------------------------------------
-
-This directory has source files to build a library that LAMMPS
-links against when using the REAX package.
-
-This library must be built with a F90 compiler, before LAMMPS is
-built, so LAMMPS can link against it.
-
-You can type "make lib-reax" from the src directory to see help on how
-to build this library via make commands, or you can do the same thing
-by typing "python Install.py" from within this directory, or you can
-do it manually by following the instructions below.
-
-Build the library using one of the provided Makefile.* files or create
-your own, specific to your compiler and system. For example:
-
-make -f Makefile.gfortran
-
-When you are done building this library, two files should
-exist in this directory:
-
-libreax.a the library LAMMPS will link against
-Makefile.lammps settings the LAMMPS Makefile will import
-
-Makefile.lammps is created by the make command, by copying one of the
-Makefile.lammps.* files. See the EXTRAMAKE setting at the top of the
-Makefile.* files.
-
-IMPORTANT: You must examine the final Makefile.lammps to insure it is
-correct for your system, else the LAMMPS build will likely fail.
-
-Makefile.lammps has settings for 3 variables:
-
-user-reax_SYSINC = leave blank for this package
-user-reax_SYSLIB = auxiliary F90 libs needed to link a F90 lib with
- a C++ program (LAMMPS) via a C++ compiler
-user-reax_SYSPATH = path(s) to where those libraries are
-
-Because you have a F90 compiler on your system, you should have these
-libraries. But you will have to figure out which ones are needed and
-where they are. Examples of common configurations are in the
-Makefile.lammps.* files.
-
--------------------------------------------------
-
-Additional build notes:
-
-The include file reax_defs.h is used by both the ReaxFF library source
-files and the LAMMPS pair_reax.cpp source file (in package src/REAX).
-It contains dimensions of statically-allocated arrays created by the
-ReaxFF library. The size of these arrays must be set small enough to
-avoid exceeding the available machine memory, and large enough to fit
-the actual data generated by ReaxFF. If you change the values in
-reax_defs.h, you must first rebuild the library and then rebuild
-LAMMPS.
-
-This library is called by functions in pair_reax.cpp. The C++ to
-FORTRAN function calls in pair_reax.cpp assume that FORTRAN object
-names are converted to C object names by appending an underscore
-character. This is generally the case, but on machines that do not
-conform to this convention, you will need to modify either the C++
-code or your compiler settings. The name conversion is handled by the
-preprocessor macro called FORTRAN in the file pair_reax_fortran.h,
-which is included by pair_reax.cpp. Different definitions of this
-macro can be obtained by adding a machine-specific macro definition to
-the CCFLAGS variable in your your LAMMPS Makefile e.g. -D_IBM. See
-pair_reax_fortran.h for more info.
diff --git a/lib/reax/cbka.blk b/lib/reax/cbka.blk
deleted file mode 100644
index 4dbe0a36c648689a974f49ccbdbc6ecd0ee77653..0000000000000000000000000000000000000000
--- a/lib/reax/cbka.blk
+++ /dev/null
@@ -1,116 +0,0 @@
-#include "reax_defs.h"
- implicit real*8 (a-h,o-z),integer(i-n)
- parameter (nneighmax=NNEIGHMAXDEF)
- parameter (nat=NATDEF) !Max number of atoms
- parameter (nattot=NATTOTDEF) !Max number of global atoms
- parameter (nsort=NSORTDEF) !Max number of atom types
- parameter (mbond=MBONDDEF) !Max number of bonds connected to one atom
- parameter (na1mx3=3*nat) !3*max number of atoms
- parameter (navib=NAVIBDEF) !for 2nd derivatives
- parameter (nbotym=NBOTYMDEF) !Max number of bond types
- parameter (nvatym=NVATYMDEF) !Max number of valency angle types
- parameter (ntotym=NTOTYMDEF) !Max number of torsion angle types
- parameter (nhbtym=NHBTYMDEF) !Max number of hydrogen bond types
- parameter (nodmtym=NODMTYMDEF) !Max number of off-diagonal Morse types
- parameter (nboallmax=NBOALLMAXDEF) !Max number of all bonds
- parameter (nbomax=NBOMAXDEF) !Max number of bonds
- parameter (nhbmax=NHBMAXDEF) !Max number of hydrogen bonds
- parameter (nvamax=NVAMAXDEF) !Max number of valency angles
- parameter (nopmax=NOPMAXDEF) !Max number of out of plane angles
- parameter (ntomax=NTOMAXDEF) !Max number of torsion angles
- parameter (npamax=NPAMAXDEF) !Max number of general parameters in force field
- parameter (nmolmax=NMOLMAXDEF) !Max number of molecules in system
- parameter (nmolset=NMOLSETDEF) !Max number of molecules in training set
- parameter (mrestra=MRESTRADEF) !Max number of restraints
- parameter (mtreg=MTREGDEF) !Max number of temperature regimes
- parameter (mtzone=MTZONEDEF) !Max number of temperature zones
- parameter (mvreg=MVREGDEF) !Max number of volume regimes
- parameter (mvzone=MVZONEDEF) !Max number of volume zones
- parameter (mereg=MEREGDEF) !Max number of electric field regimes
- parameter (mezone=MEZONEDEF) !Max number of electric field zones
- character*1 qr,qrset,qresi2
- character*2 qaset,qadd
- character*3 qresi1
- character*5 qlabel,qffty,qbgfaxes,qbgfsgn,qresi3
- character*20 qkeyw
- character*25 qfile
- character*40 qffield,qformat,qstrana2
- character*60 qremark,qremset,qmolset
- character*200 qstrana1
- common
- $/cbka/ dhbdc(nhbmax,3,3),cp(nat,3),
- $ cadd(nat,3),d2(3*navib,3*navib),
- $ veladd(3,nat),
- $ aold(3,nat),dic(3,nat),pvdw1(nsort,nsort),
- $ pvdw2(nsort,nsort),angimp(nat,6),
- $ yt(na1mx3),pt(na1mx3),gi(na1mx3),enmolset(nmolset),
- $ ai(na1mx3),bi(na1mx3),yi(na1mx3),pn(na1mx3),tbo(nat),
- $ chgbgf(nattot),
- $ abo2(nat),bor4(nat),bos(nbomax),
- $ eldef(nat),vradic(nat),
- $ vmo2(nat),
- $ ro(nbomax),dbondr(nbomax),
- $ dbosidr(nbomax),thgo(nopmax),
- $ elmol(nmolmax),
- $ elaf(nsort),vpq(nsort),
- $ rvdw(nsort),alf(nsort),eps(nsort),chat(nsort),
- $ rcore(nsort,nsort),ecore(nsort,nsort),acore(nsort,nsort),
- $ vlp2(nsort),
- $ valp2(nsort),vincr(nsort),
- $ vval3(nsort),
- $ vuncor(nbotym),
- $ vop(nsort),
- $ sigqeq(nsort),
- $ rrcha(mrestra),
- $ rmstra3(mrestra),
- $ rmcha(mrestra),
- $ rtcha(mrestra),rvcha(mrestra),
- $ v2bo(ntotym),v3bo(ntotym),
- $ eel,fctor,elr,
- $ presx2,presy2,presz2,
- $ tset2,
- $ enmol,formol,vvol,tpnrad,
- $ delvib,
- $ taut2,tincr,xmasmd,
- $ gdicmax,parc1,parc2,sumelec,
- $ xinh,fsnh,vqnh,snh,ham,errnh,sumhe,
- $ swa,swb2,swc0,swc1,swc2,swc3,swc4,swc5,swc6,
- $ swc7,plr,endpo2,ccpar,
- $ c4,estrmin,endpo,accincr,
- $ endpoold,xadd,yadd,zadd,addist,taddmol,
- $ Hug_E0, Hug_P0, Hug_V0, xImpVcm, shock_vel,
- $ shock_z_sep
- common
- $/cbka/
- $ ioop(nopmax,9),ifreqset(nmolset),
- $ ijk(nat,4),icgeopt(nmolset),
- $ irap(50),irdo(50,2),
- $ ityadd(nat),
- $ nmoloo(nat),iradic(nat),idef(nsort),nasort(nsort),
- $ ibgr1(nattot),ibgr2(nattot),idupc(6),
- $ imolsta(nat),
- $ ncent2(nbomax),irads,nrdd,nrddf,nbiolab,nuge,
- $ nbon2,npar,nodmty,ngnh,irac,nincrop,
- $ nboty,mdstep,
- $ nreac,
- $ nbonop,icelo2,
- $ iaddfreq,iveladd,invt,
- $ noop,ndtau,
- $ nelc3,nfc,nsav2,nmmax,ibh2,
- $ nmmaxold,nfcold,icellold,imodfile,
- $ icelo2old,inmov1,inmov2,nchaold,naa,nadattempt,
- $ nequi,iadj,
- $ ntest,nmm,
- $ nmolo5o,nradcount,nmollset,iflga,
- $ iperiod,ibgfversion,iremark,iconne,
- $ kx,ky,kz,iexco,iruid,ibity,nvlist,
- $ ityrad,iredo,iexx,iexy,iexz,ncellopt,
- $ ndata2,nprob,nit,i5758,ingeo,nmoloold,itemp,
- $ icgeo,ishock_type,isymm,
- $ qadd(nat),qlabel(nattot),qffty(nattot),qresi1(nattot),
- $ qresi2(nattot),qresi3(nattot),
- $ qremark(20),qformat(20),qr,qffield,
- $ qstrana1,qstrana2,qmolset(nmolset)
-***********************************************************************
-
-
diff --git a/lib/reax/cbkabo.blk b/lib/reax/cbkabo.blk
deleted file mode 100644
index 957651d00282c5b18fc9fec0440891f5f656f79c..0000000000000000000000000000000000000000
--- a/lib/reax/cbkabo.blk
+++ /dev/null
@@ -1,4 +0,0 @@
- common
- $/cbkabo/ abo(nat)
-
-
diff --git a/lib/reax/cbkatomcoord.blk b/lib/reax/cbkatomcoord.blk
deleted file mode 100644
index 711fab85a07fb1fb4c987e998d516c9171654c87..0000000000000000000000000000000000000000
--- a/lib/reax/cbkatomcoord.blk
+++ /dev/null
@@ -1,3 +0,0 @@
- common
- $/cbkatomcoord/ id(nat,3),xmasat(nat),vel(3,nat),accel(3,nat)
-
diff --git a/lib/reax/cbkbo.blk b/lib/reax/cbkbo.blk
deleted file mode 100644
index 4c7a552c7385796596ceb2ba9a9c0868bee3a942..0000000000000000000000000000000000000000
--- a/lib/reax/cbkbo.blk
+++ /dev/null
@@ -1,3 +0,0 @@
- common
- $/cbkbo/ bo(nbomax)
-
diff --git a/lib/reax/cbkboncor.blk b/lib/reax/cbkboncor.blk
deleted file mode 100644
index 96d89e3a7eaa395a1b74e712a41304f2cb5fa494..0000000000000000000000000000000000000000
--- a/lib/reax/cbkboncor.blk
+++ /dev/null
@@ -1,5 +0,0 @@
- common
- $/cbkboncor/ dbosindc(nbomax,3,2*mbond+2),dbosidc(nbomax,3,2),
- $ bo131(nsort),bo132(nsort),bo133(nsort),
- $ ovc(nbotym),v13cor(nbotym)
-
diff --git a/lib/reax/cbkbopi.blk b/lib/reax/cbkbopi.blk
deleted file mode 100644
index c58ba313065b49accb53b81a54927dfe343f3460..0000000000000000000000000000000000000000
--- a/lib/reax/cbkbopi.blk
+++ /dev/null
@@ -1,3 +0,0 @@
- common
- $/cbkbopi/ bopi(nbomax)
-
diff --git a/lib/reax/cbkbopi2.blk b/lib/reax/cbkbopi2.blk
deleted file mode 100644
index f150895b0558d097709a003bf45da18fbab56dc3..0000000000000000000000000000000000000000
--- a/lib/reax/cbkbopi2.blk
+++ /dev/null
@@ -1,3 +0,0 @@
- common
- $/cbkbopi2/ bopi2(nbomax)
-
diff --git a/lib/reax/cbkbosi.blk b/lib/reax/cbkbosi.blk
deleted file mode 100644
index 27a73ce88462cb32b36b0406cd0803bfaab7926a..0000000000000000000000000000000000000000
--- a/lib/reax/cbkbosi.blk
+++ /dev/null
@@ -1,4 +0,0 @@
- common
- $/cbkbosi/ bosi(nbomax)
-
-
diff --git a/lib/reax/cbkc.blk b/lib/reax/cbkc.blk
deleted file mode 100644
index 2a2519eb2e674cb3ae2ce5d94970a5c449144a0a..0000000000000000000000000000000000000000
--- a/lib/reax/cbkc.blk
+++ /dev/null
@@ -1,5 +0,0 @@
- common
- $/cbkc/ c(nat,3),cglobal(nattot,3),itag(nat),
- $chgglobal(nattot)
-
-
diff --git a/lib/reax/cbkch.blk b/lib/reax/cbkch.blk
deleted file mode 100644
index e3199934be7d5909b0e745f89b6f3ef473bb2229..0000000000000000000000000000000000000000
--- a/lib/reax/cbkch.blk
+++ /dev/null
@@ -1,4 +0,0 @@
- common
- $/cbkch/ ch(nat)
-
-
diff --git a/lib/reax/cbkcha.blk b/lib/reax/cbkcha.blk
deleted file mode 100644
index 3bcc21871120c3fb4949293bbc1d2ecbc900b68f..0000000000000000000000000000000000000000
--- a/lib/reax/cbkcha.blk
+++ /dev/null
@@ -1,5 +0,0 @@
- common
- $/cbkcha/ ech,syscha,chisys
- $ vfieldx,vfieldy,vfieldz,nmcharge,ioldchg
-
-
diff --git a/lib/reax/cbkcharmol.blk b/lib/reax/cbkcharmol.blk
deleted file mode 100644
index 4ffeaf7d282c8c3bcce785ace5698cedc5db676f..0000000000000000000000000000000000000000
--- a/lib/reax/cbkcharmol.blk
+++ /dev/null
@@ -1,4 +0,0 @@
- common
- $/cbkcharmol/ vmcha(nmolmax),
- $ iat1mc(nmolmax),iat2mc(nmolmax)
-
diff --git a/lib/reax/cbkchb.blk b/lib/reax/cbkchb.blk
deleted file mode 100644
index b725afb66210fcb074ec15aed8e41d4286f1332c..0000000000000000000000000000000000000000
--- a/lib/reax/cbkchb.blk
+++ /dev/null
@@ -1,3 +0,0 @@
- common
- $/cbkchb/ chi(nsort),eta(nsort),gam(nsort)
-
diff --git a/lib/reax/cbkconst.blk b/lib/reax/cbkconst.blk
deleted file mode 100644
index e23dbbf20f9f33e6f9875c0316b8e194d3ed7ca2..0000000000000000000000000000000000000000
--- a/lib/reax/cbkconst.blk
+++ /dev/null
@@ -1,5 +0,0 @@
-
- common
- $/cbkconst/ dgrrdn,one,half,three,zero,caljou,rgasc,xjouca
- $ convmd
-
diff --git a/lib/reax/cbkcovbon.blk b/lib/reax/cbkcovbon.blk
deleted file mode 100644
index b37545c15289543d40e1769b03a2defd3d26f86d..0000000000000000000000000000000000000000
--- a/lib/reax/cbkcovbon.blk
+++ /dev/null
@@ -1,7 +0,0 @@
-
-
- common
- $/cbkcovbon/ de2(nbotym),de3(nbotym),psi(nbotym),
- $ psp(nbotym),
- $ ltripstaball
-
diff --git a/lib/reax/cbkd.blk b/lib/reax/cbkd.blk
deleted file mode 100644
index 4baf7f350eba50d36523644e1742e83d15b01510..0000000000000000000000000000000000000000
--- a/lib/reax/cbkd.blk
+++ /dev/null
@@ -1,7 +0,0 @@
- integer Lvirial,Latomvirial
-
- common
- $/cbkd/ d(3,nat),estrain(nat)
-
- common
- $/cbkvirial/ atomvirial(6,nat),virial(6),Lvirial,Latomvirial
diff --git a/lib/reax/cbkdbodc.blk b/lib/reax/cbkdbodc.blk
deleted file mode 100644
index a3c9722554e3c7b675410fbe7b4d12c6c9b0a39e..0000000000000000000000000000000000000000
--- a/lib/reax/cbkdbodc.blk
+++ /dev/null
@@ -1,3 +0,0 @@
- common
- $/cbkdbodc/ dbodc(nbomax,3,2)
-
diff --git a/lib/reax/cbkdbopi2ndc.blk b/lib/reax/cbkdbopi2ndc.blk
deleted file mode 100644
index 94fde9fd0709310041cd59c9b73849541b87f5d5..0000000000000000000000000000000000000000
--- a/lib/reax/cbkdbopi2ndc.blk
+++ /dev/null
@@ -1,6 +0,0 @@
-
-
-
- common
- $/cbkdbopi2ndc/ dbopi2ndc(nbomax,3,2*mbond+2)
-
diff --git a/lib/reax/cbkdbopidc.blk b/lib/reax/cbkdbopidc.blk
deleted file mode 100644
index 559c6a77a17c4e608825556446686625cf80b875..0000000000000000000000000000000000000000
--- a/lib/reax/cbkdbopidc.blk
+++ /dev/null
@@ -1,5 +0,0 @@
-
-
- common
- $/dbopidc/ dbopi2dc(nbomax,3,2),dbopidc(nbomax,3,2)
-
diff --git a/lib/reax/cbkdbopindc.blk b/lib/reax/cbkdbopindc.blk
deleted file mode 100644
index 96285f7c86c699729d1e95ad835518bd3ece6b63..0000000000000000000000000000000000000000
--- a/lib/reax/cbkdbopindc.blk
+++ /dev/null
@@ -1,6 +0,0 @@
-
-
-
- common
- $/dbopindc/ dbopindc(nbomax,3,2*mbond+2)
-
diff --git a/lib/reax/cbkdcell.blk b/lib/reax/cbkdcell.blk
deleted file mode 100644
index c3f22240a6fc1f6f9f83efe4fea06b3fc3751e89..0000000000000000000000000000000000000000
--- a/lib/reax/cbkdcell.blk
+++ /dev/null
@@ -1,5 +0,0 @@
-
-
- common
- $/cbkdcell/ dcell(3,nat,27)
-
diff --git a/lib/reax/cbkdhdc.blk b/lib/reax/cbkdhdc.blk
deleted file mode 100644
index e5e4638f2869ddd5bdd77cdcec11aec6db610235..0000000000000000000000000000000000000000
--- a/lib/reax/cbkdhdc.blk
+++ /dev/null
@@ -1,5 +0,0 @@
-
-
- common
- $/cbkdhdc/ dhdc(nvamax,3,3)
-
diff --git a/lib/reax/cbkdistan.blk b/lib/reax/cbkdistan.blk
deleted file mode 100644
index d752173f24c3bc9d7fc1798650f5521f5b244763..0000000000000000000000000000000000000000
--- a/lib/reax/cbkdistan.blk
+++ /dev/null
@@ -1,4 +0,0 @@
- common
- $/cbkdistan/ axis(3),aaxh,baxh,caxh,iortho
-
-
diff --git a/lib/reax/cbkdrdc.blk b/lib/reax/cbkdrdc.blk
deleted file mode 100644
index 1d5615440e7296e4b9b190a83208442285b4b445..0000000000000000000000000000000000000000
--- a/lib/reax/cbkdrdc.blk
+++ /dev/null
@@ -1,5 +0,0 @@
-
-
- common
- $/cbkdrdc/ drdc(nbomax,3,2)
-
diff --git a/lib/reax/cbkefield.blk b/lib/reax/cbkefield.blk
deleted file mode 100644
index 7991f4b98eb75926d1081e54a645dd3a291b3471..0000000000000000000000000000000000000000
--- a/lib/reax/cbkefield.blk
+++ /dev/null
@@ -1,4 +0,0 @@
-
- common
- $/cbkefield/ efix,efiy,efiz,c1
-
diff --git a/lib/reax/cbkenergies.blk b/lib/reax/cbkenergies.blk
deleted file mode 100644
index e0220e88ef59b41e66e2ae4a390d92b6052705cd..0000000000000000000000000000000000000000
--- a/lib/reax/cbkenergies.blk
+++ /dev/null
@@ -1,7 +0,0 @@
-
- common
- $/cbkenergies/ eb,eoop,epen,estrc,deda(3),pressu,
- $ efi,elp,emol,ea,eres,et,eradbo,
- $ ev,eco,ecoa,ehb,sw,ew,ep,ekin
-
-
diff --git a/lib/reax/cbkeregime.blk b/lib/reax/cbkeregime.blk
deleted file mode 100644
index 198862e5f139297475a5bf2f430493e4b2356e6f..0000000000000000000000000000000000000000
--- a/lib/reax/cbkeregime.blk
+++ /dev/null
@@ -1,5 +0,0 @@
- character*5 qetype
- common
- $/cbkeregime/ qetype(mereg,mezone),nnereg(mereg),nerc,
- $ ereg(mereg,mezone),nitec(mereg)
-
diff --git a/lib/reax/cbkff.blk b/lib/reax/cbkff.blk
deleted file mode 100644
index 36ffceea0cd6f9d1e1eb362b0abebafc22e6960f..0000000000000000000000000000000000000000
--- a/lib/reax/cbkff.blk
+++ /dev/null
@@ -1,9 +0,0 @@
- character*2 qas
- common
- $/cbkff/ gamcco(nsort,nsort),vpar(npamax),vovun(nsort),
- $ stlp(nsort),aval(nsort),vlp1(nsort),
- $ vover(nbotym),valp1(nsort),
- $ vka(nvatym),qas(nsort),amas(nsort),e1(nbotym),
- $ valf(nsort),de1(nbotym),swb,nvs(nvatym,3),nso,nvaty
-
-
diff --git a/lib/reax/cbkfftorang.blk b/lib/reax/cbkfftorang.blk
deleted file mode 100644
index 4154e5565dc4310ff88a75af2735e080ddca7489..0000000000000000000000000000000000000000
--- a/lib/reax/cbkfftorang.blk
+++ /dev/null
@@ -1,8 +0,0 @@
-
-
-
-
- common
- $/cbkfftorang/ v4(ntotym),vconj(ntotym),
- $ v1(ntotym),v2(ntotym),v3(ntotym)
-
diff --git a/lib/reax/cbkh.blk b/lib/reax/cbkh.blk
deleted file mode 100644
index 7be7c5d7b3c7cca43fdec0d171a0cce44364436d..0000000000000000000000000000000000000000
--- a/lib/reax/cbkh.blk
+++ /dev/null
@@ -1,5 +0,0 @@
-
-
- common
- $/cbkh/ h(nvamax)
-
diff --git a/lib/reax/cbkhbond.blk b/lib/reax/cbkhbond.blk
deleted file mode 100644
index 7a071ef096fe8bbc834b4ba030e41d5f24596cf5..0000000000000000000000000000000000000000
--- a/lib/reax/cbkhbond.blk
+++ /dev/null
@@ -1,5 +0,0 @@
-
- common
-
- $/cbkhbond/ hhb(nhbmax)
-
diff --git a/lib/reax/cbkia.blk b/lib/reax/cbkia.blk
deleted file mode 100644
index f7ada0e8fd2a77254641539a842029ffb5c8539a..0000000000000000000000000000000000000000
--- a/lib/reax/cbkia.blk
+++ /dev/null
@@ -1,6 +0,0 @@
-
-
-
- common
- $/cbkia/ ia(nat,mbond+3),iag(nat,mbond+3)
-
diff --git a/lib/reax/cbkidbo.blk b/lib/reax/cbkidbo.blk
deleted file mode 100644
index cc3fb49331066b377caafffa282cd5f84b8b67a3..0000000000000000000000000000000000000000
--- a/lib/reax/cbkidbo.blk
+++ /dev/null
@@ -1,7 +0,0 @@
-
-
-
- common
- $/cbkidbo/ idbo(nbomax,2*mbond+2),dbondc(nbomax,3,2*mbond+2),
- $ idbo1(nbomax)
-
diff --git a/lib/reax/cbkimove.blk b/lib/reax/cbkimove.blk
deleted file mode 100644
index e65bd01e431817f9d85c64148850a854156a16ec..0000000000000000000000000000000000000000
--- a/lib/reax/cbkimove.blk
+++ /dev/null
@@ -1,6 +0,0 @@
-
-
- common
- $/cbkimove/ imove(nattot)
-
-
diff --git a/lib/reax/cbkinit.blk b/lib/reax/cbkinit.blk
deleted file mode 100644
index 45ac3396a03cf7834895297f66a3f2965cf6583c..0000000000000000000000000000000000000000
--- a/lib/reax/cbkinit.blk
+++ /dev/null
@@ -1,6 +0,0 @@
-
- character*40 qruid
- common
- $/cbkinit/ tsetor,nzero,none,ntwo,nthree,qruid,systime,
- $ ustime,two,pi,avognr,axiss(3),pset,rdndgr
-
diff --git a/lib/reax/cbklonpar.blk b/lib/reax/cbklonpar.blk
deleted file mode 100644
index 016888f28675a705338fc7590d163af3b8fcb979..0000000000000000000000000000000000000000
--- a/lib/reax/cbklonpar.blk
+++ /dev/null
@@ -1,5 +0,0 @@
-
-
- common
- $/cbklonpar/ vlp(nat),dvlpdsbo(nat)
-
diff --git a/lib/reax/cbkmolec.blk b/lib/reax/cbkmolec.blk
deleted file mode 100644
index 847ae44edbd57a01acef563385d4a0a801489cc9..0000000000000000000000000000000000000000
--- a/lib/reax/cbkmolec.blk
+++ /dev/null
@@ -1,6 +0,0 @@
-
-
-
- common
- $/cbkmolec/ nmolat2(nmolmax,nat),elmol2(nmolmax)
-
diff --git a/lib/reax/cbknmolat.blk b/lib/reax/cbknmolat.blk
deleted file mode 100644
index a89f0f677caa1d91c021d8f8a00bdf058012a6f1..0000000000000000000000000000000000000000
--- a/lib/reax/cbknmolat.blk
+++ /dev/null
@@ -1,6 +0,0 @@
-
-
-
- common
- $/cbknmolat/ nmolat(nmolmax,nat)
-
diff --git a/lib/reax/cbknonbon.blk b/lib/reax/cbknonbon.blk
deleted file mode 100644
index c0ec0feaa18501b2a29af45633d1be7000ddf22d..0000000000000000000000000000000000000000
--- a/lib/reax/cbknonbon.blk
+++ /dev/null
@@ -1,6 +0,0 @@
-
-
- common
- $/cbknonbon/ gamwco(nsort,nsort),sw1,p3co(nsort,nsort),
- $ p2co(nsort,nsort),p1co(nsort,nsort)
-
diff --git a/lib/reax/cbknubon2.blk b/lib/reax/cbknubon2.blk
deleted file mode 100644
index ecc7eafd474e7faabe36de290a0647674a24e7d4..0000000000000000000000000000000000000000
--- a/lib/reax/cbknubon2.blk
+++ /dev/null
@@ -1,5 +0,0 @@
-
-
- common
- $/cbknubon2/ nubon1(nat,mbond), nubon2(nat,mbond)
-
diff --git a/lib/reax/cbknvlbo.blk b/lib/reax/cbknvlbo.blk
deleted file mode 100644
index b9a379181109842b1069a5ca110f4a7e4f25afc1..0000000000000000000000000000000000000000
--- a/lib/reax/cbknvlbo.blk
+++ /dev/null
@@ -1,4 +0,0 @@
- common
- $/cbknvlbo/ nvlbo(nneighmax*nat)
-
-
diff --git a/lib/reax/cbknvlown.blk b/lib/reax/cbknvlown.blk
deleted file mode 100644
index d51ce5531f01adf194ac0603c2c883bb7e9fa8d4..0000000000000000000000000000000000000000
--- a/lib/reax/cbknvlown.blk
+++ /dev/null
@@ -1,2 +0,0 @@
- common
- $/cbknvlown/ nvlown(nneighmax*nat)
diff --git a/lib/reax/cbkpairs.blk b/lib/reax/cbkpairs.blk
deleted file mode 100644
index 028b0f2fac440583a29c530f9fb290063103d19b..0000000000000000000000000000000000000000
--- a/lib/reax/cbkpairs.blk
+++ /dev/null
@@ -1,4 +0,0 @@
- common
- $/cbkpairs/ nvl1(nneighmax*nat),nvl2(nneighmax*nat),nvpair,nvlself
-
-
diff --git a/lib/reax/cbkpres.blk b/lib/reax/cbkpres.blk
deleted file mode 100644
index bf14b380c4c076659c135e5ed8d0e9ff017a35ff..0000000000000000000000000000000000000000
--- a/lib/reax/cbkpres.blk
+++ /dev/null
@@ -1,4 +0,0 @@
-
- common
- $/cbkpres/ presx,presy,presz
-
diff --git a/lib/reax/cbkqa.blk b/lib/reax/cbkqa.blk
deleted file mode 100644
index 63e88e74119b201f3db2e97d8626a13375fc1fb1..0000000000000000000000000000000000000000
--- a/lib/reax/cbkqa.blk
+++ /dev/null
@@ -1,5 +0,0 @@
- character*2 qa
- common
- $/cbkqa/ qa(nattot)
-
-
diff --git a/lib/reax/cbkrbo.blk b/lib/reax/cbkrbo.blk
deleted file mode 100644
index e9b99f008aa439a268020dbe8b4e4ccdd1152858..0000000000000000000000000000000000000000
--- a/lib/reax/cbkrbo.blk
+++ /dev/null
@@ -1,5 +0,0 @@
-
-
- common
- $/cbkrbo/ rbo(nbomax),ibsym(nbomax),ib(nbomax,3)
-
diff --git a/lib/reax/cbkrestr.blk b/lib/reax/cbkrestr.blk
deleted file mode 100644
index 15169677e4034fb15e4ec2851d2d59c54fd578b9..0000000000000000000000000000000000000000
--- a/lib/reax/cbkrestr.blk
+++ /dev/null
@@ -1,12 +0,0 @@
- common
- $/cbkrestr/ vkrv(mrestra),vrstra(mrestra),vkr2v(mrestra),
- $ dismacen(mrestra),rmstra1(mrestra),
- $ rrstra(mrestra),vkrst2(mrestra),
- $ rmstra2(mrestra),rmstrax(mrestra),rmstray(mrestra),
- $ rmstraz(mrestra),cmo(nat,3),vmo1(nat),trstra(mrestra),
- $ vkrt(mrestra),vkr2t(mrestra),vkrstr(mrestra),
- $ irstrav(mrestra,3),irstra(mrestra,2),itend(mrestra),
- $ irstram(mrestra,5),itstart(mrestra),irstrat(mrestra,4),
- $ imorph
-
-
diff --git a/lib/reax/cbksrtbon1.blk b/lib/reax/cbksrtbon1.blk
deleted file mode 100644
index 9a4d425e185d6df8eb809b0616fde71ac8e9f426..0000000000000000000000000000000000000000
--- a/lib/reax/cbksrtbon1.blk
+++ /dev/null
@@ -1,13 +0,0 @@
- character*60 qmol
- common
- $/cbksrtbon1/ dbodr(nbomax),dbopidr(nbomax),
- $ dbopi2dr(nbomax),
- $ rob1(nsort,nsort),rob2(nsort,nsort),
- $ rob3(nsort,nsort),
- $ rat(nsort),rapt(nsort),vnq(nsort),bom(nbotym),
- $ pdp(nbotym),ptp(nbotym),pdo(nbotym),
- $ popi(nbotym),bop1(nbotym),bop2(nbotym),cutoff,
- $ nbs(nbotym,2),
- $ nsbma2,nsbmax,nboty2,nbonall,qfile(nmolset),qmol
-
-
diff --git a/lib/reax/cbksrthb.blk b/lib/reax/cbksrthb.blk
deleted file mode 100644
index ad035f6c0536917d95ba27d2a9bcdc3bdcb4d534..0000000000000000000000000000000000000000
--- a/lib/reax/cbksrthb.blk
+++ /dev/null
@@ -1,10 +0,0 @@
-
-
- common
- $/cbksrthb/ vhb1(nhbtym),vhb2(nhbtym),rhb(nhbtym),
- $ dehb(nhbtym),ihb(nhbmax,8),nhb,
- $ nphb(nsort),nhbs(nhbtym,3),nhbty,hbcut,
- $ lhbnew
-
-
-
diff --git a/lib/reax/cbktorang.blk b/lib/reax/cbktorang.blk
deleted file mode 100644
index 3e8c94fd5f00d452db66e72708d0215592df3c2b..0000000000000000000000000000000000000000
--- a/lib/reax/cbktorang.blk
+++ /dev/null
@@ -1,5 +0,0 @@
-
-
- common
- $/cbktorang/ dargtdc(ntomax,3,4),thg(ntomax)
-
diff --git a/lib/reax/cbktorsion.blk b/lib/reax/cbktorsion.blk
deleted file mode 100644
index 30f984b7df5ac71346f714d1672f76668734e094..0000000000000000000000000000000000000000
--- a/lib/reax/cbktorsion.blk
+++ /dev/null
@@ -1,7 +0,0 @@
-
-
-
- common
- $/cbktorsion/ nts(ntotym,4),ntoty,ntor,it(ntomax,11)
-
-
diff --git a/lib/reax/cbktregime.blk b/lib/reax/cbktregime.blk
deleted file mode 100644
index 06df64e192a466b6a27bebb03670b8f277900858..0000000000000000000000000000000000000000
--- a/lib/reax/cbktregime.blk
+++ /dev/null
@@ -1,8 +0,0 @@
- common
- $/cbktregime/ dttreg(mtreg,mtzone),tdamptreg(mtreg,mtzone),
- $ ia1treg(mtreg,mtzone),ia2treg(mtreg,mtzone),
- $ tsettreg(mtreg,mtzone),nntreg(mtreg),ittc(mtreg),
- $ nittc(mtreg),ifieldz,ifieldx,ifieldy,
- $ nrestra,nrestram,nrestrat,nrestrav,ntrc
-
-
diff --git a/lib/reax/cbkvalence.blk b/lib/reax/cbkvalence.blk
deleted file mode 100644
index 3e7bee9b600245f6de6a19e307a6d17701665708..0000000000000000000000000000000000000000
--- a/lib/reax/cbkvalence.blk
+++ /dev/null
@@ -1,5 +0,0 @@
-
-
- common
- $/cbkvalence/ nval,iv(nvamax,6)
-
diff --git a/lib/reax/cbkvregime.blk b/lib/reax/cbkvregime.blk
deleted file mode 100644
index ed2f5a45e6227be32d9cd2aaea68eccc7b38defb..0000000000000000000000000000000000000000
--- a/lib/reax/cbkvregime.blk
+++ /dev/null
@@ -1,7 +0,0 @@
- character*5 qvtype
- common
- $/cbkvregime/ ivsca(mvreg,mvzone),dvvreg(mvreg,mvzone),
- $ nnvreg(mvreg),invrc,nitvc(mvreg),
- $ qvtype(mvreg,mvzone)
-
-
diff --git a/lib/reax/cellcoord.blk b/lib/reax/cellcoord.blk
deleted file mode 100644
index 3cbee22656c71ae94a116353fff732521e34d4cd..0000000000000000000000000000000000000000
--- a/lib/reax/cellcoord.blk
+++ /dev/null
@@ -1,4 +0,0 @@
-
- common
- $/cellcoord/ tm11,tm21,tm31,tm22,tm32,tm33,angle(3),angles(3)
-
diff --git a/lib/reax/control.blk b/lib/reax/control.blk
deleted file mode 100644
index 4e84f85b9e1dfe481a00cb8b6a08e52fbaa724bc..0000000000000000000000000000000000000000
--- a/lib/reax/control.blk
+++ /dev/null
@@ -1,12 +0,0 @@
- common
- $/control/ vrange,cutof2,cutof3,vlbora,tstep,range,taut,volcha,
- $ axis1,axis2,axis3,taup,
- $ icpres,nmethod,noutpt,inpt,napp,ianaly,ncha2,
- $ nrand,ntscale,itstep,ndebug,icentr,itrout,
- $ nchaudixmolo,itrans,nsav,
- $ nrep1,ncontrol,nhop2,nsav3,ngeofor,ifreq,
- $ nprevrun,maxstp,nvel,nsurp,ncons,
- $ ncha,icell,imolde,nchaud
-*********************************************************************************
-
-
diff --git a/lib/reax/opt.blk b/lib/reax/opt.blk
deleted file mode 100644
index c72df23d5cddf32e7b0ec306514110178c9ada6c..0000000000000000000000000000000000000000
--- a/lib/reax/opt.blk
+++ /dev/null
@@ -1,23 +0,0 @@
- parameter (maxdat=5000)
- parameter (maxmdat=2500)
- parameter (maxkop=2500)
- character*80 qff
- character*60 qmdat
- character*100 qdatid
- character*2 qas2
- common
- $/opt/ fpar(7,nvatym,40),datopt(maxdat),caldat(maxdat),
- $ compdat(maxdat),weightdat(maxdat),
- $ devi(maxdat),vkop(maxkop),devkop(maxkop),sdy(3),
- $ valpar,valnew,change,vchange,
- $ molin(maxmdat,nsort),
- $ iboo(nbotym,2),idmo(nodmtym,2),ivao(nvatym,5),
- $ itoo(ntotym,7),ihbo(nhbtym,5),iheada(maxmdat),
- $ ndatm(maxmdat),iheada2(maxmdat),ichn(3),
- $ ikop1(maxkop),ikop2(maxkop),idat(maxdat),mu1(maxkop),
- $ mu2(maxkop),
- $ ndata,imam,iopt,iheatf,nkop,iagain,
- $ qdatid(maxdat),qmdat(maxmdat),qff(250),qas2(nsort)
-***********************************************************************
-
-
diff --git a/lib/reax/reax_charges.F b/lib/reax/reax_charges.F
deleted file mode 100644
index 5815501a29fe3c67696936d8edb8e26985767d62..0000000000000000000000000000000000000000
--- a/lib/reax/reax_charges.F
+++ /dev/null
@@ -1,85 +0,0 @@
-**********************************************************************
-* *
-* REAXFF Reactive force field program *
-* *
-* Developed and written by Adri van Duin, duin@wag.caltech.edu *
-* *
-* Copyright (c) 2001-2010 California Institute of Technology *
-* *
-* This is an open-source program. Feel free to modify its *
-* contents. Please keep me informed of any useful modification *
-* or addition that you made. Please do not distribute this *
-* program to others; if people are interested in obtaining *
-* a copy of this program let them contact me first. *
-* *
-**********************************************************************
-************************************************************************
-
- subroutine taper(r,r2)
-
-************************************************************************
-#include "cbka.blk"
-#include "cbkconst.blk"
-#include "cbkenergies.blk"
-#include "cbkinit.blk"
-#include "cbknonbon.blk"
-************************************************************************
-* *
-* Taper function for Coulomb interaction *
-* *
-************************************************************************
- r3=r2*r
- SW=SWC7*R3*R3*R+SWC6*R3*R3+SWC5*R3*R2+SWC4*R2*R2+SWC3*R3+SWC2*R2+
- $SWC1*R+SWC0
- SW1=7.0D0*SWC7*R3*R3+6.0D0*SWC6*R3*R2+5.0D0*SWC5*R2*R2+
- $4.0D0*SWC4*R3+THREE*SWC3*R2+TWO*SWC2*R+SWC1
- return
- end
-************************************************************************
-************************************************************************
-
- subroutine tap7th
-
-************************************************************************
-#include "cbka.blk"
-#include "cbkc.blk"
-#include "cbkconst.blk"
-#include "cbkd.blk"
-#include "cbkff.blk"
-#include "cbkh.blk"
-#include "control.blk"
-
-************************************************************************
-* *
-* 7th order taper function setup *
-* *
-************************************************************************
-c$$$ if (ndebug.eq.1) then
-c$$$C open (65,file='fort.65',status='unknown',access='append')
-c$$$ write (65,*) 'In tap7th'
-c$$$ call timer(65)
-c$$$ close (65)
-c$$$ end if
- D1=SWB-SWA
- D7=D1**7.0D0
- SWA2=SWA*SWA
- SWA3=SWA2*SWA
- SWB2=SWB*SWB
- SWB3=SWB2*SWB
-
-************************************************************************
-* 7th order taper function *
-************************************************************************
-
- SWC7= 20.0D0/D7
- SWC6= -70.0D0*(SWA+SWB)/D7
- SWC5= 84.0D0*(SWA2+3.0D0*SWA*SWB+SWB2)/D7
- SWC4= -35.0D0*(SWA3+9.0D0*SWA2*SWB+9.0D0*SWA*SWB2+SWB3)/D7
- SWC3= 140.0D0*(SWA3*SWB+3.0D0*SWA2*SWB2+SWA*SWB3)/D7
- SWC2=-210.0D0*(SWA3*SWB2+SWA2*SWB3)/D7
- SWC1= 140.0D0*SWA3*SWB3/D7
- SWC0=(-35.0D0*SWA3*SWB2*SWB2+21.0D0*SWA2*SWB3*SWB2-
- $7.0D0*SWA*SWB3*SWB3+SWB3*SWB3*SWB)/D7
-
- return
- END
diff --git a/lib/reax/reax_connect.F b/lib/reax/reax_connect.F
deleted file mode 100644
index e77875124f1f28d70373279f9302fad15c559c2b..0000000000000000000000000000000000000000
--- a/lib/reax/reax_connect.F
+++ /dev/null
@@ -1,1547 +0,0 @@
-**********************************************************************
-* *
-* REAXFF Reactive force field program *
-* *
-* Developed and written by Adri van Duin, duin@wag.caltech.edu *
-* *
-* Copyright (c) 2001-2010 California Institute of Technology *
-* *
-* This is an open-source program. Feel free to modify its *
-* contents. Please keep me informed of any useful modification *
-* or addition that you made. Please do not distribute this *
-* program to others; if people are interested in obtaining *
-* a copy of this program let them contact me first. *
-* *
-**********************************************************************
-**********************************************************************
-
- subroutine srtatom
-
-**********************************************************************
-#include "cbka.blk"
-#include "cbkatomcoord.blk"
-#include "cbkff.blk"
-#include "cbkia.blk"
-#include "cbkqa.blk"
-#include "control.blk"
-#include "opt.blk"
-#include "small.blk"
-**********************************************************************
-* *
-* Determine atom types in system *
-* *
-**********************************************************************
-* Requires the following variables
-* ndebug - opt.blk; determines whether to debug or not; everywhere
-* xmasmd - cbka.blk; some sort of atmoic mass?; srtatom, reac.f
-* molin - opt.blk; keeps info on?; srtatom
-* nso - cbka.blk; number of atoms?; srtatom, inout.f
-* nprob - cbka.blk; does?; connect.f, inout.f, reac.f
-* nasort - cbka.blk; a sorting array; srtatom
-* ia - cbka.blk; atom numbers?; poten.f, inout.f, connect.f, charges.f
-* iag - cbka.blk; ; connect.f, inout.f, poten.f, reac.f
-* xmasat - cbka.blk; does?; srtatom, reac.f
-* amas - cbka.blk; ? ; srtatom, ffinpt, molanal, ovcor
-* qa - cbka.blk; some sort of error statement variable?; srtatom, srtbon1, inout.f, radbo
-*
-c$$$ if (ndebug.eq.1) then
-c$$$C open (65,file='fort.65',status='unknown',access='append')
-c$$$ write (65,*) 'In srtatom'
-c$$$ call timer(65)
-c$$$ close (65)
-c$$$ end if
-
- xmasmd=0.0
- do i1=1,nso
- molin(nprob,i1)=0
- nasort(i1)=0
- end do
- do i1=1,na
- ia(i1,1)=0
- iag(i1,1)=0
- do i2=1,nso
- if (qa(i1).eq.qas(i2)) then
- ia(i1,1)=i2
- iag(i1,1)=i2
- molin(nprob,i2)=molin(nprob,i2)+1
- xmasat(i1)=amas(i2)
- xmasmd=xmasmd+amas(i2)
- nasort(i2)=nasort(i2)+1
- end if
- end do
- if (ia(i1,1).eq.0) then
- write (*,*)'Unknown atom type: ',qa(i1)
- stop 'Unknown atom type'
- end if
- end do
-
- return
- end
-**********************************************************************
-**********************************************************************
-
- subroutine molec
-
-**********************************************************************
-#include "cbka.blk"
-#include "cbkdcell.blk"
-#include "cbkff.blk"
-#include "cbkia.blk"
-#include "cbkmolec.blk"
-#include "cbknmolat.blk"
-#include "control.blk"
-#include "small.blk"
- dimension nmolo2(nat),iseen(nmolmax),isee2(nmolmax)
-**********************************************************************
-* *
-* Determine changes in molecules *
-* *
-**********************************************************************
-c$$$ if (ndebug.eq.1) then
-c$$$C open (65,file='fort.65',status='unknown',access='append')
-c$$$ write (65,*) 'In molec'
-c$$$ call timer(65)
-c$$$ close (65)
-c$$$ end if
- npreac=0
-
- do i1=1,nmolo
- natmol=0
- do i2=1,na
- if (ia(i2,3+mbond).eq.i1) then
- natmol=natmol+1
- nmolat(i1,natmol+1)=i2
- end if
- end do
- nmolat(i1,1)=natmol
- end do
-
- if (nmolo5.lt.nmolo5o) nradcount=0 !reset reaction counter
- do i1=1,nmolo5
- natmol=0
- do i2=1,na
- if (iag(i2,3+mbond).eq.i1) then
- natmol=natmol+1
- nmolat2(i1,natmol+1)=i2
- end if
- end do
- nmolat2(i1,1)=natmol
- end do
- nmolo5o=nmolo5
-
- do i1=nmolo+1,nmoloold
- do i2=1,nmolat(i1,1)
- nmolat(i1,1+i2)=0
- end do
- nmolat(i1,1)=0
- end do
-
- do i1=1,nmolo
- elmol(i1)=0.0
- do i2=1,nmolat(i1,1)
- ihu=nmolat(i1,i2+1)
- ity=ia(ihu,1)
- elmol(i1)=elmol(i1)+stlp(ity)
- end do
- end do
-
- do i1=1,nmolo5
- elmol2(i1)=0.0
- do i2=1,nmolat2(i1,1)
- ihu=nmolat2(i1,i2+1)
- ity=iag(ihu,1)
- elmol2(i1)=elmol2(i1)+stlp(ity)
- end do
- end do
-
- return
- end
-**********************************************************************
-**********************************************************************
-
- subroutine dista2 (n1,n2,dista,dx,dy,dz)
-
-**********************************************************************
-#include "cbka.blk"
-#include "cbkc.blk"
-**********************************************************************
-* *
-* Determine interatomic distances *
-* *
-**********************************************************************
-c$$$* if (ndebug.eq.1) then
-c$$$C* open (65,file='fort.65',status='unknown',access='append')
-c$$$* write (65,*) 'In dista2'
-c$$$* call timer(65)
-c$$$* close (65)
-c$$$* end if
-
- dx=c(n1,1)-c(n2,1)
- dy=c(n1,2)-c(n2,2)
- dz=c(n1,3)-c(n2,3)
- dista=sqrt(dx*dx+dy*dy+dz*dz)
-
- return
- end
-**********************************************************************
-**********************************************************************
-
- subroutine srtbon1(lprune,lhb,hbcut_in,lhbnew_in,ltripstaball_in)
-
-**********************************************************************
-#include "cbka.blk"
-#include "cbkabo.blk"
-#include "cbkbo.blk"
-#include "cbkbosi.blk"
-#include "cbkbopi.blk"
-#include "cbkbopi2.blk"
-#include "cbkc.blk"
-#include "cbkch.blk"
-#include "cbkconst.blk"
-#include "cbkdbopidc.blk"
-#include "cbkdrdc.blk"
-#include "cbkia.blk"
-#include "cbknubon2.blk"
-#include "cbknvlbo.blk"
-#include "cbkpairs.blk"
-#include "cbknvlown.blk"
-#include "cbkqa.blk"
-#include "cbkrbo.blk"
-#include "cellcoord.blk"
-#include "control.blk"
-#include "small.blk"
-#include "cbkdbodc.blk"
-#include "cbksrtbon1.blk"
-#include "cbkff.blk"
-#include "cbksrthb.blk"
-#include "cbkcovbon.blk"
- logical found
- integer nboncol(nboallmax)
- integer iball(nboallmax,3)
-
-**********************************************************************
-* *
-* Determine connections within the molecule *
-* *
-**********************************************************************
-c$$$ if (ndebug.eq.1) then
-c$$$C open (65,file='fort.65',status='unknown',access='append')
-c$$$ write (65,*) 'In srtbon1'
-c$$$ call timer(65)
-c$$$ close (65)
-c$$$ end if
-
-c Transfer hbcut, lhbnew, and ltripstaball from C++ calling function
- hbcut = hbcut_in
- lhbnew = lhbnew_in
- ltripstaball = ltripstaball_in
-
- do i1=1,na
- abo(i1)=0.0d0
- end do
- nbonall=0
- nbon2=0
- nsbmax=0
- nsbma2=0
-
- if (imolde.eq.0) then
-
- nmolo=0
- nmolo5=0
- end if
- if (imolde.eq.0) then
- do i1=1,na
- do i2=2,mbond+3
- ia(i1,i2)=0
- iag(i1,i2)=0
- end do
- end do
-
- else
-
- do i1=1,na
- do i2=2,mbond+2
- ia(i1,i2)=0
- iag(i1,i2)=0
- end do
- end do
-
- end if
-
- do i1=1,na
- do i2=1,mbond
- nubon1(i1,i2)=0
- nubon2(i1,i2)=0
- end do
- end do
-
-* First detect all bonds and create preliminary list
-
- do 11 ivl=1,nvpair
- if (nvlbo(ivl).eq.0) goto 11 !not in bond order range
- i1=nvl1(ivl)
- i2=nvl2(ivl)
- call dista2(i1,i2,dis,dxm,dym,dzm)
- ih1=ia(i1,1)
- ih2=ia(i2,1)
- disdx=dxm/dis
- disdy=dym/dis
- disdz=dzm/dis
- itype=0
- if (ih1.gt.ih2) then
- ih1=ia(i2,1)
- ih2=ia(i1,1)
- end if
- do i3=1,nboty2
- if (ih1.eq.nbs(i3,1).and.ih2.eq.nbs(i3,2)) itype=i3
- end do
- if (itype.eq.0.and.rat(ih1).gt.zero.and.rat(ih2).gt.zero) then
-c$$$ call mdsav(1,qfile(nprob))
- write (*,*)qa(i1),'-',qa(i2),'Fatal: Unknown bond in molecule'
- stop
- end if
-
- rhulp=dis/rob1(ih1,ih2)
-
-**********************************************************************
-* *
-* Determine bond orders *
-* *
-**********************************************************************
- rh2=zero
- rh2p=zero
- rh2pp=zero
- ehulp=zero
- ehulpp=zero
- ehulppp=zero
- if (rapt(ih1).gt.zero.and.rapt(ih2).gt.zero) then
- rhulp2=dis/rob2(ih1,ih2)
- rh2p=rhulp2**ptp(itype)
- ehulpp=exp(pdp(itype)*rh2p)
- end if
- if (vnq(ih1).gt.zero.and.vnq(ih2).gt.zero) then
- rhulp3=dis/rob3(ih1,ih2)
- rh2pp=rhulp3**popi(itype)
- ehulppp=exp(pdo(itype)*rh2pp)
- end if
-
- if (rat(ih1).gt.zero.and.rat(ih2).gt.zero) then
- rh2=rhulp**bop2(itype)
- ehulp=(1.0+cutoff)*exp(bop1(itype)*rh2)
- end if
-
- bor=ehulp+ehulpp+ehulppp
-
- j1=i1
- j2=i2
-
-**********************************************************************
-* *
-* Determine bond orders *
-* *
-**********************************************************************
- if (bor.gt.cutoff) then
- nbonall=nbonall+1
- if (nbonall.gt.nboallmax) then
- write (6,*)'nbonall = ',nbonall,
- $ ' reax_defs.h::NBOALLMAXDEF = ',NBOALLMAXDEF,
- $ ' after',ivl, ' of ',nvpair,' pairs completed.'
- stop 'Too many bonds; maybe wrong cell parameters.'
- end if
- iball(nbonall,1)=itype
- iball(nbonall,2)=j1
- iball(nbonall,3)=j2
-
- ia(i1,2)=ia(i1,2)+1
- if (ia(i1,2).gt.mbond) then
- write (6,*)'ia(i1,2) = ',ia(i1,2),
- $ ' reax_defs.h::MBONDDEF = ',MBONDDEF,
- $ ' after',ivl, ' of ',nvpair,' pairs completed.'
- stop 'Too many bonds on atom. Increase MBONDDEF'
- end if
-
- if (i1.ne.i2) then
- ia(i2,2)=ia(i2,2)+1
- if (ia(i2,2).gt.mbond) then
- write (6,*)'ia(i1,2) = ',ia(i1,2),
- $ ' reax_defs.h::MBONDDEF = ',MBONDDEF,
- $ ' after',ivl, ' of ',nvpair,' pairs completed.'
- stop 'Too many bonds on atom. Increase MBONDDEF'
- end if
- endif
-
- ia(i1,ia(i1,2)+2)=i2
- ia(i2,ia(i2,2)+2)=i1
- if (abs(de1(iball(nbonall,1))).gt.-0.01) then
- nubon2(i1,ia(i1,2))=nbonall
- nubon2(i2,ia(i2,2))=nbonall
- else
- nbonall=nbonall-1 !Inorganics
- end if
- end if
- 11 continue
-
-**********************************************************************
-* *
-* lprune controls level of bond-pruning performed to increase *
-* performance. For correct results, it should be set to 4. *
-* However, making it smaller can speed up *
-* force calculation and may not have a big effect on forces. *
-* Setting it to 0 turns off pruning, useful for debugging. *
-* *
-**********************************************************************
-*********************************************************************
-* *
-* lhb controls whether or not to unprune ghost bonds that *
-* may possibly form ghost hydrogen bonds. *
-* Setting it to 1 causes unpruning, and so is the safe option. *
-* If lprune = 0, then pruning is not used, results are exact *
-* and lhb has no effect. *
-* *
-**********************************************************************
- if (lprune .gt. 0) then
-**********************************************************************
-* *
-* Eliminate bonds that are not in 1-6 interaction *
-* with local atom, or closer. *
-* Need additional sweep to catch possible hydrogen bonds *
-* *
-**********************************************************************
-
- ntmp0 = 0
- ntmp1 = 0
- ntmp2 = 0
- ntmp3 = 0
- ntmp4 = 0
- ntmp5 = 0
- ntmp6 = 0
- ntmphb = 0
-
-* color 1 are bonds with two local atoms
-* color 2 are bonds with one local atom
-* color 3 are bonds adjacent to bond with one local atom
-
- do i1 = 1,nbonall
- if (iball(i1,2).le.na_local) then
- if (iball(i1,3).le.na_local) then
- nboncol(i1) = 1
- ntmp1 = ntmp1+1
- else
- nboncol(i1) = 2
- ntmp2 = ntmp2+1
- endif
- else if (iball(i1,3).le.na_local) then
- nboncol(i1) = 2
- ntmp2 = ntmp2+1
- else
- nboncol(i1) = 0
- endif
- end do
-
- if (lprune .ge. 3) then
- do i1 = 1,nbonall
- if (nboncol(i1).eq.2) then
- if (iball(i1,2).le.na_local) then
- i3=iball(i1,3)
- else
- i3=iball(i1,2)
- endif
-
- do i4 = 1,ia(i3,2)
- i5=nubon2(i3,i4)
- if (nboncol(i5).eq.0) then
- nboncol(i5)=3
- ntmp3 = ntmp3+1
- endif
- end do
- endif
- end do
- endif
-* color 4 bonds are part of a 1-4 interaction with local atom
-
- if (lprune .ge. 4) then
- do i1 = 1,nbonall
- if (nboncol(i1).eq.3) then
-* One end definitely has a bond of color 2
-* Find it and color bonds on other end 4
- i3=iball(i1,2)
- i3b=0
- do i4 = 1,ia(i3,2)
- i5=nubon2(i3,i4)
- if (nboncol(i5).eq.2) then
- i3b=iball(i1,3)
- endif
- end do
-
- if (i3b.eq.0) then
- i3=iball(i1,3)
- i3b=0
- do i4 = 1,ia(i3,2)
- i5=nubon2(i3,i4)
- if (nboncol(i5).eq.2) then
- i3b=iball(i1,2)
- endif
- end do
- endif
-
- if (i3b.eq.0) then
- stop 'Could not find color 2 from color 3 bond'
- endif
-
- do i4 = 1,ia(i3b,2)
- i5=nubon2(i3b,i4)
- if (nboncol(i5).eq.0) then
- nboncol(i5)=4
- ntmp4 = ntmp4+1
- endif
- end do
-
- endif
- end do
- endif
-
-* color 5 bonds are part of a 1-5 interaction with local atom
-
- if (lprune .ge. 5) then
- do i1 = 1,nbonall
- if (nboncol(i1).eq.4) then
-* One end definitely has a bond of color 3
-* Find it and color bonds on other end 5
- i3=iball(i1,2)
- i3b=0
- do i4 = 1,ia(i3,2)
- i5=nubon2(i3,i4)
- if (nboncol(i5).eq.3) then
- i3b=iball(i1,3)
- endif
- end do
-
- if (i3b.eq.0) then
- i3=iball(i1,3)
- i3b=0
- do i4 = 1,ia(i3,2)
- i5=nubon2(i3,i4)
- if (nboncol(i5).eq.3) then
- i3b=iball(i1,2)
- endif
- end do
- endif
-
- if (i3b.eq.0) then
- stop 'Could not find color 3 from color 4 bond'
- endif
-
- do i4 = 1,ia(i3b,2)
- i5=nubon2(i3b,i4)
- if (nboncol(i5).eq.0) then
- nboncol(i5)=5
- ntmp5 = ntmp5+1
- endif
- end do
-
- endif
- end do
- endif
-
-* color 6 bonds are part of a 1-6 interaction with local atom
-
- if (lprune .ge. 6) then
- do i1 = 1,nbonall
- if (nboncol(i1).eq.5) then
-* One end definitely has a bond of color 4
-* Find it and color bonds on other end 6
- i3=iball(i1,2)
- i3b=0
- do i4 = 1,ia(i3,2)
- i5=nubon2(i3,i4)
- if (nboncol(i5).eq.4) then
- i3b=iball(i1,3)
- endif
- end do
-
- if (i3b.eq.0) then
- i3=iball(i1,3)
- i3b=0
- do i4 = 1,ia(i3,2)
- i5=nubon2(i3,i4)
- if (nboncol(i5).eq.4) then
- i3b=iball(i1,2)
- endif
- end do
- endif
-
- if (i3b.eq.0) then
- stop 'Could not find color 4 from color 5 bond'
- endif
-
- do i4 = 1,ia(i3b,2)
- i5=nubon2(i3b,i4)
- if (nboncol(i5).eq.0) then
- nboncol(i5)=6
- ntmp6 = ntmp6+1
- endif
- end do
-
- endif
- end do
- endif
-
-* Catch all the possible hydrogen bonds
-* This section replicates the logic used in srthb()
- if (lhb .eq. 1) then
-c Outer loop must be Verlet list, because ia() does not store Verlet entries,
-c but it does store bond entries in nubon2()
- do ivl=1,nvpair !Use Verlet-list to find donor-acceptor pairs
-
- j1=nvl1(ivl)
- j2=nvl2(ivl)
- ihhb1=nphb(ia(j1,1))
- ihhb2=nphb(ia(j2,1))
-
- if (ihhb1.gt.ihhb2) then !Make j1 donor(H) atom and j2 acceptor(O) atom
- j2=nvl1(ivl)
- j1=nvl2(ivl)
- ihhb1=nphb(ia(j1,1))
- ihhb2=nphb(ia(j2,1))
- end if
-
-* Only need to compute bonds where j1 is local
- if (j1 .le. na_local) then
-
- if (ihhb1.eq.1.and.ihhb2.eq.2) then
- call dista2(j1,j2,dishb,dxm,dym,dzm)
- if (dishb.lt.hbcut) then
- do i23=1,ia(j1,2) !Search for acceptor atoms bound to donor atom
- if (nboncol(nubon2(j1,i23)).eq.0) then
- j3=ia(j1,2+i23)
- if (nphb(ia(j3,1)).eq.2.and.j3.ne.j2) then
- nboncol(nubon2(j1,i23))=-1
- ntmphb = ntmphb+1
- endif
- endif
- end do
- end if
- end if
- end if
- end do
- end if
-
-* Compact the list, removing all uncolored bonds
-
- nbon = 0
- do i1 = 1,nbonall
- if (nboncol(i1).eq.0) then
- ntmp0=ntmp0+1
- else
- nbon = nbon+1
-
- if (nbon.gt.nbomax) then
- write (6,*)nbon,nbomax
- write (6,*)'nbon = ',nbon,' reax_defs.h::NBOMAXDEF = ',
- $ NBOMAXDEF,' after',i1, ' of ',nbonall,
- $ ' initial bonds completed.'
- stop 'Too many pruned bonds; increase NBOMAXDEF'
- end if
-
-
- ib(nbon,1) = iball(i1,1)
- ib(nbon,2) = iball(i1,2)
- ib(nbon,3) = iball(i1,3)
- endif
- end do
-
-**********************************************************************
-* *
-* Do not perform ghost-bond pruning *
-* *
-**********************************************************************
-
- else
-
- nbon = 0
- do i1 = 1,nbonall
- nbon = nbon+1
-
- if (nbon.gt.nbomax) then
- write (6,*)nbon,nbomax
- write (6,*)'nbon = ',nbon,' reax_defs.h::NBOMAXDEF = ',
- $ NBOMAXDEF,' after',i1, ' of ',nbonall,
- $ ' initial bonds completed.'
- stop 'Too many pruned bonds; increase NBOMAXDEF'
- end if
-
- ib(nbon,1) = iball(i1,1)
- ib(nbon,2) = iball(i1,2)
- ib(nbon,3) = iball(i1,3)
- end do
-
- endif
-
- do i1=1,na
- do i2=2,mbond+2
- ia(i1,i2)=0
- iag(i1,i2)=0
- end do
- end do
-
-* Generate full set of bond data structures
-
- do 10 i0 = 1,nbon
- i1 = ib(i0,2)
- i2 = ib(i0,3)
- call dista2(i1,i2,dis,dxm,dym,dzm)
-* do 10 i1=1,na-1
-* do 10 i2=i1+1,na
-* call dista2(i1,i2,dis,dxm,dym,dzm)
- ih1=ia(i1,1)
- ih2=ia(i2,1)
-* if (dis.gt.5.0*rob) goto 10
- disdx=dxm/dis
- disdy=dym/dis
- disdz=dzm/dis
- itype=0
- if (ih1.gt.ih2) then
- ih1=ia(i2,1)
- ih2=ia(i1,1)
- end if
- do i3=1,nboty2
- if (ih1.eq.nbs(i3,1).and.ih2.eq.nbs(i3,2)) itype=i3
- end do
- if (itype.eq.0.and.rat(ih1).gt.zero.and.rat(ih2).gt.zero) then
-c$$$ call mdsav(1,qfile(nprob))
- write (*,*)qa(i1),'-',qa(i2),'Fatal: Unknown bond in molecule'
- stop
- end if
-
- rhulp=dis/rob1(ih1,ih2)
-
-**********************************************************************
-* *
-* Determine bond orders *
-* *
-**********************************************************************
- rh2=zero
- rh2p=zero
- rh2pp=zero
- ehulp=zero
- ehulpp=zero
- ehulppp=zero
- if (rapt(ih1).gt.zero.and.rapt(ih2).gt.zero) then
- rhulp2=dis/rob2(ih1,ih2)
- rh2p=rhulp2**ptp(itype)
- ehulpp=exp(pdp(itype)*rh2p)
- end if
- if (vnq(ih1).gt.zero.and.vnq(ih2).gt.zero) then
- rhulp3=dis/rob3(ih1,ih2)
- rh2pp=rhulp3**popi(itype)
- ehulppp=exp(pdo(itype)*rh2pp)
- end if
-
- if (rat(ih1).gt.zero.and.rat(ih2).gt.zero) then
- rh2=rhulp**bop2(itype)
- ehulp=(1.0+cutoff)*exp(bop1(itype)*rh2)
- end if
-
- bor=ehulp+ehulpp+ehulppp
- borsi=ehulp
- borpi=ehulpp
- borpi2=ehulppp
- dbordrob=bop2(itype)*bop1(itype)*rh2*(1.0/dis)*ehulp+
- $ptp(itype)*pdp(itype)*rh2p*(1.0/dis)*ehulpp+
- $popi(itype)*pdo(itype)*rh2pp*(1.0/dis)*ehulppp
- dborsidrob=bop2(itype)*bop1(itype)*rh2*(1.0/dis)*ehulp
- dborpidrob=ptp(itype)*pdp(itype)*rh2p*(1.0/dis)*ehulpp
- dborpi2drob=popi(itype)*pdo(itype)*rh2pp*(1.0/dis)*ehulppp
-
- nbon2=nbon2+1
- j1=i1
- j2=i2
-
-**********************************************************************
-* *
-* Determine bond orders *
-* *
-**********************************************************************
- ib(i0,1)=itype
- ib(i0,2)=j1
- ib(i0,3)=j2
- ibsym(i0)=ivl
- drdc(i0,1,1)=disdx
- drdc(i0,2,1)=disdy
- drdc(i0,3,1)=disdz
- drdc(i0,1,2)=-disdx
- drdc(i0,2,2)=-disdy
- drdc(i0,3,2)=-disdz
- abo(i1)=abo(i1)+bor-cutoff
- if (i1.ne.i2) abo(i2)=abo(i2)+bor-cutoff
- bo(i0)=bor-cutoff
- bos(i0)=bor-cutoff
- bosi(i0)=borsi-cutoff
- bopi(i0)=borpi
- bopi2(i0)=borpi2
- rbo(i0)=dis
- dbodr(i0)=dbordrob
-* dbosidr(i0)=dborsidrob
- dbopidr(i0)=dborpidrob
- dbopi2dr(i0)=dborpi2drob
- dbodc(i0,1,1)=dbodr(i0)*drdc(i0,1,1)
- dbodc(i0,2,1)=dbodr(i0)*drdc(i0,2,1)
- dbodc(i0,3,1)=dbodr(i0)*drdc(i0,3,1)
- dbodc(i0,1,2)=dbodr(i0)*drdc(i0,1,2)
- dbodc(i0,2,2)=dbodr(i0)*drdc(i0,2,2)
- dbodc(i0,3,2)=dbodr(i0)*drdc(i0,3,2)
-* dbosidc(i0,1,1)=dbosidr(i0)*drdc(i0,1,1)
-* dbosidc(i0,2,1)=dbosidr(i0)*drdc(i0,2,1)
-* dbosidc(i0,3,1)=dbosidr(i0)*drdc(i0,3,1)
-* dbosidc(i0,1,2)=dbosidr(i0)*drdc(i0,1,2)
-* dbosidc(i0,2,2)=dbosidr(i0)*drdc(i0,2,2)
-* dbosidc(i0,3,2)=dbosidr(i0)*drdc(i0,3,2)
- dbopidc(i0,1,1)=dbopidr(i0)*drdc(i0,1,1)
- dbopidc(i0,2,1)=dbopidr(i0)*drdc(i0,2,1)
- dbopidc(i0,3,1)=dbopidr(i0)*drdc(i0,3,1)
- dbopidc(i0,1,2)=dbopidr(i0)*drdc(i0,1,2)
- dbopidc(i0,2,2)=dbopidr(i0)*drdc(i0,2,2)
- dbopidc(i0,3,2)=dbopidr(i0)*drdc(i0,3,2)
- dbopi2dc(i0,1,1)=dbopi2dr(i0)*drdc(i0,1,1)
- dbopi2dc(i0,2,1)=dbopi2dr(i0)*drdc(i0,2,1)
- dbopi2dc(i0,3,1)=dbopi2dr(i0)*drdc(i0,3,1)
- dbopi2dc(i0,1,2)=dbopi2dr(i0)*drdc(i0,1,2)
- dbopi2dc(i0,2,2)=dbopi2dr(i0)*drdc(i0,2,2)
- dbopi2dc(i0,3,2)=dbopi2dr(i0)*drdc(i0,3,2)
- ia(i1,2)=ia(i1,2)+1
- if (i1.ne.i2) ia(i2,2)=ia(i2,2)+1
- ia(i1,ia(i1,2)+2)=i2
- ia(i2,ia(i2,2)+2)=i1
- if (ia(i1,2).gt.nsbma2) nsbma2=ia(i1,2)
- if (ia(i2,2).gt.nsbma2) nsbma2=ia(i2,2)
- if (bor.gt.cutof3) then
- iag(i1,2)=iag(i1,2)+1
- iag(i2,2)=iag(i2,2)+1
- iag(i1,iag(i1,2)+2)=i2
- iag(i2,iag(i2,2)+2)=i1
- nubon1(i1,iag(i1,2))=i0
- nubon1(i2,iag(i2,2))=i0
- if (iag(i1,2).gt.nsbmax) nsbmax=iag(i1,2)
- if (iag(i2,2).gt.nsbmax) nsbmax=iag(i2,2)
- end if
- nubon2(i1,ia(i1,2))=i0
- nubon2(i2,ia(i2,2))=i0
-
- 10 continue
-
-**********************************************************************
-* *
-* Sort molecules *
-* *
-**********************************************************************
- imolde = 1
- if (imolde.eq.1) return !fixed molecular definitions
-
- FOUND=.FALSE.
- DO 31 K1=1,NA
- IF (IA(K1,3+mbond).EQ.0) FOUND=.TRUE.
- 31 IF (IA(K1,3+mbond).GT.NMOLO) NMOLO=IA(K1,3+mbond)
- IF (.NOT.FOUND) GOTO 32
-************************************************************************
-* *
-* Molecule numbers are assigned. No restrictions are made for the *
-* sequence of the numbers in the connection table. *
-* *
-************************************************************************
- N3=1
- 34 N2=N3
- NMOLO=NMOLO+1
- if (nmolo.gt.nmolmax) then
- write (*,*)nmolmax
- write (*,*)'Too many molecules in system; increase nmolmax'
- write (*,*)'nmolmax = ',nmolmax
- write (*,*)'nmolo = ',nmolo
- write (*,*)'n2 = ',n2
- stop 'Too many molecules in system'
- end if
- IA(N2,3+mbond)=NMOLO
- 37 FOUND=.FALSE.
- DO 36 N1=N2+1,NA
- IF (IA(N1,3+mbond).NE.0) GOTO 36
- DO 35 L=1,mbond
- IF (IA(N1,l+2).EQ.0) GOTO 36
- IF (IA(IA(N1,l+2),3+mbond).EQ.NMOLO) THEN
- FOUND=.TRUE.
- IA(N1,3+mbond)=NMOLO
- GOTO 36
- ENDIF
- 35 CONTINUE
- 36 CONTINUE
- IF (FOUND) GOTO 37
- DO 33 N3=N2+1,NA
- 33 IF (IA(N3,3+mbond).EQ.0) GOTO 34
-************************************************************************
-* *
-* The assigned or input molecule numbers are checked for their *
-* consistency. *
-* *
-************************************************************************
- 32 FOUND=.FALSE.
- DO 42 N1=1,NA
- DO 41 L=1,mbond
- IF (IA(N1,L+2).EQ.0) GOTO 42
- IF (IA(IA(N1,L+2),3+mbond).NE.IA(N1,3+mbond)) THEN
- FOUND=.TRUE.
- ENDIF
- 41 CONTINUE
- 42 CONTINUE
- IF (FOUND) THEN
- write (7,1000)NA,qmol
- do i1=1,NA
- write (7,1100)i1,ia(i1,1),(ia(i1,2+i2),i2=1,nsbmax),
- $ia(i1,3+mbond)
- end do
- write (7,*)tm11,tm22,tm33,angle(1),angle(2),angle(3)
- STOP' Mol.nrs. not consistent; maybe wrong cell parameters'
- end if
-**********************************************************************
-* *
-* Sort molecules again *
-* This sort is on iag, enforces bond order cutoff *
-* *
-**********************************************************************
- FOUND=.FALSE.
- DO 61 K1=1,NA
- IF (IAG(K1,3+mbond).EQ.0) FOUND=.TRUE.
- 61 IF (IAG(K1,3+mbond).GT.NMOLO5) NMOLO5=IAG(K1,3+mbond)
- IF (.NOT.FOUND) GOTO 62
-************************************************************************
-* *
-* Molecule numbers are assigned. No restrictions are made for the *
-* sequence of the numbers in the connection table. *
-* *
-************************************************************************
- N3=1
- 64 N2=N3
- NMOLO5=NMOLO5+1
- if (nmolo5.gt.nmolmax) stop 'Too many molecules in system'
- IAG(N2,3+mbond)=NMOLO5
- 67 FOUND=.FALSE.
- DO 66 N1=N2+1,NA
- IF (IAG(N1,3+mbond).NE.0) GOTO 66
- DO 65 L=1,mbond
- IF (IAG(N1,l+2).EQ.0) GOTO 66
- IF (IAG(IAG(N1,l+2),3+mbond).EQ.NMOLO5) THEN
- FOUND=.TRUE.
- IAG(N1,3+mbond)=NMOLO5
- GOTO 66
- ENDIF
- 65 CONTINUE
- 66 CONTINUE
- IF (FOUND) GOTO 67
- DO 63 N3=N2+1,NA
- 63 IF (IAG(N3,3+mbond).EQ.0) GOTO 64
-************************************************************************
-* *
-* The assigned or input molecule numbers are checked for their *
-* consistency. *
-* *
-************************************************************************
- 62 FOUND=.FALSE.
- DO 72 N1=1,NA
- DO 71 L=1,mbond
- IF (IAG(N1,L+2).EQ.0) GOTO 72
- IF (IAG(IAG(N1,L+2),3+mbond).NE.IAG(N1,3+mbond)) THEN
- FOUND=.TRUE.
- ENDIF
- 71 CONTINUE
- 72 CONTINUE
- IF (FOUND) THEN
- write (7,1000)NA,qmol
- do i1=1,NA
- write (7,1100)i1,iag(i1,1),(iag(i1,2+i2),i2=1,nsbmax),
- $iag(i1,3+mbond)
- end do
- write (7,*)tm11,tm22,tm33,angle(1),angle(2),angle(3)
- STOP' Mol.nrs. not consistent; maybe wrong cell parameters'
- ENDIF
-
-**********************************************************************
-* *
-* Format part *
-* *
-**********************************************************************
- 1000 format (i3,2x,a60)
- 1100 format (8i3)
- end
-**********************************************************************
-**********************************************************************
-
- subroutine srtang
-
-**********************************************************************
-#include "cbka.blk"
-#include "cbkbo.blk"
-#include "cbknubon2.blk"
-#include "cbkff.blk"
-#include "cbkia.blk"
-#include "cbkrbo.blk"
-#include "cbkvalence.blk"
-#include "cellcoord.blk"
-#include "control.blk"
-#include "small.blk"
-
- dimension a(3),b(3),j(3)
- dimension ityva(100)
-
-**********************************************************************
-* *
-* Find valency angles in molecule *
-* *
-**********************************************************************
-c$$$ if (ndebug.eq.1) then
-c$$$C open (65,file='fort.65',status='unknown',access='append')
-c$$$ write (65,*) 'In srtang'
-c$$$ call timer(65)
-c$$$ close (65)
-c$$$ end if
-
- nval=0
- if (nvaty.eq.0) return
- do iindexatom=1,na
- inumbonds=ia(iindexatom,2)
- do jindexbond=1,inumbonds-1
- jindexbondlist = nubon2(iindexatom,jindexbond)
- if (bo(jindexbondlist).lt.cutof2) goto 51
- k4=ib(jindexbondlist,2)
- k5=ib(jindexbondlist,3)
- do kindexbond=jindexbond+1,inumbonds
- kindexbondlist = nubon2(iindexatom,kindexbond)
- iju=0
- if (bo(kindexbondlist).lt.cutof2) goto 50
- if (bo(jindexbondlist)*bo(kindexbondlist).lt.0.001) goto 50
- k7=ib(kindexbondlist,2)
- k8=ib(kindexbondlist,3)
-
-* Exclude angles that have no local atoms.
-* Angles with non-local center atom are not needed for angle
-* energies, but are needed to construct torsions.
- if ( k4 .le. na_local .or.
- $ k5 .le. na_local .or.
- $ k7 .le. na_local .or.
- $ k8 .le. na_local) then
-
- if (k4.eq.k7.and.k5.eq.k8.and.k4.ne.k8.and.k5.ne.k7) then
- nval=nval+1
- iv(nval,2)=k5
- iv(nval,3)=k4
- iv(nval,4)=k8
- iv(nval,5)=jindexbondlist
- iv(nval,6)=kindexbondlist
- nval=nval+1
- iv(nval,2)=k4
- iv(nval,3)=k5
- iv(nval,4)=k7
- iv(nval,5)=jindexbondlist
- iv(nval,6)=kindexbondlist
- iju=2
- write(6,*) 'Aaaah!'
- end if
- if (iju.eq.2) goto 50
-
- if (k4.eq.k8.and.k5.eq.k7.and.k4.ne.k7.and.k5.ne.k8) then
- nval=nval+1
- iv(nval,2)=k5
- iv(nval,3)=k4
- iv(nval,4)=k7
- iv(nval,5)=jindexbondlist
- iv(nval,6)=kindexbondlist
- nval=nval+1
- iv(nval,2)=k4
- iv(nval,3)=k5
- iv(nval,4)=k8
- iv(nval,5)=jindexbondlist
- iv(nval,6)=kindexbondlist
- iju=2
- write(6,*) 'Aaaah!'
- end if
- if (iju.eq.2) goto 50
-
- if (k4.eq.k7) then
- nval=nval+1
- iv(nval,2)=k5
- iv(nval,3)=k4
- iv(nval,4)=k8
- iv(nval,5)=jindexbondlist
- iv(nval,6)=kindexbondlist
- iju=1
- end if
- if (iju.eq.1) goto 50
-
- if (k4.eq.k8) then
- nval=nval+1
- iv(nval,2)=k5
- iv(nval,3)=k4
- iv(nval,4)=k7
- iv(nval,5)=jindexbondlist
- iv(nval,6)=kindexbondlist
- iju=1
- end if
- if (iju.eq.1) goto 50
-
- if (k5.eq.k7) then
- nval=nval+1
- iv(nval,2)=k4
- iv(nval,3)=k5
- iv(nval,4)=k8
- iv(nval,5)=jindexbondlist
- iv(nval,6)=kindexbondlist
- iju=1
- end if
- if (iju.eq.1) goto 50
-
- if (k5.eq.k8) then
- nval=nval+1
- iv(nval,2)=k4
- iv(nval,3)=k5
- iv(nval,4)=k7
- iv(nval,5)=jindexbondlist
- iv(nval,6)=kindexbondlist
- iju=1
- end if
- if (iju.eq.1) goto 50
-
- write (6,*)'nval = ',nval,
- $ ' after',iindexatom, ' of ',na,' atoms completed.'
- stop 'Adjacent bonds did not make an angle'
-
- endif
-
- 50 continue
-
- if (nval.gt.nvamax) then
- write (6,*)'nval = ',nval,' reax_defs.h::NVAMAXDEF = ',
- $ NVAMAXDEF,
- $ ' after',iindexatom, ' of ',na,' atoms completed.'
- stop 'Too many valency angles. Increase NVAMAXDEF'
- endif
-
- if (iju.gt.0) then
-**********************************************************************
-* *
-* Determine force field types of angles *
-* *
-**********************************************************************
- ityva(1)=0
- ih1=ia(iv(nval,2),1)
- ih2=ia(iv(nval,3),1)
- ih3=ia(iv(nval,4),1)
- if (ih3.lt.ih1) then
- ih3=ia(iv(nval,2),1)
- ih2=ia(iv(nval,3),1)
- ih1=ia(iv(nval,4),1)
- end if
-
- nfound=0
- do i3=1,nvaty
- if (ih1.eq.nvs(i3,1).and.ih2.eq.nvs(i3,2).and.
- $ih3.eq.nvs(i3,3)) then
- nfound=nfound+1
- ityva(nfound)=i3
- end if
- end do
-
- if (ityva(1).eq.0.or.abs(vka(ityva(1))).lt.0.001) then !Valence angle does not exist in force field;ignore
- nval=nval-1
- ihul=0
- else
- iv(nval,1)=ityva(1)
- ihul=1
-
- do i3=1,nfound-1 !Found multiple angles of the same type
- nval=nval+1
- iv(nval,1)=ityva(i3+1)
- do i4=2,6
- iv(nval,i4)=iv(nval-1,i4)
- end do
-
- end do
-
- end if
-
- if (iju.eq.2) then
- ityva(1)=0
- ih1=ia(iv(nval-ihul,2),1)
- ih2=ia(iv(nval-ihul,3),1)
- ih3=ia(iv(nval-ihul,4),1)
- if (ih3.lt.ih1) then
- ih3=ia(iv(nval-ihul,2),1)
- ih2=ia(iv(nval-ihul,3),1)
- ih1=ia(iv(nval-ihul,4),1)
- end if
-
- nfound=0
- do i3=1,nvaty
- if (ih1.eq.nvs(i3,1).and.ih2.eq.nvs(i3,2).and.
- $ih3.eq.nvs(i3,3)) then
- nfound=nfound+1
- ityva(nfound)=i3
- end if
- end do
-
- if (ityva(1).eq.0.or.abs(vka(ityva(1))).lt.0.001) then !Valence angle does not exist in force field;ignore
- if (ihul.eq.1) then
- do i3=1,6
- iv(nval-1,i3)=iv(nval,i3)
- end do
- end if
- nval=nval-1
- else
- iv(nval-ihul,1)=ityva(1)
-
- do i3=1,nfound-1 !Found multiple angles of the same type
- nval=nval+1
- iv(nval,1)=ityva(i3+1)
- do i4=2,6
- iv(nval,i4)=iv(nval-1,i4)
- end do
-
- end do
-
- end if
-
- end if
-
- end if
-
- end do
- 51 continue
- end do
- end do
-
- nbonop=0
-
- return
- end
-**********************************************************************
-**********************************************************************
-
- subroutine srttor
-
-**********************************************************************
-#include "cbka.blk"
-#include "cbkc.blk"
-#include "cbkbo.blk"
-#include "cbkrbo.blk"
-#include "cbkia.blk"
-#include "cbktorsion.blk"
-#include "cbkvalence.blk"
-#include "cellcoord.blk"
-#include "control.blk"
-#include "small.blk"
-#include "cbknubon2.blk"
-**********************************************************************
-* *
-* Find torsion angles in molecule *
-* *
-**********************************************************************
-c$$$ if (ndebug.eq.1) then
-c$$$ open (65,file='fort.65',status='unknown',access='append')
-c$$$ write (65,*) 'In srttor'
-c$$$ call timer(65)
-c$$$ close (65)
-c$$$ end if
- ntor=0
- if (ntoty.eq.0) return
- do 61 i1=1,nbon
- k2=ib(i1,2)
- k3=ib(i1,3)
-c Only compute interaction if both atoms local
-c are local or else flip a coin
- if (k2 .gt. na_local) go to 61
- if (k3 .gt. na_local) then
- if (itag(k2) .lt. itag(k3)) go to 61
- if (itag(k2) .eq. itag(k3)) then
- if(c(k2,3) .gt. c(k3,3)) go to 61
- if(c(k2,3) .eq. c(k3,3) .and.
- $ c(k2,2) .gt. c(k3,2)) go to 61
- if(c(k2,3) .eq. c(k3,3) .and.
- $ c(k2,2) .eq. c(k3,2) .and.
- $ c(k2,1) .gt. c(k3,1)) go to 61
- endif
- endif
-
- iob1=ia(k2,2)
- iob2=ia(k3,2)
- do 60 i2=1,iob1 !Atoms connected to k2
- k4=ia(k2,2+i2)
- ibo2=nubon2(k2,i2)
- do 60 i3=1,iob2 !Atoms connected to k3
- k5=ia(k3,2+i3)
- ibo3=nubon2(k3,i3)
- bopr=bo(i1)*bo(ibo2)*bo(ibo3)
- if (bopr.gt.cutof2.and.k2.ne.k5.and.k3.ne.k4.and.k4.ne.k5) then
-
- ntor=ntor+1
- it(ntor,2)=k4
- it(ntor,3)=k2
- it(ntor,4)=k3
- it(ntor,5)=k5
- it(ntor,6)=ibo2
- it(ntor,7)=i1
- it(ntor,8)=ibo3
-
-**********************************************************************
-* *
-* Determine force field types of torsion angles *
-* *
-**********************************************************************
- ity=0
- ih1=ia(it(ntor,2),1)
- ih2=ia(it(ntor,3),1)
- ih3=ia(it(ntor,4),1)
- ih4=ia(it(ntor,5),1)
-
- if (ih2.gt.ih3) then
- ih1=ia(it(ntor,5),1)
- ih2=ia(it(ntor,4),1)
- ih3=ia(it(ntor,3),1)
- ih4=ia(it(ntor,2),1)
- end if
-
- if (ih2.eq.ih3.and.ih4.lt.ih1) then
- ih1=ia(it(ntor,5),1)
- ih2=ia(it(ntor,4),1)
- ih3=ia(it(ntor,3),1)
- ih4=ia(it(ntor,2),1)
- end if
-
- do i4=1,ntoty
- if (ih1.eq.nts(i4,1).and.ih2.eq.nts(i4,2).and.ih3.eq.nts(i4,3)
- $.and.ih4.eq.nts(i4,4)) ity=i4
- end do
-
- if (ity.eq.0) then
- do i4=1,ntoty
- if (nts(i4,1).eq.0.and.ih2.eq.nts(i4,2).and.ih3.eq.nts(i4,3)
- $.and.nts(i4,4).eq.0) ity=i4
- end do
- end if
-
- if (ity.eq.0) then
- ntor=ntor-1 !Torsion angle does not exist in force field: ignore
- else
- it(ntor,1)=ity
- end if
-
- end if
-
- 60 continue
- 61 continue
-
- if (ntor.gt.ntomax) stop 'Too many torsion angles'
-* do i1=1,ntor
-* write (41,'(20i4)')i1,it(i1,1),it(i1,2),it(i1,3),
-* $it(i1,4),it(i1,5),it(i1,6),it(i1,7),it(i1,8)
-* end do
-
- return
- end
-**********************************************************************
-**********************************************************************
-
- subroutine srtoop
-
-**********************************************************************
-#include "cbka.blk"
-#include "cbkbo.blk"
-#include "cbkrbo.blk"
-#include "cbkvalence.blk"
-#include "control.blk"
-#include "small.blk"
-**********************************************************************
-c$$$ if (ndebug.eq.1) then
-c$$$C open (65,file='fort.65',status='unknown',access='append')
-c$$$ write (65,*) 'In srtoop'
-c$$$ call timer(65)
-c$$$ close (65)
-c$$$ end if
-**********************************************************************
-* *
-* Find out of plane angles in molecule *
-* *
-**********************************************************************
- noop=0
- do i1=1,nval
- k2=iv(i1,2)
- k3=iv(i1,3)
- k4=iv(i1,4)
- k5=iv(i1,5)
- k6=iv(i1,6)
- do i2=1,nbon
- k7=ib(i2,2)
- k8=ib(i2,3)
- if (bo(i2).gt.cutof2) then
- if (k7.eq.k3.and.k8.ne.k4.and.k8.ne.k2) then
- noop=noop+1
- ioop(noop,2)=k8
- ioop(noop,3)=k3
- ioop(noop,4)=k2
- ioop(noop,5)=k4
- ioop(noop,6)=i2
- ioop(noop,7)=iv(i1,5)
- ioop(noop,8)=iv(i1,6)
- ioop(noop,9)=i1
- end if
- if (k8.eq.k3.and.k7.ne.k4.and.k7.ne.k2) then
- noop=noop+1
- ioop(noop,2)=k7
- ioop(noop,3)=k3
- ioop(noop,4)=k2
- ioop(noop,5)=k4
- ioop(noop,6)=i2
- ioop(noop,7)=iv(i1,5)
- ioop(noop,8)=iv(i1,6)
- ioop(noop,9)=i1
- end if
- end if
- end do
- end do
-
- do i1=1,noop
- call caltor(ioop(i1,2),ioop(i1,3),ioop(i1,4),ioop(i1,5),hoop)
- end do
-
-**********************************************************************
- return
- end
-**********************************************************************
-
-**********************************************************************
-
- subroutine srthb
-
-**********************************************************************
-#include "cbka.blk"
-#include "cbkc.blk"
-#include "cbkbo.blk"
-#include "cbkconst.blk"
-#include "cbkia.blk"
-#include "cbkrbo.blk"
-#include "cbksrthb.blk"
-#include "control.blk"
-#include "small.blk"
-#include "cbkpairs.blk"
-#include "cbknvlown.blk"
-#include "cbknubon2.blk"
-**********************************************************************
-* *
-* Find hydrogen bonds in molecule *
-* *
-**********************************************************************
-c$$$ if (ndebug.eq.1) then
-c$$$ open (65,file='fort.65',status='unknown',access='append')
-c$$$ write (65,*) 'In srthb'
-c$$$ call timer(65)
-c$$$ close (65)
-c$$$ end if
- nhb=0
-**********************************************************************
-* *
-* Locate donor/acceptor bonds *
-* *
-**********************************************************************
-c Outer loop must be Verlet list, because ia() does not store Verlet entries,
-c but it does store bond entries in nubon2()
-c
-c The problem with using the nvlown ownership criterion
-c is that it would require that we unprune every bond that is within
-c certain distance, as well as its first and second neighbor bonds.
-c
-c For the ownership criterion based on H atom location no unpruning is required.
-c Apparently lprune=4 is sufficient here, implying that we need to capture first and
-c second neighbor bonds of the O-H bond, and of course we need to include all hydrogen
-c bond partners within hbcut.
-c
-
- do 20 ivl=1,nvpair !Use Verlet-list to find donor-acceptor pairs
-
- j1=nvl1(ivl)
- j2=nvl2(ivl)
- ity1=ia(j1,1)
- ity2=ia(j2,1)
- ihhb1=nphb(ia(j1,1))
- ihhb2=nphb(ia(j2,1))
-
- if (ihhb1.gt.ihhb2) then !Make j1 donor(H) atom and j2 acceptor(O) atom
- j2=nvl1(ivl)
- j1=nvl2(ivl)
- ity1=ia(j1,1)
- ity2=ia(j2,1)
- ihhb1=nphb(ia(j1,1))
- ihhb2=nphb(ia(j2,1))
- end if
-
-* Only need to compute bonds where j1 is local
- if (j1 .le. na_local) then
-
- if (ihhb1.eq.1.and.ihhb2.eq.2) then
- call dista2(j1,j2,dishb,dxm,dym,dzm)
- if (dishb.lt.hbcut) then
- do 10 i23=1,ia(j1,2) !Search for acceptor atoms bound to donor atom
- j3=ia(j1,2+i23)
- ity3=ia(j3,1)
- nbohb=nubon2(j1,i23)
- if (nphb(ity3).eq.2.and.j3.ne.j2.and.bo(nbohb).gt.0.01) then
-**********************************************************************
-* *
-* Accept hydrogen bond and find hydrogen bond type *
-* *
-**********************************************************************
- nhb=nhb+1
-
- if (nhb.gt.nhbmax) then
- write (*,*)nhb,nhbmax
- write (*,*)'Maximum number of hydrogen bonds exceeded'
- stop 'Maximum number of hydrogen bonds exceeded'
- end if
-
- ihb(nhb,1)=0
-
- do i3=1,nhbty
- if (ity3.eq.nhbs(i3,1).and.ity1.eq.nhbs(i3,2).and.ity2.eq.
- $nhbs(i3,3)) ihb(nhb,1)=i3
- end do
-
- if (ihb(nhb,1).eq.0) then !Hydrogen bond not in force field
- nhb=nhb-1
-* write (*,*)'Warning: added hydrogen bond ',ity3,ity1,ity2
-* nhbty=nhbty+1
-* nhbs(nhbty,1)=ity3
-* nhbs(nhbty,2)=ity1
-* nhbs(nhbty,3)=ity2
-* rhb(nhbty)=2.70
-* dehb(nhbty)=zero
-* vhb1(nhbty)=5.0
-* vhb2(nhbty)=20.0
-* ihb(nhb,1)=nhbty
- end if
-
- ihb(nhb,2)=j3
- ihb(nhb,3)=j1
- ihb(nhb,4)=j2
- ihb(nhb,5)=nbohb
- ihb(nhb,6)=k1
- ihb(nhb,7)=k2
- ihb(nhb,8)=k3
-* write (64,*)nhb,ihb(nhb,1),j3,j1,j2,nbohb,k1,k2,k3,bo(nbohb),
-* $dishb
-
- end if
-
- 10 continue
-
- end if
- end if
- end if
- 20 end do
-
-* stop 'end in srthb'
- return
- end
-**********************************************************************
diff --git a/lib/reax/reax_defs.h b/lib/reax/reax_defs.h
deleted file mode 100644
index e28533fa9bdb76d409953fed553ab9739c8ef6f5..0000000000000000000000000000000000000000
--- a/lib/reax/reax_defs.h
+++ /dev/null
@@ -1,70 +0,0 @@
-#define PORTABLECOMMENTFLAG
-#ifndef PORTABLECOMMENTFLAG
-// This is just a way to have portable comments
-// for both C++ and FORTRAN preprocessing.
- /* ///:EOH~ */
- /* */
- /* This file contains array dimension parameters for all the main */
- /* ReaxFF data structures, some of which need to be directly accessed */
- /* by Grasp C++ functions. If they are set too small, the calculation */
- /* will run out of allocated memory. If they are set too big, the machine */
- /* will not be able to allocate enough memory. */
- /* */
-
- /* NNEIGHMAXDEF = Max number of neighbors / NATDEF */
- /* NATDEF = Max number of atoms */
- /* NATTOTDEF = Max number of global atoms */
- /* NSORTDEF = Max number of atom types */
- /* MBONDDEF = Max number of bonds connected to one atom */
- /* NAVIBDEF = for 2nd derivatives */
- /* NBOTYMDEF = Max number of bond types */
- /* NVATYMDEF = Max number of valency angle types */
- /* NTOTYMDEF = Max number of torsion angle types */
- /* NHBTYMDEF = Max number of hydrogen bond types */
- /* NODMTYMDEF = Max number of off-diagonal Morse types */
- /* NBOALLMAXDEF = Max number of all bonds */
- /* NBOMAXDEF = Max number of bonds */
- /* NHBMAXDEF = Max number of hydrogen bonds */
- /* NVAMAXDEF = Max number of valency angles */
- /* NOPMAXDEF = Max number of out of plane angles */
- /* NTOMAXDEF = Max number of torsion angles */
- /* NPAMAXDEF = Max number of general parameters in force field */
- /* NMOLMAXDEF = Max number of molecules in system */
- /* NMOLSETDEF = Max number of molecules in training set */
- /* MRESTRADEF = Max number of restraints */
- /* MTREGDEF = Max number of temperature regimes */
- /* MTZONEDEF = Max number of temperature zones */
- /* MVREGDEF = Max number of volume regimes */
- /* MVZONEDEF = Max number of volume zones */
- /* MEREGDEF = Max number of electric field regimes */
- /* MEZONEDEF = Max number of electric field zones */
-#endif
-
-#define NNEIGHMAXDEF 120
-#define NATDEF 40000
-#define NATTOTDEF 39744
-#define NSORTDEF 20
-#define MBONDDEF 20
-#define NAVIBDEF 50
-#define NBOTYMDEF 200
-#define NVATYMDEF 200
-#define NTOTYMDEF 200
-#define NHBTYMDEF 200
-#define NODMTYMDEF 20
-#define NBOALLMAXDEF 180000
-#define NBOMAXDEF 90000
-#define NHBMAXDEF 400000
-#define NVAMAXDEF 300000
-#define NOPMAXDEF 00010
-#define NTOMAXDEF 65000
-#define NPAMAXDEF 50
-#define NMOLMAXDEF 2000
-#define NMOLSETDEF 1500
-#define MRESTRADEF 100
-#define MTREGDEF 100
-#define MTZONEDEF 5
-#define MVREGDEF 100
-#define MVZONEDEF 6
-#define MEREGDEF 100
-#define MEZONEDEF 3
-
diff --git a/lib/reax/reax_inout.F b/lib/reax/reax_inout.F
deleted file mode 100644
index 944400a9680af2213c7e0c46cb5a8d2895b7ed92..0000000000000000000000000000000000000000
--- a/lib/reax/reax_inout.F
+++ /dev/null
@@ -1,3870 +0,0 @@
-**********************************************************************
-* *
-* REAXFF Reactive force field program *
-* *
-* Developed and written by Adri van Duin, duin@wag.caltech.edu *
-* *
-* Copyright (c) 2001-2010 California Institute of Technology *
-* *
-* This is an open-source program. Feel free to modify its *
-* contents. Please keep me informed of any useful modification *
-* or addition that you made. Please do not distribute this *
-* program to others; if people are interested in obtaining *
-* a copy of this program let them contact me first. *
-* *
-**********************************************************************
-**********************************************************************
-
- subroutine ffinpt
-
-**********************************************************************
-#include "cbka.blk"
-#include "cbkboncor.blk"
-#include "cbkconst.blk"
-#include "cbkcovbon.blk"
-#include "cbkff.blk"
-#include "cbkfftorang.blk"
-#include "cbknonbon.blk"
-#include "cbksrthb.blk"
-#include "cbktorsion.blk"
-#include "cellcoord.blk"
-#include "control.blk"
-#include "opt.blk"
-#include "valang.blk"
-#include "cbksrtbon1.blk"
-#include "cbkchb.blk"
- dimension rcore2(nsort),ecore2(nsort),acore2(nsort)
-**********************************************************************
-* *
-* Read in force field *
-* *
-**********************************************************************
-c$$$ if (ndebug.eq.1) then
-c$$$C open (65,file='fort.65',status='unknown',access='append')
-c$$$ write (65,*) 'In ffinpt'
-c$$$ call timer(65)
-c$$$ close (65)
-c$$$ end if
- open (4,file='ffield.reax',status='old')
- rewind (4)
- iline=0
- read (4,'(a40)',end=990,err=990)qffield
- iline=iline+1
-**********************************************************************
-* *
-* Read in general force field parameters *
-* *
-**********************************************************************
- read (4,1100,end=990,err=990)npar
- iline=iline+1
- do i1=1,npar
- read (4,1300,end=990,err=990)vpar(i1)
- iline=iline+1
- end do
- cutoff=0.01*vpar(30)
- swa=vpar(12)
- if (abs(swa).gt.0.01) write (*,*)
- $'Warning: non-zero value for lower Taper-radius cutoff'
- swb=vpar(13)
- if (swb.lt.zero) stop
- $'Negative value for upper Taper-radius cutoff'
- if (swb.lt.5.0) write (*,*)
- $'Warning: very low value for upper Taper-radius cutoff:',swb
-**********************************************************************
-* *
-* Read in atom type data *
-* *
-**********************************************************************
- read (4,1100,end=990,err=990) nso
- iline=iline+1
- read (4,*,end=990,err=990)
- iline=iline+1
- read (4,*,end=990,err=990)
- iline=iline+1
- read (4,*,end=990,err=990)
- iline=iline+1
- if (nso.gt.nsort) stop 'Maximum number of atom types exceeded'
- do i1=1,nso
- read (4,1200,end=990,err=990)qas(i1),rat(i1),aval(i1),amas(i1),
- $rvdw(i1),eps(i1),gam(i1),rapt(i1),stlp(i1)
- iline=iline+1
- read (4,1250,end=990,err=990)alf(i1),vop(i1),valf(i1),
- $valp1(i1),valp2(i1),chi(i1),eta(i1),vnphb
- iline=iline+1
- read (4,1250,end=990,err=990)vnq(i1),vlp1(i1),vincr(i1),
- $bo131(i1),bo132(i1),bo133(i1),sigqeq(i1),default
- iline=iline+1
- read (4,1250,end=990,err=990)vovun(i1),vval1(i1),vrom,
- $vval3(i1),vval4(i1),rcore2(i1),ecore2(i1),acore2(i1)
- iline=iline+1
- idef(i1)=int(default)
- nphb(i1)=int(vnphb)
- end do
-**********************************************************************
-* *
-* Calculate van der Waals and Coulomb pair-parameters *
-* *
-**********************************************************************
- do i1=1,nso
- do i2=1,nso
- rcore(i1,i2)=sqrt(rcore2(i1)*rcore2(i2))
- ecore(i1,i2)=sqrt(ecore2(i1)*ecore2(i2))
- acore(i1,i2)=sqrt(acore2(i1)*acore2(i2))
- p1co(i1,i2)=sqrt(4.0*rvdw(i1)*rvdw(i2))
- p2co(i1,i2)=sqrt(eps(i1)*eps(i2))
- p3co(i1,i2)=sqrt(alf(i1)*alf(i2))
- gamwh=sqrt(vop(i1)*vop(i2))
- gamwco(i1,i2)=1.0/gamwh**vpar(29)
- gamch=sqrt(gam(i1)*gam(i2))
- gamcco(i1,i2)=1.0/gamch**3
- rob1(i1,i2)=0.50*(rat(i1)+rat(i2))
- rob2(i1,i2)=0.50*(rapt(i1)+rapt(i2))
- rob3(i1,i2)=0.50*(vnq(i1)+vnq(i2))
- end do
- end do
-**********************************************************************
-* *
-* Read in bond type data *
-* *
-**********************************************************************
- read (4,1100,end=990,err=990)nboty
- iline=iline+1
- read (4,*,end=990,err=990)
- iline=iline+1
- if (2*nboty.gt.nbotym) stop 'Maximum nr. of bond types exceeded'
- ih=0
- do i1=1,nboty
- ih=ih+1
- read (4,1400,end=990,err=990)nbs(ih,1),nbs(ih,2),de1(ih),
- $de2(ih),de3(ih),psi(ih),pdo(ih),v13cor(ih),popi(ih),vover(ih)
- iline=iline+1
- read (4,1450,end=990,err=990)psp(ih),pdp(ih),ptp(ih),
- $bom(ih),bop1(ih),bop2(ih),ovc(ih),vuncor(ih)
- iline=iline+1
- if (nbs(ih,1).ne.nbs(ih,2)) then
- ih=ih+1
- nbs(ih,1)=nbs(ih-1,2)
- nbs(ih,2)=nbs(ih-1,1)
- de1(ih)=de1(ih-1)
- de2(ih)=de2(ih-1)
- de3(ih)=de3(ih-1)
- psi(ih)=psi(ih-1)
- pdo(ih)=pdo(ih-1)
- v13cor(ih)=v13cor(ih-1)
- vover(ih)=vover(ih-1)
- psp(ih)=psp(ih-1)
- pdp(ih)=pdp(ih-1)
- ptp(ih)=ptp(ih-1)
- bop1(ih)=bop1(ih-1)
- bop2(ih)=bop2(ih-1)
-* bop3(ih)=bop3(ih-1)
-* bop4(ih)=bop4(ih-1)
- bom(ih)=bom(ih-1)
- popi(ih)=popi(ih-1)
- ovc(ih)=ovc(ih-1)
- end if
- end do
- nboty2=ih
-**********************************************************************
-* *
-* Read in off-diagonal parameters *
-* *
-**********************************************************************
- read (4,1100,end=990,err=990)nodmty
- iline=iline+1
- if (nodmty.gt.nodmtym)
- $stop 'Maximum nr. of off-diagonal Morse types exceeded'
- ih=0
- do i1=1,nodmty
- ih=ih+1
- read (4,1400,end=990,err=990)nodm1,nodm2,deodmh,rodmh,godmh,
- $rsig,rpi,rpi2
- iline=iline+1
- if (rsig.gt.zero) rob1(nodm1,nodm2)=rsig
- if (rsig.gt.zero) rob1(nodm2,nodm1)=rsig
- if (rpi.gt.zero) rob2(nodm1,nodm2)=rpi
- if (rpi.gt.zero) rob2(nodm2,nodm1)=rpi
- if (rpi2.gt.zero) rob3(nodm1,nodm2)=rpi2
- if (rpi2.gt.zero) rob3(nodm2,nodm1)=rpi2
- if (rodmh.gt.zero) p1co(nodm1,nodm2)=2.0*rodmh
- if (rodmh.gt.zero) p1co(nodm2,nodm1)=2.0*rodmh
- if (deodmh.gt.zero) p2co(nodm1,nodm2)=deodmh
- if (deodmh.gt.zero) p2co(nodm2,nodm1)=deodmh
- if (godmh.gt.zero) p3co(nodm1,nodm2)=godmh
- if (godmh.gt.zero) p3co(nodm2,nodm1)=godmh
- end do
-**********************************************************************
-* *
-* Read in valency angle and conjugation type data *
-* *
-**********************************************************************
- read (4,1100,end=990,err=990)nvaty
- iline=iline+1
- if (nvaty.gt.nvatym)
- $stop 'Maximum nr. of valency angle types exceeded'
- do i1=1,nvaty
- read (4,1500,end=990,err=990)nvs(i1,1),nvs(i1,2),
- $nvs(i1,3),th0(i1),vka(i1),vka3(i1),vka8(i1),vkac(i1),vkap(i1),
- $vval2(i1)
- iline=iline+1
- end do
-**********************************************************************
-* *
-* Read in torsion angle type data *
-* *
-**********************************************************************
- read (4,1100,end=990,err=990)ntoty
- iline=iline+1
- if (ntoty.gt.ntotym)
- $stop 'Maximum nr. of torsion angle types exceeded'
- do i1=1,ntoty
- read (4,1600,end=990,err=990)nts(i1,1),nts(i1,2),nts(i1,3),
- $nts(i1,4),v1(i1),
- $v2(i1),v3(i1),v4(i1),vconj(i1),v2bo(i1),v3bo(i1)
- iline=iline+1
- end do
-**********************************************************************
-* *
-* Read in hydrogen bond type data *
-* *
-**********************************************************************
- read (4,1100,end=990,err=990)nhbty
- iline=iline+1
- if (nhbty.gt.nhbtym)
- $stop 'Maximum nr. of hydrogen bond types exceeded'
- do i1=1,nhbty
- read (4,1500,end=990,err=990)nhbs(i1,1),nhbs(i1,2),
- $nhbs(i1,3),rhb(i1),dehb(i1),vhb1(i1),vhb2(i1)
- iline=iline+1
- end do
-**********************************************************************
-* *
-* Calculate vdWaals interaction parameters *
-* *
-**********************************************************************
- do i1=1,nso
- do i2=1,nso
- rr=(rvdw(i1)+rvdw(i2))
- rr2=rr*rr
- eps2=sqrt(eps(i1)*eps(i2))
- rr6=rr2*rr2*rr2
- pvdw1(i1,i2)=eps2*rr6*rr6
- pvdw1(i2,i1)=eps2*rr6*rr6
- pvdw2(i1,i2)=2.0*eps2*rr6
- pvdw2(i2,i1)=2.0*eps2*rr6
- end do
- end do
-**********************************************************************
-* *
-* Error part *
-* *
-**********************************************************************
- goto 999
- 990 write (*,*)'Error or end-of-file reading unit 4 on line:',iline
- stop
- 999 continue
- close(4)
-**********************************************************************
-* *
-* Format part *
-* *
-**********************************************************************
- 1100 format (i3,2x,a2,3x,3d22.15)
- 1200 format (1x,a2,10f9.4)
- 1250 format (3x,10f9.4)
- 1300 format (f10.4)
- 1400 format (2i3,8f9.4)
- 1450 format (6x,8f9.4)
- 1500 format (3i3,7f9.4)
- 1600 format (4i3,7f9.4)
- return
- end
-**********************************************************************
-***********************************************************************
-
- subroutine mdsav(node)
-
-***********************************************************************
-#include "cbka.blk"
-#include "cbkabo.blk"
-#include "cbkatomcoord.blk"
-#include "cbkbo.blk"
-#include "cbkc.blk"
-#include "cbkch.blk"
-#include "cbkconst.blk"
-#include "cbkdistan.blk"
-#include "cbkenergies.blk"
-#include "cbkia.blk"
-#include "cbkinit.blk"
-#include "cbklonpar.blk"
-#include "cbknubon2.blk"
-#include "cbkqa.blk"
-#include "cbktregime.blk"
-#include "cbksrtbon1.blk"
-#include "cellcoord.blk"
-#include "control.blk"
-#include "opt.blk"
-#include "small.blk"
-
- dimension idum(mbond+3),bodum(mbond+3),qat2(2)
- character*25 qfileh
- character*33 qfile2
- character*4 qext
- character*6 qmdfi
- character *7 var
- character *3 qat2,pepname
- character *1 qrtemp
-************************************************************************
-* *
-* Save coordinates, velocities and accelerations of MD-system *
-* *
-************************************************************************
-c$$$ if (ndebug.eq.1) then
-c$$$C open (65,file='fort.65',status='unknown',access='append')
-c$$$ write (65,*) 'In mdsav'
-c$$$ call timer(65)
-c$$$ close (65)
-c$$$ end if
-
-************************************************************************
-c
-c This is just for test purposes
-c
-************************************************************************
-c$$$ write(6,*) '***************************'
-c$$$ write(6,*) 'mdsav node number is ',node
-c$$$ write(6,*) '***************************'
- return
-
-
- qfileh='Unknown'
- qmdfi='moldyn'
- pepname=' '
- ipeptide=0
- if (ni.eq.2) qmdfi='molsav'
-
- if (iopt.eq.0) then
-
- do i1=1,mbond+3
- idum(i1)=nzero
- bodum(i1)=zero
- end do
-C if (napp.eq.1)
-C $open (7,file='fort.7',status='unknown',access='append')
- if (napp.ne.1)
- $open (7,file='fort.7',status='unknown')
- nsbmaxh=5*((nsbmax/5)+1)
- write (7,100)na,qmol,mdstep,nsbmaxh
- if (nbiolab.eq.1) write (67,101)na,qmol
- do i1=1,na
- bosum=0.0
- do i3=1,nsbmax
- if (iag(i1,2+i3).gt.0) bosum=bosum+bo(nubon1(i1,i3))
- end do
- if (nsbmax.lt.5) then
- write (7,200)i1,iag(i1,1),(iag(i1,2+i2),i2=1,iag(i1,2)),
- $(idum(i2),i2=1,5-iag(i1,2)),
- $iag(i1,3+mbond),(bo(nubon1(i1,i2)),i2=1,iag(i1,2)),
- $(bodum(i2),i2=1,5-iag(i1,2)),abo(i1),vlp(i1),ch(i1)
- if (nbiolab.eq.1) then !Delphi-connection table output
- write (67,201)i1,iag(i1,1),(iag(i1,2+i2),i2=1,iag(i1,2))
- end if
- else if (nsbmax.lt.10) then
- write (7,210)i1,iag(i1,1),(iag(i1,2+i2),i2=1,iag(i1,2)),
- $(idum(i2),i2=1,10-iag(i1,2)),
- $iag(i1,3+mbond),(bo(nubon1(i1,i2)),i2=1,iag(i1,2)),
- $(bodum(i2),i2=1,10-iag(i1,2)),abo(i1),vlp(i1),ch(i1)
- else if (nsbmax.lt.15) then
- write (7,220)i1,iag(i1,1),(iag(i1,2+i2),i2=1,iag(i1,2)),
- $(idum(i2),i2=1,15-iag(i1,2)),
- $iag(i1,3+mbond),(bo(nubon1(i1,i2)),i2=1,iag(i1,2)),
- $(bodum(i2),i2=1,15-iag(i1,2)),abo(i1),vlp(i1),ch(i1)
- else if (nsbmax.lt.20) then
- write (7,230)i1,iag(i1,1),(iag(i1,2+i2),i2=1,iag(i1,2)),
- $(idum(i2),i2=1,20-iag(i1,2)),
- $iag(i1,3+mbond),(bo(nubon1(i1,i2)),i2=1,iag(i1,2)),
- $(bodum(i2),i2=1,20-iag(i1,2)),abo(i1),vlp(i1),ch(i1)
- else if (nsbmax.lt.25) then
- write (7,240)i1,iag(i1,1),(iag(i1,2+i2),i2=1,iag(i1,2)),
- $(idum(i2),i2=1,25-iag(i1,2)),
- $iag(i1,3+mbond),(bo(nubon1(i1,i2)),i2=1,iag(i1,2)),
- $(bodum(i2),i2=1,25-iag(i1,2)),abo(i1),vlp(i1),ch(i1)
- else if (nsbmax.gt.25) then
- write (7,250)i1,iag(i1,1),(iag(i1,2+i2),i2=1,iag(i1,2)),
- $(idum(i2),i2=1,35-iag(i1,2)),
- $iag(i1,3+mbond),(bo(nubon1(i1,i2)),i2=1,iag(i1,2)),
- $(bodum(i2),i2=1,35-iag(i1,2)),abo(i1),vlp(i1),ch(i1)
- end if
- end do
- boss=zero
- vlps=0.0
-C if (napp.eq.1)
-C $open (8,file='fort.8',status='unknown',access='append')
- if (napp.ne.1)
- $open (8,file='fort.8',status='unknown')
- nsbmaxh=5*((nsbma2/5)+1)
- write (8,100)na,qmol,mdstep,nsbmaxh
- chsum=0.0
- do i1=1,na
- bosum=0.0
- do i3=1,nsbma2
- if (ia(i1,2+i3).gt.0) bosum=bosum+bo(nubon2(i1,i3))
- end do
- if (nsbma2.lt.5) then
- write (8,200)i1,ia(i1,1),(ia(i1,2+i2),i2=1,ia(i1,2)),
- $(idum(i2),i2=1,5-ia(i1,2)),
- $ia(i1,3+mbond),(bo(nubon2(i1,i2)),i2=1,ia(i1,2)),
- $(bodum(i2),i2=1,5-ia(i1,2)),abo(i1),vlp(i1),ch(i1)
- else if (nsbma2.lt.10) then
- write (8,210)i1,ia(i1,1),(ia(i1,2+i2),i2=1,ia(i1,2)),
- $(idum(i2),i2=1,10-ia(i1,2)),
- $ia(i1,3+mbond),(bo(nubon2(i1,i2)),i2=1,ia(i1,2)),
- $(bodum(i2),i2=1,10-ia(i1,2)),abo(i1),vlp(i1),ch(i1)
- else if (nsbma2.lt.15) then
- write (8,220)i1,ia(i1,1),(ia(i1,2+i2),i2=1,ia(i1,2)),
- $(idum(i2),i2=1,15-ia(i1,2)),
- $ia(i1,3+mbond),(bo(nubon2(i1,i2)),i2=1,ia(i1,2)),
- $(bodum(i2),i2=1,15-ia(i1,2)),abo(i1),vlp(i1),ch(i1)
- else if (nsbma2.lt.20) then
- write (8,230)i1,ia(i1,1),(ia(i1,2+i2),i2=1,ia(i1,2)),
- $(idum(i2),i2=1,20-ia(i1,2)),
- $ia(i1,3+mbond),(bo(nubon2(i1,i2)),i2=1,ia(i1,2)),
- $(bodum(i2),i2=1,20-ia(i1,2)),abo(i1),vlp(i1),ch(i1)
- else if (nsbma2.lt.25) then
- write (8,240)i1,ia(i1,1),(ia(i1,2+i2),i2=1,ia(i1,2)),
- $(idum(i2),i2=1,25-ia(i1,2)),
- $ia(i1,3+mbond),(bo(nubon2(i1,i2)),i2=1,ia(i1,2)),
- $(bodum(i2),i2=1,25-ia(i1,2)),abo(i1),vlp(i1),ch(i1)
- end if
- boss=boss+bosum/2.0
- vlps=vlps+vlp(i1)
- chsum=chsum+ch(i1)
- end do
- write (7,*)2.0*boss,vlps,2.0*boss+2.0*vlps,chsum
- close(8)
- close(7)
-
- end if
-
- if (noutpt.eq.0) then
- write (var,'(f7.4)')float(mdstep/nsav)/1d4
- if (ni.eq.0) open (unit=67,file=qmdfi//var(3:7),
- $status='unknown')
- write (67,300)qmol
- do i1=1,na
- write (67,400)i1,qa(i1),(c(i1,i2),i2=1,3)
- end do
- write (67,*)
- close(67)
- end if
-
- if (noutpt.eq.2) then
-C open (88,file='moldyn.bgf',status='unknown',access='append')
- call writebgf(88)
- close (88)
- end if
-
- if ((ni.eq.1.and.iopt.eq.0).or.(ni.eq.1.and.iopt.eq.1.and.
- $iflga.eq.1)) then
- qrtemp=qr
- if (qr.eq.'I') qr='C'
- if (qfileh.eq.' ') then
- write (*,*)'Warning: no file name given; use Unknown'
- qfileh='Unknown'
- end if
- qfile2=qfileh
- if (imodfile.eq.0) then
- istart=1
- qstrana1(1:25)=qfileh
- call stranal(istart,iend,vout,iout,1)
- qfile2=qfileh(istart:iend-1)//".geo"
- end if
- call writegeo(98)
-
- if (imodfile.eq.1.or.iopt.eq.0) then
- open (88,file=qfile2,status='unknown')
- call writegeo(88)
- close (88)
- end if
-
- qr=qrtemp
-
- if (iopt.eq.0) then
-
- do i1=1,na
- write (56,410) i1,ch(i1)
- write (55,410) i1,chgbgf(i1)
- end do
-**********************************************************************
-* *
-* Write .pdb output file *
-* *
-**********************************************************************
- open (unit=47,file='output.pdb',status='unknown')
- do i1=1,na
- write (47,412)'ATOM ',i1,qa(i1),pepname,ipeptide,c(i1,1),
- $c(i1,2),c(i1,3),1.0,2.2,qa(i1)
- end do
- write (47,*) 'TER'
- write (47,*) 'END'
- close (47)
-
- if (nsurp.eq.0) then
- if (kx.gt.0.or.ky.gt.0.or.kz.gt.0) then
- qrtemp=qr
-**********************************************************************
-* *
-* Write crystal structure including periodic images *
-* *
-**********************************************************************
-* mux=(1+kx+kx)
-* muy=(1+ky+ky)
-* muz=(1+kz+kz)
-* qr='F'
-* write (86,'(2x,a1,1x,a60)')qr,qmol
-* qr=qrtemp
-* write (86,'(3f10.4)')mux*axiss(1),muy*axiss(2),muz*axiss(3)
-* write (86,'(3f10.4)')angle(1),angle(2),angle(3)
-* do i1=1,na
-* write (86,'(i4,1x,a2,3x,3d22.15)')i1,qa(i1),(c(i1,i2),i2=1,3)
-* end do
-* nhulp=na+1
-* do k1=-kx,kx
-* do k2=-ky,ky
-* do k3=-kz,kz
-* if (k1.ne.0.or.k2.ne.0.or.k3.ne.0) then
-* do i1=1,na
-* cx=c(i1,1)+k1*tm11
-* cy=c(i1,2)+k1*tm21+k2*tm22
-* cz=c(i1,3)+k1*tm31+k2*tm32+k3*tm33
-* write (86,'(i4,1x,a2,3x,3d22.15)')nhulp,qa(i1),cx,cy,cz
-* nhulp=nhulp+1
-* end do
-* end if
-* end do
-* end do
-* end do
-* write (86,*)
-**********************************************************************
-* *
-* Write crystal structure with extra unit cells *
-* *
-**********************************************************************
- mux=1+iexx
- muy=1+iexy
- muz=1+iexz
- qr='F'
- write (85,'(2x,a1,1x,a60)')qr,qmol
- qr=qrtemp
- write (85,'(3f10.4)')mux*axiss(1),muy*axiss(2),muz*axiss(3)
- write (85,'(3f10.4)')angle(1),angle(2),angle(3)
- do i1=1,na
- write (85,'(i4,1x,a2,3x,3d22.15)')i1,qa(i1),(c(i1,i2),i2=1,3)
- end do
- nhulp=na+1
- do k1=0,iexx
- do k2=0,iexy
- do k3=0,iexz
- if (k1.ne.0.or.k2.ne.0.or.k3.ne.0) then
- do i1=1,na
- cx=c(i1,1)+k1*tm11
- cy=c(i1,2)+k1*tm21+k2*tm22
- cz=c(i1,3)+k1*tm31+k2*tm32+k3*tm33
- write (85,'(i4,1x,a2,3x,3d22.15)')nhulp,qa(i1),cx,cy,cz
- nhulp=nhulp+1
- end do
- end if
- end do
- end do
- end do
- write (85,*)
-
- end if
- end if
- end if
-
- end if
-
- if (ni.eq.0.or.ni.eq.2) then
-**********************************************************************
-* *
-* Write ASCII trajectory file *
-* *
-**********************************************************************
- if (ni.eq.0) open(unit=66,file=qmdfi//'.vel',status='unknown')
- if (ni.eq.2) then
- write (var,'(f7.4)')float(mdstep/nsav3)/1d4
- open (unit=66,file=qmdfi//var(3:7),status='unknown')
- end if
- write (66,500)axis(1),axis(2),axis(3)
- write (66,550)angle(1),angle(2),angle(3)
- write (66,600)na,((c(i,j),j=1,3),qlabel(i),i=1,na)
- write (66,700)((vel(j,i),j=1,3),i=1,na)
- write (66,800)((accel(j,i),j=1,3),i=1,na)
- write (66,900)((aold(j,i),j=1,3),i=1,na)
- write (66,1000)tempmd
- write (66,1050)
- close (66)
- end if
- if (ni.ne.2.and.iopt.eq.0) then
-
-C open (unit=68,file='xmolout',status='unknown',access='append')
- write (68,1200)na
- write (68,1300)qmol,mdstep+nit+nprevrun,estrc,
- $axis(1),axis(2),axis(3),angle(1),angle(2),angle(3)
- do i1=1,na
- if (ixmolo.eq.0) write (68,1400)qa(i1),(c(i1,i2),i2=1,3)
- if (ixmolo.eq.1) write (68,1400)qa(i1),(c(i1,i2),i2=1,3),
- $(vel(i2,i1)/1e+10,i2=1,3),iag(i1,3+mbond)
- if (ixmolo.eq.2) write (68,1401)qa(i1),(c(i1,i2),i2=1,3),
- $iag(i1,3+mbond)
- end do
- close (68)
-
- if (itrout.ne.0) then
-C open (unit=69,file='xmolout2',status='unknown',access='append')
- write (69,1200)na
- write (69,1300)qmol,mdstep+nit+nprevrun,estrc,
- $axis(1),axis(2),axis(3),angle(1),angle(2),angle(3)
- do i1=1,na
- if (ixmolo.eq.0) write (69,1400)qa(i1),(cp(i1,i2),i2=1,3)
- if (ixmolo.eq.1) write (69,1400)qa(i1),(cp(i1,i2),i2=1,3),
- $(vel(i2,i1)/1e+10,i2=1,3),iag(i1,3+mbond)
- if (ixmolo.eq.2) write (68,1401)qa(i1),(c(i1,i2),i2=1,3),
- $iag(i1,3+mbond)
- end do
- close (69)
- end if
-
- call molanal
- end if
-**********************************************************************
-* *
-* Generate BIOGRAF output-file *
-* *
-**********************************************************************
- if ((ni.eq.1.and.iopt.eq.0).or.(ni.eq.1.and.iopt.eq.1.and.
- $iflga.eq.1)) then
-
- if (qfileh.eq.' ') then
- write (*,*)'Warning: no file name given; use Unknown'
- qfileh='Unknown'
- end if
- qfile2=qfileh
- if (imodfile.eq.0) then
- istart=1
- qstrana1(1:25)=qfileh
- call stranal(istart,iend,vout,iout,1)
- qfile2=qfileh(istart:iend-1)//".bgf"
- end if
- call writebgf(90)
-
- if (imodfile.eq.1.or.iopt.eq.0) then
- open (88,file=qfile2,status='unknown')
- call writebgf(88)
- close (88)
- end if
-
- end if
-
- return
-**********************************************************************
-* *
-* Format part *
-* *
-**********************************************************************
- 100 format (i4,1x,a40,'Iteration:',i8,' #Bonds:',i4)
- 101 format (i3,2x,a40)
- 200 format (8i4,8f7.3)
- 201 format (8i3)
- 210 format (13i4,13f7.3)
- 220 format (18i4,18f7.3)
- 230 format (23i4,23f7.3)
- 240 format (28i4,28f7.3)
- 250 format (38i4,38f7.3)
- 300 format (2x,a1,1x,a60)
- 301 format (2x,a1,1x,f6.2,a60)
- 302 format (2x,a1,1x,2f6.2,a60)
- 310 format (2x,a1,1x,a60)
- 320 format (3f10.4)
- 400 format (i4,1x,a2,3x,3(d21.14,1x),1x,a5,1x,i5)
- 410 format (i4,f12.6)
- 412 format(A6,I5,1x,A2,3x,A3,2x,i4,4x,3f8.3,f6.2,f6.2,4x,2x,A6)
- 500 format (1x,'Lattice parameters:',/(3f15.8))
- 550 format (3f15.8)
- 600 format (i4,1x,'Atom coordinates (Angstrom):',/
- $(3d24.15,1x,a5))
- 700 format (1x,'Atom velocities (Angstrom/s):',/(3d24.15))
- 800 format (1x,'Atom accelerations (Angstrom/s**2):',/(3d24.15))
- 900 format (1x,'Previous atom accelerations:',/(3d24.15))
- 1000 format (1x,'MD-temperature (K):',/(1d24.15))
- 1050 format (1x,'Connections, bond orders and lone pairs:')
- 1100 format (8i3,8f8.4)
- 1200 format (i4)
- 1300 format (a40,i6,f12.4,6f7.2)
- 1400 format (a2,3f10.5,3f15.5,i6)
- 1401 format (a2,3f10.5,i6)
- 1500 format ('BIOGRF',i4)
- 1600 format ('XTLGRF',i4)
- 1700 format ('DESCRP ',a60)
- 1800 format ('REMARK ',a60)
- 1900 format ('FFIELD ',a40)
- 2000 format ('RUTYPE ',a40)
- 2100 format ('CRYSTX ',6f11.5)
- 2200 format ('CELLS ',6i5)
- 2300 format ('# At1 At2 R12 Force1 Force2 ',
- $'dR12/dIteration(MD only)')
- 2400 format ('BOND RESTRAINT ',2i4,f8.4,f8.2,f8.5,f10.7)
- 2500 format ('# At1 At2 At3 Angle Force1 Force2',
- $' dAngle/dIteration (MD only)')
- 2600 format ('ANGLE RESTRAINT ',3i4,2f8.2,f8.4,f9.6)
- 2700 format ('# At1 At2 At3 At3 Angle Force1 ',
- $'Force2 dAngle/dIteration (MD only)')
- 2800 format ('TORSION RESTRAINT ',4i4,2f8.2,f8.4,f9.6)
- 2900 format ('FORMAT ATOM (a6,1x,i5,1x,a5,1x,a3,1x,a1,1x,a5,',
- $'3f10.5,1x,a5,i3,i2,1x,f8.5)')
- 3000 format ('HETATM',1x,i5,1x,a5,1x,a3,1x,a1,1x,a5,3f10.5,1x,
- $a5,i3,i2,1x,f8.5)
- 3100 format ('FORMAT CONECT (a6,12i6)')
- 3200 format ('CONECT',12i6)
- 3300 format ('UNIT ENERGY kcal')
- 3400 format ('ENERGY',5x,f14.6)
- 3500 format ('END')
- end
-
-************************************************************************
-************************************************************************
-
- subroutine readc
-
-************************************************************************
-#include "cbka.blk"
-#include "cbkc.blk"
-#include "cbkcha.blk"
-#include "cbkconst.blk"
-#include "cbkdistan.blk"
-#include "cbkinit.blk"
-#include "cbktregime.blk"
-#include "control.blk"
-#include "opt.blk"
-#include "small.blk"
-
- character*6 qident
- character*20 qhulp
-* dimension qident(100)
-************************************************************************
-* *
-* Read control file *
-* *
-************************************************************************
-c$$$c if (ndebug.eq.1) then
-c$$$C open (65,file='fort.65',status='unknown',access='append')
-c$$$c write (65,*) 'In readc'
-c$$$c call timer(65)
-c$$$c close (65)
-c$$$c end if
- if (mdstep.gt.0.or.nit.gt.0) nmmsav=nmm
-************************************************************************
-* *
-* Set default values *
-* *
-************************************************************************
- nreac=0
- axis1=200.0d0
- axis2=200.0d0
- axis3=200.0d0
- cutof2=0.001d0
- cutof3=0.300d0
- tsetor=298.0d0
- tset2=298.0d0
- pset=0.0d0
- tincr=0.0d0
- tstep=0.5d0
-* swa=0.0 !Moved to force field
-* swb=12.5 !Moved to force field
- taut=2.5d0
- taut2=2.5d0
- ndtau=50000
- taup=500.0d0
- vqnd=100.0d0
- errnh=1.0d0
- range=2.5d0
- maxstp=1000
- nequi=0
- nmethod=3
- ncha=3
- ncha2=1
- nchaud=1
- nvlist=25
- nrep1=5
- nsav=50
- icheck=0
- ivels=0
- itfix=0
- ncontrol=25
- noutpt=0
- napp=0
- nsurp=0
- ncons=2
- nrand=0
- nmm=0
- endpo=1.0d0
- endpo2=1.0d0
- nfc=50
- nsav2=50
- nmmax=50
- i5758=0
- parc1=1.0d0
- parc2=0.001d0
- icell=0
- ingeo=1
- ccpar=1.0005d0
- icelo2=0
- nrdd=0
- nrddf=200000
- nbiolab=0
-c ngeofor=0
- nincrop=0
- accerr=2.50d0
- vrange=2.50d0
- vlbora=5.00d0
- nsav3=1000
- nhop2=25
- nprevrun=0
- ndebug=0
- volcha=10.00d0
- ixmolo=0
- inpt=0
- iconne=0
- imolde=0
- ianaly=0
- icentr=0
- itrans=0
- itrout=0
- tpnrad=300.0d0
- ityrad=3
- iexx=1
- iexy=1
- iexz=1
- syscha=0.00d0
- inmov1=0
- inmov2=0
- vfield=0.00d0
- itstep=0
- ifreq=0
- isymm=1
- icpres=0
- delvib=0.0001d0
-c shock variables
- shock_vel = 2.d0 ! impact velocity for shock simulations (nm/ps)
- shock_z_sep = 10.0d0 ! separation z value to apply initial velocities in shocks
- ishock_type = 0.0d0 ! shock type. 0: simple impact; 1: compressing c axis
-c Hugoniostat variables
- Hug_E0 = 0.d0 ! Reference energy
- Hug_P0 = 0.d0 ! Reference pressure
- Hug_V0 = 0.d0 ! Reference volume
-c Shear flow simulations for viscosity
- xImpVcm = 1.d0 ! velocity applied in shear simulations (in nm/ps), left half mover at -xImpVcm and right at +xImpVcm
-c$$$************************************************************************
-c$$$* *
-c$$$* Read control-file *
-c$$$* *
-c$$$************************************************************************
-c$$$ open (10,file='control',status='old')
-c$$$ 10 read (10,'(a20)',end=20,err=30)qhulp
-c$$$ if (qhulp(1:1).eq.'#') goto 10
-c$$$ read (qhulp,*,err=30)vhulp
-c$$$ read (qhulp,'(8x,a6)',err=30)qident
-c$$$ if (qident.eq.'Hug_V0') Hug_P0=vhulp
-c$$$ if (qident.eq.'Hug_P0') Hug_V0=vhulp
-c$$$ if (qident.eq.'Hug_E0') Hug_E0=vhulp
-c$$$ if (qident.eq.'shea_v') xImpVcm=vhulp
-c$$$ if (qident.eq.'shok_t') ishock_type=int(vhulp)
-c$$$ if (qident.eq.'shok_z') shock_z_sep=vhulp
-c$$$ if (qident.eq.'shok_v') shock_vel=vhulp
-c$$$ if (qident.eq.'nreac') nreac=int(vhulp)
-c$$$ if (qident.eq.'axis1') axis1=vhulp
-c$$$ if (qident.eq.'axis2') axis2=vhulp
-c$$$ if (qident.eq.'axis3') axis3=vhulp
-c$$$ if (qident.eq.'cutof2') cutof2=vhulp
-c$$$ if (qident.eq.'cutof3') cutof3=vhulp
-c$$$ if (qident.eq.'mdtemp') tsetor=vhulp
-c$$$ if (qident.eq.'mdtem2') tset2=vhulp
-c$$$ if (qident.eq.'mdpres') pset=vhulp*0.001
-c$$$ if (qident.eq.'tincr') tincr=vhulp
-c$$$ if (qident.eq.'tstep') tstep=vhulp
-c$$$* if (qident.eq.'lowtap') swa=vhulp !Moved to force field
-c$$$* if (qident.eq.'uptap') swb=vhulp !Moved to force field
-c$$$ if (qident.eq.'tdamp1') taut=vhulp
-c$$$ if (qident.eq.'tdamp2') taut2=vhulp
-c$$$ if (qident.eq.'ntdamp') ndtau=int(vhulp)
-c$$$ if (qident.eq.'pdamp1') taup=vhulp
-c$$$ if (qident.eq.'tdhoov') vqnd=vhulp
-c$$$ if (qident.eq.'achoov') errnh=vhulp/100.0
-c$$$ if (qident.eq.'range') range=vhulp
-c$$$ if (qident.eq.'nmdit') maxstp=int(vhulp)
-c$$$ if (qident.eq.'nmdeqi') nequi=int(vhulp)
-c$$$ if (qident.eq.'imdmet') nmethod=int(vhulp)
-c$$$ if (qident.eq.'icharg') ncha=int(vhulp)
- nchaold=ncha
-c$$$ if (qident.eq.'ichaen') ncha2=int(vhulp)
-c$$$ if (qident.eq.'ichupd') nchaud=int(vhulp)
-c$$$ if (qident.eq.'iout1') nrep1=int(vhulp)
-c$$$ if (qident.eq.'iout2') nsav=int(vhulp)
-c$$$ if (qident.eq.'icheck') ntest=int(vhulp)
-c$$$ if (qident.eq.'ivels') nvel=int(vhulp)
-c$$$ if (qident.eq.'itfix') ntscale=int(vhulp)
-c$$$ if (qident.eq.'irecon') ncontrol=int(vhulp)
-c$$$ if (qident.eq.'iout3') noutpt=int(vhulp)
-c$$$ if (qident.eq.'iappen') napp=int(vhulp)
-c$$$ if (qident.eq.'isurpr') nsurp=int(vhulp)
-c$$$ if (qident.eq.'itdmet') ncons=int(vhulp)
-c$$$ if (qident.eq.'iravel') nrand=int(vhulp)
-c$$$ if (qident.eq.'imetho') nmm=int(vhulp)
-c$$$ if (qident.eq.'endmm') endpo=vhulp
- endpoold=endpo
-c$$$ if (qident.eq.'endmd') endpo2=vhulp
-c$$$ if (qident.eq.'imaxmo') nfc=int(vhulp)
- nfcold=nfc
-c$$$ if (qident.eq.'iout4') nsav2=int(vhulp)
-c$$$ if (qident.eq.'imaxit') nmmax=int(vhulp)
- nmmaxold=nmmax
-c$$$ if (qident.eq.'iout5') i5758=int(vhulp)
-c$$$ if (qident.eq.'parsca') parc1=vhulp
-c$$$ if (qident.eq.'parext') parc2=vhulp
-c$$$ if (qident.eq.'icelop') icell=int(vhulp)
- icellold=icell
-c$$$ if (qident.eq.'igeopt') ingeo=int(vhulp)
-c$$$ if (qident.eq.'celopt') ccpar=vhulp
-c$$$ if (qident.eq.'icelo2') icelo2=int(vhulp)
- icelo2old=icelo2
-c$$$ if (qident.eq.'ideve1') nrdd=int(vhulp)
-c$$$ if (qident.eq.'ideve2') nrddf=int(vhulp)
-c$$$ if (qident.eq.'ibiola') nbiolab=int(vhulp)
-c$$$c if (qident.eq.'igeofo') ngeofor=int(vhulp)
-c$$$ if (qident.eq.'iincop') nincrop=int(vhulp)
-c$$$ if (qident.eq.'accerr') accincr=vhulp
-c$$$ if (qident.eq.'iout6') nsav3=int(vhulp)
-c$$$ if (qident.eq.'irten') nhop2=int(vhulp)
-c$$$ if (qident.eq.'npreit') nprevrun=int(vhulp)
-c$$$ if (qident.eq.'idebug') ndebug=int(vhulp)
-c$$$ if (qident.eq.'volcha') volcha=vhulp
-c$$$ if (qident.eq.'ixmolo') ixmolo=int(vhulp)
-c$$$ if (qident.eq.'inpt') inpt=int(vhulp)
-c$$$ if (qident.eq.'iconne') iconne=int(vhulp)
-c$$$ if (qident.eq.'imolde') imolde=int(vhulp)
-c$$$ if (qident.eq.'ianaly') ianaly=int(vhulp)
-c$$$ if (qident.eq.'icentr') icentr=int(vhulp)
-c$$$ if (qident.eq.'itrans') itrans=int(vhulp)
-c$$$ if (qident.eq.'itrout') itrout=int(vhulp)
-c$$$ if (qident.eq.'nvlist') nvlist=int(vhulp)
-c$$$ if (qident.eq.'vrange') vrange=vhulp
-c$$$ if (qident.eq.'vlbora') vlbora=vhulp
-c$$$ if (qident.eq.'tpnrad') tpnrad=vhulp
-c$$$ if (qident.eq.'ityrad') ityrad=int(vhulp)
-c$$$ if (qident.eq.'iexx') iexx=int(vhulp)
-c$$$ if (qident.eq.'iexy') iexy=int(vhulp)
-c$$$ if (qident.eq.'iexz') iexz=int(vhulp)
-c$$$ if (qident.eq.'syscha') syscha=vhulp
-c$$$ if (qident.eq.'inmov1') inmov1=int(vhulp)
-c$$$ if (qident.eq.'inmov2') inmov2=int(vhulp)
-c$$$ if (qident.eq.'itstep') itstep=int(vhulp)
-c$$$ if (qident.eq.'ifreq') ifreq=int(vhulp)
-c$$$ if (qident.eq.'isymm') isymm=int(vhulp)
-c$$$ if (qident.eq.'icpres') icpres=int(vhulp)
-c$$$ if (qident.eq.'delvib') delvib=vhulp
-c$$$ goto 10
-c$$$ 20 continue
- close (10)
- axis(1)=axis1
- axis(2)=axis2
- axis(3)=axis3
- if (axiss(1).gt.zero) then
- axis(1)=axiss(1)
- axis(2)=axiss(2)
- axis(3)=axiss(3)
- end if
- if (tincr.lt.0.0001.and.tincr.gt.-0.0001) tset=tsetor
- iequi=1
- if (nequi.gt.0) iequi=0
- if (iopt.eq.1.and.napp.eq.1) then
- stop 'No fort.7 and fort.8 append with iopt=1 !'
- end if
- if (mdstep.gt.0.or.nit.gt.0) nmm=nmmsav
- if (mdstep.gt.0.and.itstep.eq.1) then
- tstepmax=tstep
- tstep=tstep*(tsetor/tempmd)
- if (tstep.gt.tstepmax) tstep=tstepmax
- end if
- tstep=1.0d-15*tstep
- taus=taut
- taut=1.0d-15*taut
- taut2=1.0d-15*taut2
- taup=1.0d-15*taup
- ts2=tstep/2.0
- ts22=tstep*ts2
- return
- 30 continue
- write (*,*)'Error reading control-file'
- stop 'Error reading control-file'
-************************************************************************
-* *
-* Format part *
-* *
-************************************************************************
- 1050 format (f7.3)
- 1055 format (f7.4)
- 1056 format (f9.4)
- 1060 format (i8)
- 1070 format (f7.5)
- end
-************************************************************************
-************************************************************************
-
- subroutine staint
-
-************************************************************************
-#include "cbka.blk"
-#include "cbkdcell.blk"
-#include "cbkqa.blk"
-#include "control.blk"
-#include "small.blk"
-#include "cbkc.blk"
-#include "cbkconst.blk"
- dimension bvt(nat,4)
-************************************************************************
-* *
-* Generate cartesian coordinates from internal coordinate input *
-* *
-************************************************************************
-c$$$ if (ndebug.eq.1) then
-c$$$C open (65,file='fort.65',status='unknown',access='append')
-c$$$ write (65,*) 'In staint'
-c$$$ call timer(65)
-c$$$ close (65)
-c$$$ end if
- k=0
- 10 read (3,1200,end=20,err=20)(ijk(k+1,k1),k1=1,3),k2,qa(k+1),
- $bvt(k+1,3),bvt(k+1,2),bvt(k+1,1)
- qlabel(k+1)=qa(k+1)
- qresi1(k+1)=' '
- qresi2(k+1)=' '
- qresi3(k+1)=' '
- qffty(k+1)=' '
- if (k2.ne.k+1) then
- write (*,*)'Wrong order in internal coordinates at atom:',k2
- goto 20
-* stop 'Wrong order in internal coordinates'
- end if
- k=k+1
- if (k.gt.nat) then
- write (*,*)na,nat
- stop 'Maximum number of atoms exceeded'
- end if
- goto 10
- 20 continue
- na=k
-
-************************************************************************
-* *
-* CALCULATION OF CARTESIAN COORDINATES FROM INTERNAL COORDINAATES *
-* *
-************************************************************************
-
- 12 C(1,1)=ZERO
- C(1,2)=ZERO
- C(1,3)=ZERO
- C(2,1)=BVT(2,1)
- C(2,2)=ZERO
- C(2,3)=ZERO
- HR=(BVT(3,2)-90.0D0)*DGRRDN
- C(3,1)=C(2,1)+BVT(3,1)*SIN(HR)
- C(3,2)=BVT(3,1)*COS(HR)
- C(3,3)=ZERO
- DO 32 K1=4,NA
- J=IJK(K1,2)
- KB=K1-1
- XH=C(J,1)
- YH=C(J,2)
- ZH=C(J,3)
- DO 13 K2=1,KB
- C(K2,1)=C(K2,1)-XH
- C(K2,2)=C(K2,2)-YH
- C(K2,3)=C(K2,3)-ZH
- DO 13 K3=1,3
- 13 IF (ABS(C(K2,K3)).LT.1.0D-15) C(K2,K3)=1.0D-15
- K=IJK(K1,3)
- P2=C(K,2)*C(K,2)+C(K,3)*C(K,3)
- IF (P2.NE.ZERO) THEN
- P=SQRT(P2)
- Q=SQRT(C(K,1)*C(K,1)+P2)
- SA=C(K,2)/P
- CA=C(K,3)/P
- SB=-C(K,1)/Q
- CB=P/Q
- ELSE
- SA=ZERO
- CA=ONE
- SB=ONE
- CB=ZERO
- ENDIF
- DO 16 K2=1,KB
- AZ=C(K2,1)
- BZ=C(K2,2)
- C(K2,1)=AZ*CB+BZ*SB*SA+C(K2,3)*SB*CA
- C(K2,2)=BZ*CA-C(K2,3)*SA
- 16 C(K2,3)=-AZ*SB+BZ*CB*SA+C(K2,3)*CB*CA
- IF (C(K,3).LE.ZERO) THEN
- DO 17 K2=1,KB
- 17 C(K2,3)=-C(K2,3)
- ENDIF
- I=IJK(K1,1)
- IF (1.0D5*ABS(C(I,1)).LE.ABS(C(I,2))) THEN
- T1=HALF*PI
- ELSE
- YX=ABS(C(I,2)/C(I,1))
- T1=ATAN(YX)
- ENDIF
- IF (C(I,1).GE.ZERO.AND.C(I,2).LT.ZERO) T1=TWO*PI-T1
- IF (C(I,1).LT.ZERO.AND.C(I,2).GE.ZERO) T1=PI-T1
- IF (C(I,1).LT.ZERO.AND.C(I,2).LT.ZERO) T1=T1+PI
- DO 31 K2=1,KB
- IF (C(K2,1).EQ.ZERO.AND.C(K2,2).EQ.ZERO) GOTO 31
- IF (1.0D5*ABS(C(K2,1)).LT.ABS(C(K2,2))) THEN
- T2=HALF*PI
- ELSE
- YX=ABS(C(K2,2)/C(K2,1))
- T2=ATAN(YX)
- ENDIF
- IF (C(K2,1).GE.ZERO.AND.C(K2,2).LT.ZERO) T2=TWO*PI-T2
- IF (C(K2,1).LT.ZERO.AND.C(K2,2).GE.ZERO) T2=PI-T2
- IF (C(K2,1).LT.ZERO.AND.C(K2,2).LT.ZERO) T2=T2+PI
- T3=T2-T1
- IF (T3.LT.ZERO)T3=T3+TWO*PI
- RZ=SQRT(C(K2,1)*C(K2,1)+C(K2,2)*C(K2,2))
- C(K2,1)=RZ*COS(T3)
- C(K2,2)=RZ*SIN(T3)
- 31 CONTINUE
- HR=(BVT(K1,2)-90.0D0)*DGRRDN
- HT=BVT(K1,3)*DGRRDN
- CHR=COS(HR)
- C(K1,1)=BVT(K1,1)*CHR*COS(HT)
- C(K1,2)=BVT(K1,1)*CHR*SIN(HT)
- 32 C(K1,3)=C(IJK(K1,3),3)+BVT(K1,1)*SIN(HR)
-
- return
- 1200 FORMAT(4I3,1X,A2,3F10.5,4X,I1,F10.5)
- end
-************************************************************************
-************************************************************************
-
- subroutine outint
-
-************************************************************************
-#include "cbka.blk"
-#include "cbkabo.blk"
-#include "cbkbo.blk"
-#include "cbkconst.blk"
-#include "cbkia.blk"
-#include "cbkinit.blk"
-#include "cbknubon2.blk"
-#include "cbkqa.blk"
-#include "cbktregime.blk"
-#include "control.blk"
-#include "small.blk"
-#include "cbksrtbon1.blk"
-************************************************************************
-* *
-* Output internal coordinates *
-* *
-************************************************************************
- dimension dvdc(3,3),dargdc(3,3)
-c$$$ if (ndebug.eq.1) then
-c$$$C open (65,file='fort.65',status='unknown',access='append')
-c$$$ write (65,*) 'In outint'
-c$$$ call timer(65)
-c$$$ close (65)
-c$$$ end if
- write (91,50)qmol
- open (82,file='output.MOP',status='unknown')
- write (82,*)
- write (82,'(a40)')qmol
- write (82,*)
- close (82)
-
-* IF (NMOLO.GT.1) THEN
-* WRITE(6,*)' OUTPUT INTERNAL COORDINATES NOT POSSIBLE FOR ',
-* $'CALCULATION ON MORE THAN ONE MOLECULE'
-* RETURN
-* END IF
-
-************************************************************************
-* *
-* Output of internal coordinates. *
-* First 3 atoms of other input file. *
-* *
-************************************************************************
- N1=1
- N2=2
- N3=3
-C open (82,file='output.MOP',status='unknown',access='append')
- write(91,100)N1,qa(n1)
- write(82,'(2x,a2,f12.6,i3,f12.6,i3,f12.6,i3,1x,3i4)')qa(n1),
- $zero,nzero,zero,nzero,zero,nzero,nzero,nzero,nzero
- call dista2(n1,n2,rr,dx,dy,dz)
- write(91,200)N1,N2,qa(n2),RR
- write(82,'(2x,a2,f12.6,i3,f12.6,i3,f12.6,i3,1x,3i4)')qa(n2),
- $rr,none,zero,nzero,zero,nzero,n1,nzero,nzero
- close (82)
-
- call dista2(n2,n3,rr,dx,dy,dz)
- hv=zero
- call calvalres(n1,n2,n3,arg,hv,dvdc,dargdc)
- WRITE(91,300)N1,N2,N3,qa(n3),rdndgr*HV,RR
-C open (82,file='output.MOP',status='unknown',access='append')
- write(82,'(2x,a2,f12.6,i3,f12.6,i3,f12.6,i3,1x,3i4)')qa(n3),
- $rr,none,rdndgr*hv,none,zero,nzero,n2,n1,nzero
- close (82)
-
- naih=3
-
- do i1=naih+1,na
- bomax=zero
- j1=0
- do i2=1,ia(i1,2)
- iob=ia(i1,2+i2)
- ncubo=nubon2(i1,i2)
- if (bo(ncubo).gt.bomax.and.iob.lt.i1) then
- bomax=bo(ncubo)
- j1=iob
- end if
- end do
- if (j1.eq.0) j1=i1-1
- call dista2(j1,i1,rr,dx,dy,dz)
-
- bomax=zero
- j2=0
- do i2=1,ia(j1,2)
- iob=ia(j2,2+i2)
- ncubo=nubon2(j1,i2)
- if (bo(ncubo).gt.bomax.and.iob.lt.i1.and.
- $abo(iob).gt.bo(ncubo)+0.2) then
- bomax=bo(ncubo)
- j2=iob
- end if
- end do
- if (j2.eq.0) j2=i1-2
- if (j2.eq.j1) j2=j2+1
-
- call calvalres(j2,j1,i1,arg,hh,dvdc,dargdc)
-
- bomax=zero
- j3=0
- do i2=1,ia(j2,2)
- iob=ia(j2,2+i2)
- ncubo=nubon2(j2,i2)
- if (bo(ncubo).gt.bomax.and.iob.lt.i1.and.iob.ne.j1) then
- bomax=bo(ncubo)
- j3=iob
- end if
- end do
- if (j3.eq.0) j3=i1-3
- if (j3.eq.j2.and.j3.ne.j1-1) j3=j3+1
- if (j3.eq.j2.and.j3.ne.j1-2) j3=j3+2
- if (j3.eq.j1.and.j3.ne.j2-1) j3=j3+1
- if (j3.eq.j1.and.j3.ne.j2-2) j3=j3+2
-
- call caltor(j3,j2,j1,i1,ht)
-
- write(91,400)j3,j2,j1,i1,qa(i1),ht,rdndgr*hh,rr
-C open (82,file='output.MOP',status='unknown',access='append')
- write(82,'(2x,a2,f12.6,i3,f12.6,i3,f12.6,i3,1x,3i4)')qa(i1),
- $rr,none,rdndgr*hh,none,ht,none,j1,j2,j3
- close (82)
- end do
-
- close(82)
- return
- 50 format (' I',2x,a60)
- 100 FORMAT(9X,I3,1x,a2)
- 200 FORMAT(6X,2I3,1x,a2,20X,F10.5)
- 300 FORMAT(3X,3I3,1x,a2,10X,2F10.5)
- 400 FORMAT(4I3,1x,a2,3F10.5)
-
- end
-************************************************************************
-************************************************************************
-
- subroutine outres
-
-************************************************************************
-#include "cbka.blk"
-#include "cbkbo.blk"
-#include "cbkch.blk"
-#include "cbkd.blk"
-#include "cbkenergies.blk"
-#include "cbkh.blk"
-#include "cbkimove.blk"
-#include "cbkrbo.blk"
-#include "cbktorang.blk"
-#include "cbktorsion.blk"
-#include "cbktregime.blk"
-#include "cbkvalence.blk"
-#include "control.blk"
-#include "opt.blk"
-#include "small.blk"
-#include "cbkinit.blk"
-
-************************************************************************
-* *
-* Output molecular data *
-* *
-************************************************************************
- dimension isort(100),iad1(100),iad2(100),iad3(100),iad4(100)
- character*60 qm2
-c$$$ if (ndebug.eq.1) then
-c$$$C open (65,file='fort.65',status='unknown',access='append')
-c$$$ write (65,*) 'In outres'
-c$$$ call timer(65)
-c$$$ close (65)
-c$$$ end if
- read (9,100,end=50)idata,qm2
-* if (qm2.ne.qmol) then
-* write (*,*)'Wrong molecule in outres-file'
-* write (*,*)qmol
-* write (*,*)qm2
-* return
-* end if
- do 25 i1=1,idata
- read (9,200)isort(i1),iad1(i1),iad2(i1),iad3(i1),iad4(i1)
- ndata2=ndata2+1
-
- if (isort(i1).eq.1) then
-* do i2=1,nbon
-* if (ib(i2,2).eq.iad1(i1).and.ib(i2,3).eq.iad2(i1)) then
-* if (iopt.ne.1) write (81,*)iad1(i1),iad2(i1),rbo(i2)
-* caldat(ndata2)=rbo(i2)
-* end if
-* end do
- call dista2(iad1(i1),iad2(i1),dish,dx,dy,dz)
- write (81,*)iad1(i1),iad2(i1),dish
- caldat(ndata2)=dish
- end if
-
- if (isort(i1).eq.2) then
- do i2=1,nval
- if (iv(i2,2).eq.iad1(i1).and.iv(i2,3).eq.iad2(i1).and.
- $iv(i2,4).eq.iad3(i1)) then
- if (iopt.ne.1) write (81,*)iad1(i1),iad2(i1),
- $iad3(i1),h(i2)*rdndgr
- caldat(ndata2)=h(i2)*rdndgr
- end if
- end do
- end if
-
- if (isort(i1).eq.3) then
- do i2=1,ntor
- if (it(i2,2).eq.iad1(i1).and.it(i2,3).eq.iad2(i1).and.
- $it(i2,4).eq.iad3(i1).and.it(i2,5).eq.iad4(i1)) then
- if (iopt.ne.1) write (81,*)iad1(i1),iad2(i1),iad3(i1),iad4(i1),
- $abs(thg(i2))
- caldat(ndata2)=abs(thg(i2))
- end if
- end do
- end if
-
- if (isort(i1).eq.4) then
- if (iopt.ne.1) write (81,*)estrmin
- caldat(ndata2)=estrmin
- end if
-
- if (isort(i1).eq.5) then
- if (iopt.ne.1) write (81,*)estrmin
- caldat(ndata2)=estrmin
- end if
-
- if (isort(i1).eq.6) then
- if (iopt.ne.1) write (81,*)iad1(i1),axiss(iad1(i1))
- caldat(ndata2)=axiss(iad1(i1))
- end if
-
- if (isort(i1).eq.7) then
- if (iopt.ne.1) write (81,*)eco
- caldat(ndata2)=eco
- end if
-
- if (isort(i1).eq.8) then
- do i2=1,nbon
- if (ib(i2,2).eq.iad1(i1).and.ib(i2,3).eq.iad2(i1)) then
- if (iopt.ne.1) write (81,*)iad1(i1),iad2(i1),bo(i2)
- caldat(ndata2)=bo(i2)
- end if
- end do
- end if
-
- if (isort(i1).eq.9) then
- if (iopt.ne.1) write (81,*)ch(iad1(i1))
- caldat(ndata2)=ch(iad1(i1))
- end if
-
- if (isort(i1).eq.10) then
- rmsg=0.0
- nmovh=0
- do i2=1,na
- do i3=1,3
- rmsg=rmsg+imove(i2)*d(i3,i2)*d(i3,i2)
- nmovh=nmovh+imove(i2)
- end do
- end do
- rmsg=sqrt(rmsg/float(nmovh*3))
-
- if (iopt.ne.1) write (81,*)rmsg
- caldat(ndata2)=rmsg
- end if
-
- if (isort(i1).eq.11) then
- if (iopt.ne.1) write (81,*)1000.0*pressu
- caldat(ndata2)=1000.0*pressu
- end if
-
- 25 continue
-
- 50 return
-************************************************************************
-* *
-* Format part *
-* *
-************************************************************************
- 100 format (i3,a60)
- 200 format (5i3)
- end
-************************************************************************
-************************************************************************
-
- subroutine readgeo
-
-************************************************************************
-#include "cbka.blk"
-#include "cbkc.blk"
-#include "cbkconst.blk"
-#include "cbkdistan.blk"
-#include "cbkinit.blk"
-#include "cbkqa.blk"
-#include "cbksrtbon1.blk"
-#include "cbktregime.blk"
-#include "cellcoord.blk"
-#include "control.blk"
-#include "small.blk"
- character*80 qromb
- character*25 qfileh
-c$$$ if (ndebug.eq.1) then
-c$$$C open (65,file='fort.65',status='unknown',access='append')
-c$$$ write (65,*) 'In readgeo'
-c$$$ call timer(65)
-c$$$ close (65)
-c$$$ end if
-
- if (ngeofor.eq.-1) return
-
-**********************************************************************
-* *
-* Read in system geometry *
-* *
-**********************************************************************
- if (ngeofor.eq.0) then
- call readdelphi (qfileh,iend,naold)
- namov=na
- end if
-
- if (ngeofor.eq.1) then
- call readbgf(iend,naold)
- end if
-
-
-
- if (ngeofor.eq.2) then
-**********************************************************************
-* *
-* Read in free format (xmol) geometry *
-* *
-**********************************************************************
- qr='1'
- read (3,'(i6)')na
- namov=na
- read (3,'(a60)')qmol
- do i1=1,na
- read (3,'(a80)')qromb
- ifirstchar=80
- do i2=1,80
- if (qromb(i2:i2).ne.' '.and.i2.lt.ifirstchar) ifirstchar=i2
- end do
- read (qromb(ifirstchar:80),'(a2)')qa(i1)
- read (qromb(ifirstchar+2:80),*)c(i1,1),c(i1,2),c(i1,3)
- qlabel(i1)=qa(i1)
- qresi1(i1)=' '
- qresi2(i1)=' '
- qresi3(i1)=' '
- qffty(i1)=' '
- end do
- ibity=1
- axiss(1)=-1.0
- end if
-
-
- if (ngeofor.eq.3) then
-**********************************************************************
-* *
-* Read in ChemDraw CC1-file *
-* *
-**********************************************************************
- qr='1'
- read (3,*)na
- namov=na
- read (3,'(a60)')qmol
- do i1=1,na
- read (3,'(2x,a2,5x,3f12.6)')qa(i1),c(i1,1),c(i1,2),c(i1,3)
- end do
- end if
-
- if (ngeofor.eq.4) then
-**********************************************************************
-* *
-* Read in .pdb-format *
-* *
-**********************************************************************
- qr='C'
- call readpdb(iendf)
- namov=na
- ibity=1
- axiss(1)=-1.0
- qfile(nprob)=qmol
- if (iendf.eq.1) stop 'End-of-file while reading in .pdb'
- end if
-
-**********************************************************************
-* *
-* Set up periodic system *
-* *
-**********************************************************************
- axis(1)=axiss(1)
- axis(2)=axiss(2)
- axis(3)=axiss(3)
- angle(1)=angles(1)
- angle(2)=angles(2)
- angle(3)=angles(3)
- if (axiss(1).lt.zero) then
- axis(1)=axis1
- axis(2)=axis2
- axis(3)=axis3
- angle(1)=90.0
- angle(2)=90.0
- angle(3)=90.0
- end if
- halfa=angle(1)*dgrrdn
- hbeta=angle(2)*dgrrdn
- hgamma=angle(3)*dgrrdn
- sinalf=sin(halfa)
- cosalf=cos(halfa)
- sinbet=sin(hbeta)
- cosbet=cos(hbeta)
- cosphi=(cos(hgamma)-cosalf*cosbet)/(sinalf*sinbet)
- if (cosphi.gt.1.0) cosphi=1.0
- sinphi=sqrt(one-cosphi*cosphi)
- tm11=axis(1)*sinbet*sinphi
- tm21=axis(1)*sinbet*cosphi
- tm31=axis(1)*cosbet
- tm22=axis(2)*sinalf
- tm32=axis(2)*cosalf
- tm33=axis(3)
-
- return
- end
-************************************************************************
-************************************************************************
-
- subroutine readdelphi (qfileh,iend,naold)
-
-************************************************************************
-#include "cbka.blk"
-#include "cbkc.blk"
-#include "cbkconst.blk"
-#include "cbkd.blk"
-#include "cbkdcell.blk"
-#include "cbkdistan.blk"
-#include "cbkff.blk"
-#include "cbkh.blk"
-#include "cbkinit.blk"
-#include "cbkqa.blk"
-#include "cbkrestr.blk"
-#include "cbksrtbon1.blk"
-#include "cbktregime.blk"
-#include "cellcoord.blk"
-#include "control.blk"
-#include "opt.blk"
-#include "small.blk"
- character*25 qfileh
-**********************************************************************
-* *
-* Read in geometries in Delphi-format (xyz) *
-* *
-**********************************************************************
-c$$$ if (ndebug.eq.1) then
-c$$$C open (65,file='fort.65',status='unknown',access='append')
-c$$$ write (65,*) 'In readdelphi'
-c$$$ call timer(65)
-c$$$ close (65)
-c$$$ end if
-
- if (imodfile.eq.1) then
- open (3,file=qfileh,status='old')
- end if
- nmmax=nmmaxold
- nfc=nfcold
- ibity=1
- iredo=1
- endpo=endpoold
- icell=icellold
- icelo2=icelo2old
- iend=0
- read (3,1000,end=900)qr,qmol
-**********************************************************************
-* *
-* Read in restraint information (optional) *
-* *
-**********************************************************************
- if (qr.eq.'R'.or.qr.eq.'P'.or.qr.eq.'X') then
- qmol=qmol(7:60)
- qmolset(nuge)=qmol
- read (18,1070,end=4,err=4) nrestra
- do i1=1,nrestra
- read (18,1090)irstra(i1,1),irstra(i1,2),rrstra(i1),vkrstr(i1),
- $vkrst2(i1),rrcha(i1)
- end do
- 4 continue
- end if
-**********************************************************************
-* *
-* Read in torsion restraint information (optional) *
-* *
-**********************************************************************
- if (qr.eq.'T'.or.qr.eq.'X') then
- if (qr.eq.'T') then
- qmol=qmol(7:60)
- qmolset(nuge)=qmol
- end if
- read (28,1070,end=6,err=6) nrestrat
- do i1=1,nrestrat
- read (28,1091)irstrat(i1,1),irstrat(i1,2),irstrat(i1,3),
- $irstrat(i1,4),trstra(i1),vkrt(i1),vkr2t(i1),rtcha(i1)
- end do
- 6 continue
- end if
-**********************************************************************
-* *
-* Read in valency angle restraint information (optional) *
-* *
-**********************************************************************
- if (qr.eq.'V') then
- qmol=qmol(7:60)
- qmolset(nuge)=qmol
- read (38,1070,end=7,err=7) nrestrav
- do i1=1,nrestrav
- read (38,1092)irstrav(i1,1),irstrav(i1,2),irstrav(i1,3),
- $vrstra(i1),vkrv(i1),vkr2v(i1)
- end do
- 7 continue
- end if
-**********************************************************************
-* *
-* Read in geometry *
-* *
-**********************************************************************
- ibh2=0
- iequi=1
- iexco=0
- if (nequi.gt.0) iequi=0
- axiss(1)=-1.0
-
- if (qr.eq.'O'.or.qr.eq.'L') stop 'Not xyz-format'
-
- if (qr.eq.'I') then !Delphi internal coordinates
- if (nsurp.ge.2) stop 'Int.coordinates only with 1 gemetry'
- call staint
- goto 20
- end if
-
- if (qr.eq.'B') then !Previous geometry with volume reduction
- read (3,*)
- vred=(1.0-0.01*volcha)**(0.33333)
- iexco=1
- na=naold
- do i1=1,3
- qmol=qmol
- axiss(i1)=vred*axis(i1)
- angles(i1)=angle(i1)
- do i2=1,na
- c(i2,i1)=vred*c(i2,i1)
- end do
- end do
-
- halfa=angles(1)*dgrrdn
- hbeta=angles(2)*dgrrdn
- hgamma=angles(3)*dgrrdn
- sinalf=sin(halfa)
- cosalf=cos(halfa)
- sinbet=sin(hbeta)
- cosbet=cos(hbeta)
- cosphi=(cos(hgamma)-cosalf*cosbet)/(sinalf*sinbet)
- if (cosphi.gt.1.0) cosphi=1.0
- sinphi=sqrt(one-cosphi*cosphi)
- tm11=axiss(1)*sinbet*sinphi
- tm21=axiss(1)*sinbet*cosphi
- tm31=axiss(1)*cosbet
- tm22=axiss(2)*sinalf
- tm32=axiss(2)*cosalf
- tm33=axiss(3)
- kx=int(2.0*swb/tm11)
- ky=int(2.0*swb/tm22)
- kz=int(2.0*swb/tm33)
- ibity=2
-
- goto 20
- end if
-
- if (qr.eq.'S') then !Previous geometry with volume expansion
- read (3,*)
- vexp=(1.0+0.01*volcha)**(0.33333)
- na=naold
- iexco=1
- do i1=1,3
- qmol=qmol
- axiss(i1)=vexp*axis(i1)
- angles(i1)=angle(i1)
- do i2=1,na
- c(i2,i1)=vexp*c(i2,i1)
- end do
- end do
-
- halfa=angles(1)*dgrrdn
- hbeta=angles(2)*dgrrdn
- hgamma=angles(3)*dgrrdn
- sinalf=sin(halfa)
- cosalf=cos(halfa)
- sinbet=sin(hbeta)
- cosbet=cos(hbeta)
- cosphi=(cos(hgamma)-cosalf*cosbet)/(sinalf*sinbet)
- if (cosphi.gt.1.0) cosphi=1.0
- sinphi=sqrt(one-cosphi*cosphi)
- tm11=axiss(1)*sinbet*sinphi
- tm21=axiss(1)*sinbet*cosphi
- tm31=axiss(1)*cosbet
- tm22=axiss(2)*sinalf
- tm32=axiss(2)*cosalf
- tm33=axiss(3)
- kx=int(2.0*swb/tm11)
- ky=int(2.0*swb/tm22)
- kz=int(2.0*swb/tm33)
- ibity=2
-
- goto 20
- end if
-
- if (qr.eq.'F'.or.qr.eq.'Y'.or.qr.eq.'3'.or.qr.eq.'5'.
- $or.qr.eq.'P') then
- kx=0
- ky=0
- kz=0
- ibity=2
- read(3,1005)axiss(1),axiss(2),axiss(3)
- read(3,1005)angles(1),angles(2),angles(3)
-
- halfa=angles(1)*dgrrdn
- hbeta=angles(2)*dgrrdn
- hgamma=angles(3)*dgrrdn
- sinalf=sin(halfa)
- cosalf=cos(halfa)
- sinbet=sin(hbeta)
- cosbet=cos(hbeta)
- cosphi=(cos(hgamma)-cosalf*cosbet)/(sinalf*sinbet)
- if (cosphi.gt.1.0) cosphi=1.0
- sinphi=sqrt(one-cosphi*cosphi)
- tm11=axiss(1)*sinbet*sinphi
- tm21=axiss(1)*sinbet*cosphi
- tm31=axiss(1)*cosbet
- tm22=axiss(2)*sinalf
- tm32=axiss(2)*cosalf
- tm33=axiss(3)
- kx=int(2.0*swb/tm11)
- ky=int(2.0*swb/tm22)
- kz=int(2.0*swb/tm33)
-
- end if
-
- if (qr.eq.'M'.or.qr.eq.'A') then
- nmmsav=nmm
- nmm=2
- end if
-
- if (qr.eq.'A') nmm=1
-
- if (qr.eq.'D') then
- endpo=endpo/25
- nmmax=nmmax*5
- qruid='HIGH PRECISION'
- end if
-
- if (qr.eq.'H') then
- nmmax=nmmax/10
- qruid='LOW PRECISION'
- end if
-
- if (qr.eq.'1'.or.qr.eq.'5') then
- nmm=1
- nmmax=1
- qruid='SINGLE POINT'
- end if
-
- if (qr.eq.'Y') then
- icell=0
- qruid='NO CELL OPT'
- end if
-
- 10 read (3,1100,end=20,err=20)ir,qa(na+1),(c(na+1,i2),i2=1,3)
- qlabel(na+1)=qa(na+1)
- qresi1(na+1)=' '
- qresi2(na+1)=' '
- qresi3(na+1)=' '
- qffty(na+1)=' '
- if (ir.eq.0) goto 20
- na=na+1
-
- if (na.gt.nat) then
- write (*,*)'Maximum number of atom exceeded ',na,nat
- stop 'Maximum number of atoms exceeded'
- end if
-
- goto 10
- 20 continue
-
- if (imodfile.eq.1) close (3)
-
- return
- 900 iend=1
- return
- 1000 format (2x,a1,1x,a60)
- 1005 format (3f10.4)
- 1070 format (i3)
- 1090 format (2i4,2f8.4,f8.6,f10.8)
- 1091 format (4i4,2f8.4,3f8.6)
- 1092 format (3i4,2f8.4,2f8.6)
- 1100 format (i4,1x,a2,3x,3d22.15,1x,a5,1x,i5)
- end
-************************************************************************
-************************************************************************
-
- subroutine readbgf(iendf,naold)
-
-************************************************************************
-#include "cbka.blk"
-#include "cbkc.blk"
-#include "cbkcha.blk"
-#include "cbkcharmol.blk"
-#include "cbkconst.blk"
-#include "cbkd.blk"
-#include "cbkdcell.blk"
-#include "cbkdistan.blk"
-#include "cbkenergies.blk"
-#include "cbkff.blk"
-#include "cbkh.blk"
-#include "cbkimove.blk"
-#include "cbkinit.blk"
-#include "cbkqa.blk"
-#include "cbkrestr.blk"
-#include "cbksrtbon1.blk"
-#include "cbktregime.blk"
-#include "cellcoord.blk"
-#include "control.blk"
-#include "opt.blk"
-#include "small.blk"
- character*80 qromb
- character*2 qrom
- character*5 quen
- character*5 qlabhulp
- character*25 qfileh
- character*200 qhulp
-**********************************************************************
-* *
-* Read in BIOGRAF-geometry *
-* *
-**********************************************************************
-c$$$ if (ndebug.eq.1) then
-c$$$C open (65,file='fort.65',status='unknown',access='append')
-c$$$ write (65,*) 'In readbgf'
-c$$$ call timer(65)
-c$$$ close (65)
-c$$$ end if
-
- iendf=0
- ienread=0
- iredo=0
- qremark(1)=' '
- enmol=zero
- formol=zero
-c$$$ if (imodfile.eq.1) then
-c$$$ open (3,file=qfileh,status='old')
-c$$$ end if
- open (3,file='fort.3',status='old')
- read (3,'(a40)',end=900)qromb
- ibity=0
- if (qromb(1:6).eq.'BIOGRF') ibity=1
- if (qromb(1:6).eq.'XTLGRF') ibity=2
- if (ibity.eq.0) then
- write (*,*)qromb(1:6)
- stop 'Unknown Biograf-file'
- end if
- read (qromb,'(6x,i4)')ibgfversion
- if (ibity.eq.1) qr='C'
- if (ibity.eq.2) qr='F'
- iremark=0
- iformat=0
- iline=0
- iexco=0
- iruid=1
- vvol=1.0
- nmcharge=0
- nmmax=nmmaxold
- nfc=nfcold
- ncha=nchaold
- endpo=endpoold
- icell=icellold
- icelo2=icelo2old
- axiss(1)=-1.0
-
- 30 read (3,'(a200)',end=46,err=40)qhulp
- qstrana1(1:200)=qhulp
- iline=iline+1
- irecog=0
-
- if (qhulp(1:6).eq.'DESCRP') then
- read (qhulp,'(7x,a40)',end=46,err=46)qmol
- irecog=1
- end if
-
- if (qhulp(1:6).eq.'REMARK') then
- if (iremark.lt.20) iremark=iremark+1
- read (qhulp,'(7x,a40)',end=46,err=46)qremark(iremark)
- irecog=1
- end if
-
- if (qhulp(1:6).eq.'FORMAT') then
- if (iformat.lt.20) iformat=iformat+1
- read(qhulp,'(7x,a40)',end=46,err=46)qformat(iformat)
- irecog=1
- end if
-
- if (qhulp(1:7).eq.'VCHANGE') then
- read (qhulp(8:60),*)vvol
- vred=(1.0+(vvol-1.0))**(0.33333333)
- iexco=1
- na=naold
- qmol=qmol
- do i1=1,3
- axiss(i1)=vred*axis(i1)
- angles(i1)=angle(i1)
- do i2=1,na
- cglobal(i2,i1)=vred*cglobal(i2,i1)
- end do
- end do
-
- halfa=angles(1)*dgrrdn
- hbeta=angles(2)*dgrrdn
- hgamma=angles(3)*dgrrdn
- sinalf=sin(halfa)
- cosalf=cos(halfa)
- sinbet=sin(hbeta)
- cosbet=cos(hbeta)
- cosphi=(cos(hgamma)-cosalf*cosbet)/(sinalf*sinbet)
- if (cosphi.gt.1.0) cosphi=1.0
- sinphi=sqrt(one-cosphi*cosphi)
- tm11=axiss(1)*sinbet*sinphi
- tm21=axiss(1)*sinbet*cosphi
- tm31=axiss(1)*cosbet
- tm22=axiss(2)*sinalf
- tm32=axiss(2)*cosalf
- tm33=axiss(3)
- kx=int(2.0*swb/tm11)
- ky=int(2.0*swb/tm22)
- kz=int(2.0*swb/tm33)
- ibity=2
- irecog=1
- end if
-
- if (qhulp(1:7).eq.'VCHANGX') then
- read (qhulp(8:60),*)vvol
- vred=vvol
- iexco=1
- na=naold
- qmol=qmol
- do i1=1,3
- axiss(i1)=axis(i1)
- angles(i1)=angle(i1)
- do i2=1,na
- cglobal(i2,i1)=cglobal(i2,i1)
- end do
- end do
-
- axiss(1)=vred*axiss(1)
- do i2=1,na
- cglobal(i2,1)=vred*cglobal(i2,1)
- end do
-
- halfa=angles(1)*dgrrdn
- hbeta=angles(2)*dgrrdn
- hgamma=angles(3)*dgrrdn
- sinalf=sin(halfa)
- cosalf=cos(halfa)
- sinbet=sin(hbeta)
- cosbet=cos(hbeta)
- cosphi=(cos(hgamma)-cosalf*cosbet)/(sinalf*sinbet)
- if (cosphi.gt.1.0) cosphi=1.0
- sinphi=sqrt(one-cosphi*cosphi)
- tm11=axiss(1)*sinbet*sinphi
- tm21=axiss(1)*sinbet*cosphi
- tm31=axiss(1)*cosbet
- tm22=axiss(2)*sinalf
- tm32=axiss(2)*cosalf
- tm33=axiss(3)
- kx=int(2.0*swb/tm11)
- ky=int(2.0*swb/tm22)
- kz=int(2.0*swb/tm33)
- ibity=2
- irecog=1
- end if
-
- if (qhulp(1:7).eq.'VCHANGY') then
- read (qhulp(8:60),*)vvol
- vred=vvol
- iexco=1
- na=naold
- qmol=qmol
- do i1=1,3
- axiss(i1)=axis(i1)
- angles(i1)=angle(i1)
- do i2=1,na
- cglobal(i2,i1)=cglobal(i2,i1)
- end do
- end do
-
- axiss(2)=vred*axiss(2)
- do i2=1,na
- cglobal(i2,2)=vred*cglobal(i2,2)
- end do
-
- halfa=angles(1)*dgrrdn
- hbeta=angles(2)*dgrrdn
- hgamma=angles(3)*dgrrdn
- sinalf=sin(halfa)
- cosalf=cos(halfa)
- sinbet=sin(hbeta)
- cosbet=cos(hbeta)
- cosphi=(cos(hgamma)-cosalf*cosbet)/(sinalf*sinbet)
- if (cosphi.gt.1.0) cosphi=1.0
- sinphi=sqrt(one-cosphi*cosphi)
- tm11=axiss(1)*sinbet*sinphi
- tm21=axiss(1)*sinbet*cosphi
- tm31=axiss(1)*cosbet
- tm22=axiss(2)*sinalf
- tm32=axiss(2)*cosalf
- tm33=axiss(3)
- kx=int(2.0*swb/tm11)
- ky=int(2.0*swb/tm22)
- kz=int(2.0*swb/tm33)
- ibity=2
- irecog=1
- end if
-
- if (qhulp(1:7).eq.'VCHANGZ') then
- read (qhulp(8:60),*)vvol
- vred=vvol
- iexco=1
- na=naold
- qmol=qmol
-
- do i1=1,3
- axiss(i1)=axis(i1)
- angles(i1)=angle(i1)
- do i2=1,na
- cglobal(i2,i1)=cglobal(i2,i1)
- end do
- end do
-
- axiss(3)=vred*axiss(3)
- do i2=1,na
- cglobal(i2,3)=vred*cglobal(i2,3)
- end do
-
- halfa=angles(1)*dgrrdn
- hbeta=angles(2)*dgrrdn
- hgamma=angles(3)*dgrrdn
- sinalf=sin(halfa)
- cosalf=cos(halfa)
- sinbet=sin(hbeta)
- cosbet=cos(hbeta)
- cosphi=(cos(hgamma)-cosalf*cosbet)/(sinalf*sinbet)
- if (cosphi.gt.1.0) cosphi=1.0
- sinphi=sqrt(one-cosphi*cosphi)
- tm11=axiss(1)*sinbet*sinphi
- tm21=axiss(1)*sinbet*cosphi
- tm31=axiss(1)*cosbet
- tm22=axiss(2)*sinalf
- tm32=axiss(2)*cosalf
- tm33=axiss(3)
- kx=int(2.0*swb/tm11)
- ky=int(2.0*swb/tm22)
- kz=int(2.0*swb/tm33)
- ibity=2
- irecog=1
- end if
-
- if (qhulp(1:6).eq.'CRYSTX') then
- read (qhulp,'(8x,6f11.5)',end=46,err=46)axiss(1),
- $axiss(2),axiss(3),angles(1),angles(2),angles(3)
- kx=0
- ky=0
- kz=0
- halfa=angles(1)*dgrrdn
- hbeta=angles(2)*dgrrdn
- hgamma=angles(3)*dgrrdn
- sinalf=sin(halfa)
- cosalf=cos(halfa)
- sinbet=sin(hbeta)
- cosbet=cos(hbeta)
- cosphi=(cos(hgamma)-cosalf*cosbet)/(sinalf*sinbet)
- if (cosphi.gt.1.0) cosphi=1.0
- sinphi=sqrt(one-cosphi*cosphi)
- tm11=axiss(1)*sinbet*sinphi
- tm21=axiss(1)*sinbet*cosphi
- tm31=axiss(1)*cosbet
- tm22=axiss(2)*sinalf
- tm32=axiss(2)*cosalf
- tm33=axiss(3)
- kx=int(2.0*swb/tm11)
- ky=int(2.0*swb/tm22)
- kz=int(2.0*swb/tm33)
- qr='F'
- if (nmmax.eq.1.and.nmmaxold.gt.1) qr='5'
- if (icell.eq.0.and.icellold.gt.0) qr='Y'
- ibity=2
- irecog=1
- end if
-
- if (qhulp(1:6).eq.'PERIOD') then
- read (qhulp,'(7x,i3)',end=46,err=46)iperiod
- irecog=1
- end if
-
- if (qhulp(1:4).eq.'AXES') then
- read (qhulp,'(7x,a3)',end=46,err=46)qbgfaxes
- irecog=1
- end if
-
- if (qhulp(1:6).eq.'SGNAME') then
- read (qhulp,'(7x,a3)',end=46,err=46)qbgfsgn
- irecog=1
- end if
-
-* if (qhulp(1:5).eq.'CELLS') then
-* read (qhulp,'(7x,*)',end=40,err=40)kx,ky,kz
-* irecog=1
-* end if
-
- if (qhulp(1:6).eq.'HETATM') then
- if (ibgfversion.lt.400) then
- read (qhulp,
- $'(7x,i5,1x,a5,1x,a3,1x,a1,1x,a5,3f10.5,1x,a5,i3,i2,1x,f8.5)'
- $,end=40,err=40)
- $ir,qlabel(na+1),qresi1(na+1),qresi2(na+1),qresi3(na+1),
- $cglobal(na+1,1),cglobal(na+1,2),
- $cglobal(na+1,3),qffty(na+1),ibgr1(na+1),ibgr2(na+1),
- $chgglobal(na+1)
- else
- stop 'Unsupported Biograf-version'
- end if
- qlabhulp=qlabel(na+1)
- if (qlabhulp(1:1).eq.' ') qlabhulp=qlabhulp(2:5)
- if (qlabhulp(1:1).eq.' ') qlabhulp=qlabhulp(2:4)
- if (qlabhulp(1:1).eq.' ') qlabhulp=qlabhulp(2:3)
- if (qlabhulp(1:1).eq.'C ') qa(na+1)='C '
- if (qlabhulp(1:2).eq.'Ca') qa(na+1)='Ca'
- if (qlabhulp(1:2).eq.'Cl') qa(na+1)='Cl'
- if (qlabhulp(1:2).eq.'Cu') qa(na+1)='Cu'
- if (qlabhulp(1:2).eq.'Co') qa(na+1)='Co'
- if (qlabhulp(1:1).eq.'H ') qa(na+1)='H '
- if (qlabhulp(1:2).eq.'He') qa(na+1)='He'
- if (qlabhulp(1:1).eq.'N ') qa(na+1)='N '
- if (qlabhulp(1:2).eq.'Ni') qa(na+1)='Ni'
- if (qlabhulp(1:1).eq.'O ') qa(na+1)='O '
- if (qlabhulp(1:1).eq.'B ') qa(na+1)='B '
- if (qlabhulp(1:1).eq.'F ') qa(na+1)='F '
- if (qlabhulp(1:2).eq.'Fe') qa(na+1)='Fe'
- if (qlabhulp(1:1).eq.'P ') qa(na+1)='P '
- if (qlabhulp(1:1).eq.'S ') qa(na+1)='S '
- if (qlabhulp(1:1).eq.'Y ') qa(na+1)='Y '
- if (qlabhulp(1:2).eq.'Al ') qa(na+1)='Al'
- if (qlabhulp(1:2).eq.'Au ') qa(na+1)='Au'
- if (qlabhulp(1:2).eq.'Si') qa(na+1)='Si'
- if (qlabhulp(1:2).eq.'Pt') qa(na+1)='Pt'
- if (qlabhulp(1:2).eq.'Mo') qa(na+1)='Mo'
- if (qlabhulp(1:2).eq.'Mg') qa(na+1)='Mg'
- if (qlabhulp(1:2).eq.'Ar') qa(na+1)='Ar'
- if (qlabhulp(1:2).eq.'Zr') qa(na+1)='Zr'
- if (qlabhulp(1:2).eq.'Ti') qa(na+1)='Ti'
- if (qlabhulp(1:2).eq.'Ru') qa(na+1)='Ru'
- if (qlabhulp(1:2).eq.'Ba') qa(na+1)='Ba'
- if (qlabhulp(1:2).eq.'Bi') qa(na+1)='Bi'
- if (qlabhulp(1:2).eq.'Li') qa(na+1)='Li'
- if (qlabhulp(1:2).eq.'V ') qa(na+1)='V '
- if (qlabhulp(1:2).eq.'X ') qa(na+1)='X '
- na=na+1
- if (na.gt.nattot) then
- write (*,*)'Number of atoms:read ',na
- write (*,*)'Maximum number of atoms: ',nattot
- stop
- $'Maximum number of atoms exceeded; increase nattot in cbka.blk'
- end if
- irecog=1
- end if
-
- if (qhulp(1:6).eq.'RUTYPE') then !run-type identifiers
- irecrun=0
- read (qhulp,'(7x,a40)',end=46,err=46)qruid
-
- if (qruid(1:10).eq.'NORMAL RUN') then
- iruid=0
- irecrun=1
- end if
-
- if (qruid(1:14).eq.'HIGH PRECISION') then
- endpo=endpo/25
- nmmax=nmmax*5
- qr='D'
- iruid=1
- irecrun=1
- end if
-
- if (qruid(1:13).eq.'LOW PRECISION') then
- nmmax=nmmax/10
- qr='H'
- iruid=1
- irecrun=1
- end if
-
- if (qruid(1:12).eq.'SINGLE POINT') then
- iruid=1
- nmmax=1
- qr='1'
- if (ibity.eq.2) qr='5'
- irecrun=1
- end if
-
- if (qruid(1:11).eq.'NO CELL OPT') then
- iruid=1
- icell=0
- if (ibity.eq.2) qr='Y'
- irecrun=1
- end if
-
- if (qruid(1:8).eq.'CELL OPT') then
- iruid=1
- icell=1
- iexco=0 !Override from VCHANGE
- read (qruid,'(8x,i6)',end=46,err=46)ncellopt
- if (ncellopt.eq.2) icell=2 !cell optimisation during energy minimisation
- if (ncellopt.eq.3) icelo2=4 !c/a optimisation
- if (ncellopt.eq.4) icelo2=1 !only a optimisation
- if (ncellopt.eq.5) icelo2=2 !only b optimisation
- if (ncellopt.eq.6) icelo2=3 !only c optimisation
- if (ncellopt.eq.7) then
- icelo2=4 !c/a optimisation
- icell=2 !cell optimisation during energy minimisation
- end if
- if (ibity.eq.2) qr='F'
- irecrun=1
- end if
-
- if (qruid(1:6).eq.'MAXMOV') then
- iruid=1
- read (qruid,'(6x,i6)',end=46,err=46)nfc
- irecrun=1
- end if
-
- if (qruid(1:4).eq.'REDO') then
- iruid=1
- read (qruid,'(4x,i6)',end=46,err=46)iredo
- irecrun=1
- end if
-
- if (qruid(1:5).eq.'MAXIT') then
- iruid=1
- read (qruid,'(6x,i6)',end=46,err=46)nmmax
- if (qruid(14:18).eq.'ENDPO') then
- read (qruid,'(18x,f6.3)',end=46,err=46)endpo
- end if
- irecrun=1
- end if
- if (qruid(1:5).eq.'ENDPO') then
- iruid=1
- read (qruid,'(6x,f6.3)',end=46,err=46)endpo
- irecrun=1
- end if
-
- if (qruid(1:9).eq.'CHARGEMET') then
- iruid=1
- read (qruid,'(9x,i6)',end=46,err=46)ncha
- irecrun=1
- end if
-
- if (irecrun.eq.0) then
- write (*,*)'Warning: ignored RUTYPE identifier ',qruid(1:12)
- end if
-
- irecog=1
- end if
-
- if (qhulp(1:14).eq.'BOND RESTRAINT') then
- nrestra=nrestra+1
- istart=15
- call stranal(istart,iend,vout,iout,1)
- irstra(nrestra,1)=iout
- istart=iend
- call stranal(istart,iend,vout,iout,1)
- irstra(nrestra,2)=iout
- istart=iend
- call stranal(istart,iend,vout,iout,1)
- rrstra(nrestra)=vout
- istart=iend
- call stranal(istart,iend,vout,iout,1)
- vkrstr(nrestra)=vout
- istart=iend
- call stranal(istart,iend,vout,iout,1)
- vkrst2(nrestra)=vout
- istart=iend
- call stranal(istart,iend,vout,iout,1)
- rrcha(nrestra)=vout
- istart=iend
- call stranal(istart,iend,vout,iout,1)
- itstart(nrestra)=iout
- istart=iend
- call stranal(istart,iend,vout,iout,1)
- itend(nrestra)=iout
- istart=iend
-* read (qhulp,'(15x,2i4,f8.4,f8.2,f8.5,f10.7)',end=46,err=46)
-* $irstra(nrestra,1),irstra(nrestra,2),rrstra(nrestra),
-* $vkrstr(nrestra),vkrst2(nrestra),rrcha(nrestra)
- qr='R'
- irecog=1
- end if
-
- if (qhulp(1:15).eq.'ANGLE RESTRAINT') then
- nrestrav=nrestrav+1
- read (qhulp,'(16x,3i4,2f8.2,f8.4,f9.6)',end=46,err=46)
- $irstrav(nrestrav,1),irstrav(nrestrav,2),irstrav(nrestrav,3),
- $vrstra(nrestrav),vkrv(nrestrav),vkr2v(nrestrav),
- $rvcha(nrestrav)
- qr='V'
- irecog=1
- end if
-
- if (qhulp(1:17).eq.'TORSION RESTRAINT') then
- nrestrat=nrestrat+1
- read (qhulp,'(18x,4i4,2f8.2,f8.4,f9.6)',end=46,err=46)
- $irstrat(nrestrat,1),irstrat(nrestrat,2),irstrat(nrestrat,3),
- $irstrat(nrestrat,4),trstra(nrestrat),vkrt(nrestrat),
- $vkr2t(nrestrat),rtcha(nrestrat)
- qr='T'
- irecog=1
- end if
-
- if (qhulp(1:16).eq.'MASCEN RESTRAINT') then
- nrestram=nrestram+1
- istart=17
- call stranal(istart,iend,vout,iout,1)
- istart=iend
- irstram(nrestram,1)=0
- if (qstrana2.eq.'x') irstram(nrestram,1)=1
- if (qstrana2.eq.'y') irstram(nrestram,1)=2
- if (qstrana2.eq.'z') irstram(nrestram,1)=3
- if (qstrana2.eq.'p') irstram(nrestram,1)=4 !fixed center of mass
- if (irstram(nrestram,1).eq.0)
- $stop 'Error in mass centre restraint'
- call stranal(istart,iend,vout,iout,1)
- istart=iend
- irstram(nrestram,2)=iout
- call stranal(istart,iend,vout,iout,1)
- istart=iend
- irstram(nrestram,3)=iout
- call stranal(istart,iend,vout,iout,1)
- istart=iend
- rmstra1(nrestram)=vout
- call stranal(istart,iend,vout,iout,1)
- istart=iend
- if (irstram(nrestram,1).le.3) irstram(nrestram,4)=iout
- if (irstram(nrestram,1).eq.4) rmstra2(nrestram)=vout
- call stranal(istart,iend,vout,iout,1)
- istart=iend
- if (irstram(nrestram,1).le.3) irstram(nrestram,5)=iout
- if (irstram(nrestram,1).eq.4) rmstra3(nrestram)=vout
- call stranal(istart,iend,vout,iout,1)
- istart=iend
- if (irstram(nrestram,1).le.3) rmstra2(nrestram)=vout
- call stranal(istart,iend,vout,iout,1)
- istart=iend
- if (irstram(nrestram,1).le.3) rmstra3(nrestram)=vout
- call stranal(istart,iend,vout,iout,1)
- istart=iend
- if (irstram(nrestram,1).le.3) rmcha(nrestram)=vout
- irecog=1
- end if
-
- if (qhulp(1:9).eq.'MOLCHARGE') then
- nmcharge=nmcharge+1
- istart=10
- call stranal(istart,iend,vout,iout,1)
- istart=iend
- iat1mc(nmcharge)=iout
- call stranal(istart,iend,vout,iout,1)
- istart=iend
- iat2mc(nmcharge)=iout
- call stranal(istart,iend,vout,iout,1)
- istart=iend
- vmcha(nmcharge)=vout
- irecog=1
- end if
-
- if (qhulp(1:8).eq.'FIXATOMS') then
- istart=9
- call stranal(istart,iend,vout,iout,1)
- if1=iout
- istart=iend
- call stranal(istart,iend,vout,iout,1)
- if2=iout
- do i12=if1,if2
- imove(i12)=0
- end do
- irecog=1
- end if
-
- if (qhulp(1:11).eq.'UNIT ENERGY') then
- eenconv=zero
- read (qhulp,'(14x,a5)',end=46,err=46)quen
- if (quen.eq.'eV') eenconv=23.0408
- if (quen.eq.'EV') eenconv=23.0408
- if (quen.eq.'ev') eenconv=23.0408
- if (quen.eq.'h') eenconv=627.5
- if (quen.eq.'H') eenconv=627.5
- if (quen.eq.'kcal') eenconv=1.0
- if (quen.eq.'kCal') eenconv=1.0
- if (quen.eq.'KCAL') eenconv=1.0
- if (eenconv.eq.zero) then
- write (*,*)quen,': unknown energy unit; assuming kcal/mol'
- eenconv=1.0
- end if
- irecog=1
- end if
-
- if (qhulp(1:6).eq.'ENERGY') then
- read (qhulp(7:80),*,end=46,err=46)enmol
- ienread=1
- irecog=1
- end if
-
- if (qhulp(1:6).eq.'GEOUPD') then
- icgeopt(nprob)=0
- icgeo=0
- irecog=1
- end if
-
- if (qhulp(1:9).eq.'NO GEOUPD') then
- icgeopt(nprob)=1
- icgeo=1
- irecog=1
- end if
-
- if (qhulp(1:9).eq.'FREQUENCY') then
- ifreqset(nprob)=1
- ifreq=1
- irecog=1
- end if
-
-* if (qhulp(1:5).eq.'FORCE') then
-* read (qhulp(6:80),*,end=46,err=46)formol
-* ienread=1
-* irecog=1
-* end if
-
- if (qhulp(1:6).eq.'FFIELD') goto 30
- if (qhulp(1:6).eq.'CONECT') goto 30
- if (qhulp(1:5).eq.'ORDER') goto 30
- if (qhulp(1:1).eq.'#') goto 30
- if (qhulp(1:3).eq.'END') goto 45
-
- if (irecog.eq.0) then
- write (*,*)'Warning: ignored line starting with: ',qhulp(1:10)
- end if
-
- goto 30
-
- 40 write (*,*)'Error on line ',iline+1,' of Biograf-input'
- stop
- 45 read (3,*,err=46,end=46)
- 46 continue
- if (ienread.eq.1) then
- if (eenconv.eq.zero) then
- write (*,*)'No energy unit given; assuming kcal/mol'
- eenconv=1.0
- end if
- enmol=enmol*eenconv !Convert energies to kcal/mol
- end if
-
- namov=0 !calculate number of moving atoms
- do i1=1,na
- if (imove(i1).eq.1) namov=namov+1
- end do
-
- if (imodfile.eq.1) close (3)
- return
- 900 iendf=1
- return
- end
-************************************************************************
-************************************************************************
-
- subroutine readpdb (iendf)
-
-************************************************************************
-#include "cbka.blk"
-#include "cbkc.blk"
-#include "cbkqa.blk"
-#include "control.blk"
-#include "opt.blk"
-#include "small.blk"
-#include "cbksrtbon1.blk"
- character*200 qhulp
-**********************************************************************
-* *
-* Read in .pdb-geometry *
-* *
-**********************************************************************
-c$$$ if (ndebug.eq.1) then
-c$$$C open (65,file='fort.65',status='unknown',access='append')
-c$$$ write (65,*) 'In readpdb'
-c$$$ call timer(65)
-c$$$ close (65)
-c$$$ end if
- iendf=1
- qmol='pdb_in'
- 5 read (3,'(a200)',end=10,err=900) qhulp
- qstrana1(1:200)=qhulp
- istart=1
- call stranal(istart,iend,vout,iout,1)
- istart=iend
-
- if (qstrana2(1:6).eq.'HEADER') then
- call stranal(istart,iend,vout,iout,1)
- istart=iend
- qmol=qstrana2(1:20)
- end if
-
- if (qstrana2(1:6).eq.'HETATM'.or.qstrana2(1:4).eq.'ATOM') then
- call stranal(istart,iend,vout,iout,1)
- istart=iend
- call stranal(istart,iend,vout,iout,1)
- istart=iend
- qa(na+1)=qstrana2(1:2)
- call stranal(istart,iend,vout,iout,1)
- istart=iend
- call stranal(istart,iend,vout,iout,1)
- istart=iend
- call stranal(istart,iend,vout,iout,1)
- istart=iend
- c(na+1,1)=vout
- call stranal(istart,iend,vout,iout,1)
- istart=iend
- c(na+1,2)=vout
- call stranal(istart,iend,vout,iout,1)
- istart=iend
- c(na+1,3)=vout
- na=na+1
- end if
-
- if (qstrana2(1:3).eq.'END'.or.qstrana2(2:4).eq.'END') then
- iendf=0
- goto 10
- end if
-
- goto 5
- 10 continue
- return
- 900 write (*,*)'Error reading in .pdb-format'
- stop 'Error reading in .pdb-format'
- end
-************************************************************************
-************************************************************************
-
- subroutine readtreg
-
-************************************************************************
-#include "cbka.blk"
-#include "cbktregime.blk"
-#include "control.blk"
-#include "small.blk"
- dimension isumattreg(mtreg)
- character*200 qrom
-**********************************************************************
-* *
-* Read in temperature regime *
-* *
-**********************************************************************
-c$$$ if (ndebug.eq.1) then
-c$$$C open (65,file='fort.65',status='unknown',access='append')
-c$$$ write (65,*) 'In readtreg'
-c$$$ call timer(65)
-c$$$ close (65)
-c$$$ end if
- ntrc=0
- open (19,file='tregime.in',status='old',err=60)
- 10 read (19,'(a200)',end=50,err=900)qrom
- qstrana1(1:200)=qrom
- if (qrom(1:1).eq.'#') goto 10
- istart=1
- ntrc=ntrc+1
- if (ntrc.gt.mtreg) then
- write (*,*)'Too many temperature regimes in tregime.in;',
- $' inrease mtreg in cbka.blk'
- stop 'Too many temperature regimes in tregime.in'
- end if
- call stranal(istart,iend,vout,iout,1)
- nittc(ntrc)=iout
- istart=iend
-
- if (ntrc.gt.1) then
- if (nittc(ntrc).lt.nittc(ntrc-1)) then
- ntrc=ntrc-1
- write (*,*)'Warning: wrong order or empty line in tregime.in'
- write (*,*)'Ignored lines below iteration:',nittc(ntrc)
- goto 50
- end if
- end if
-
- call stranal(istart,iend,vout,iout,1)
- nntreg(ntrc)=iout
- if (nntreg(ntrc).gt.mtzone) then
- write (*,*)'Too many temperature zones in tregime.in;',
- $' inrease mtzone in cbka.blk'
- stop 'Too many temperature zones in tregime.in'
- end if
- istart=iend
- isumattreg(ntrc)=0
- do i1=1,nntreg(ntrc)
- call stranal(istart,iend,vout,iout,1)
- ia1treg(ntrc,i1)=iout
- istart=iend
- call stranal(istart,iend,vout,iout,1)
- ia2treg(ntrc,i1)=iout
- istart=iend
- isumattreg(ntrc)=isumattreg(ntrc)+1+ia2treg(ntrc,i1)-
- $ia1treg(ntrc,i1)
- call stranal(istart,iend,vout,iout,1)
- tsettreg(ntrc,i1)=vout
- istart=iend
- call stranal(istart,iend,vout,iout,1)
- tdamptreg(ntrc,i1)=vout
- istart=iend
- call stranal(istart,iend,vout,iout,1)
- dttreg(ntrc,i1)=vout
- istart=iend
- end do
- goto 10
- 50 continue
- close (19)
- 60 continue
-**********************************************************************
-* *
-* Check consistency temperature programs in tregime.in *
-* *
-**********************************************************************
- if (ntrc.gt.0) then
- do i1=1,ntrc
- if (isumattreg(i1).ne.na) then
- write (*,*)'Inconsistency in temperature regime nr.',i1
- write (*,*)'Number of atoms defined in tregime.in:',
- $isumattreg(i1)
- write (*,*)'Number of atoms in system:',na
- stop 'Inconsistency in tregime.in'
- end if
- end do
- end if
-
- return
- 900 stop 'Error reading tregime.in'
- end
-************************************************************************
-************************************************************************
-
- subroutine readvreg
-
-************************************************************************
-#include "cbka.blk"
-#include "cbkc.blk"
-#include "cbkvregime.blk"
-#include "control.blk"
- character*200 qrom
-**********************************************************************
-* *
-* Read in volume regime *
-* *
-**********************************************************************
-c$$$ if (ndebug.eq.1) then
-c$$$C open (65,file='fort.65',status='unknown',access='append')
-c$$$ write (65,*) 'In readvreg'
-c$$$ call timer(65)
-c$$$ close (65)
-c$$$ end if
- nvrc=0
- open (19,file='vregime.in',status='old',err=60)
- 10 read (19,'(a200)',end=50,err=900)qrom
- qstrana1(1:200)=qrom
- if (qrom(1:1).eq.'#') goto 10
- istart=1
- nvrc=nvrc+1
- if (nvrc.gt.mvreg) then
- write (*,*)'Too many volume regimes in vregime.in;',
- $' inrease mvreg in cbka.blk'
- stop 'Too many volume regimes in vregime.in'
- end if
-
- call stranal(istart,iend,vout,iout,1)
- nitvc(nvrc)=iout
- istart=iend
-
- if (nvrc.gt.1) then
- if (nitvc(nvrc).lt.nitvc(nvrc-1)) then
- nvrc=nvrc-1
- write (*,*)'Warning: wrong order or empty line in vregime.in'
- write (*,*)'Ignored lines below iteration:',nitvc(nvrc)
- goto 50
- end if
- end if
-
- call stranal(istart,iend,vout,iout,1)
- nnvreg(nvrc)=iout
- if (nnvreg(nvrc).gt.mvzone) then
- write (*,*)'Too many volume regimes in vregime.in;',
- $' inrease mvzone in cbka.blk'
- stop 'Too many volume zones in vregime.in'
- end if
- istart=iend
- do i1=1,nnvreg(nvrc)
- call stranal(istart,iend,vout,iout,1)
- if (qstrana2(1:1).ne.'a'.and.qstrana2(1:1).ne.'b'.and.
- $qstrana2(1:1).ne.'c'.and.qstrana2(1:4).ne.'alfa'.and.
- $qstrana2(1:4).ne.'beta'.and.qstrana2(1:5).ne.'gamma') then
- write (*,*)qstrana2
- write (*,*)'Invalid cell parameter type in vregime.in ;',
- $' use a,b,c,alfa,beta or gamma'
- stop 'Invalid cell parameter type in vregime.in'
- end if
- qvtype(nvrc,i1)=qstrana2
- istart=iend
- call stranal(istart,iend,vout,iout,1)
- dvvreg(nvrc,i1)=vout
- istart=iend
- call stranal(istart,iend,vout,iout,1)
- ivsca(nvrc,i1)=1
- if (qstrana2(1:1).eq.'n') ivsca(nvrc,i1)=0
- istart=iend
- end do
- goto 10
- 50 continue
- close (19)
- 60 continue
- return
- 900 stop 'Error reading vregime.in'
- end
-************************************************************************
-************************************************************************
-
- subroutine readereg
-
-************************************************************************
-#include "cbka.blk"
-#include "cbkeregime.blk"
-#include "control.blk"
- character*200 qrom
-**********************************************************************
-* *
-* Read in electric field regime *
-* *
-**********************************************************************
-c$$$ if (ndebug.eq.1) then
-c$$$C open (65,file='fort.65',status='unknown',access='append')
-c$$$ write (65,*) 'In readereg'
-c$$$ call timer(65)
-c$$$ close (65)
-c$$$ end if
- nerc=0
- open (19,file='eregime.in',status='old',err=60)
- 10 read (19,'(a200)',end=50,err=900)qrom
- qstrana1(1:200)=qrom
- if (qrom(1:1).eq.'#') goto 10
- istart=1
- nerc=nerc+1
- if (nerc.gt.mereg) then
- write (*,*)'Too many electric field regimes in eregime.in;',
- $' inrease mereg in cbka.blk'
- stop 'Too many electric field regimes in eregime.in'
- end if
- call stranal(istart,iend,vout,iout,1)
- nitec(nerc)=iout
-
- if (nerc.gt.1) then
- if (nitec(nerc).lt.nitec(nerc-1)) then
- nerc=nerc-1
- write (*,*)'Warning: wrong order or empty line in eregime.in'
- write (*,*)'Ignored lines below iteration:',nitec(nerc)
- goto 50
- end if
- end if
-
- istart=iend
- call stranal(istart,iend,vout,iout,1)
- nnereg(nerc)=iout
- if (nnereg(nerc).gt.mezone) then
- write (*,*)'Too many electric field zones in eregime.in;',
- $' inrease mezone in cbka.blk'
- stop 'Too many electric field zones in vregime.in'
- end if
- istart=iend
- do i1=1,nnereg(nerc)
- call stranal(istart,iend,vout,iout,1)
- if (qstrana2(1:1).ne.'x'.and.qstrana2(1:1).ne.'y'.and.
- $qstrana2(1:1).ne.'z') then
- write (*,*)qstrana2
- write (*,*)'Invalid field direction in eregime.in ;',
- $' use x,y or z'
- stop 'Invalid field direction in eregime.in'
- end if
- qetype(nerc,i1)=qstrana2
- istart=iend
- call stranal(istart,iend,vout,iout,1)
- ereg(nerc,i1)=vout
- istart=iend
- end do
- goto 10
- 50 continue
- close (19)
- 60 continue
- return
- 900 stop 'Error reading vregime.in'
- end
-************************************************************************
-************************************************************************
-
- subroutine readaddmol
-
-************************************************************************
-#include "cbka.blk"
-#include "cbkatomcoord.blk"
-#include "cbkc.blk"
-#include "cbkff.blk"
-#include "cbkh.blk"
-#include "control.blk"
- character*80 qromb
- character*200 qhulp
- character*5 qlabhulp
-**********************************************************************
-* *
-* Read in molecule coordinates. This molecule will be added to *
-* the system at regular intervals *
-* Accepts only .bgf-format *
-* *
-**********************************************************************
-c$$$ if (ndebug.eq.1) then
-c$$$C open (65,file='fort.65',status='unknown',access='append')
-c$$$ write (65,*) 'In readaddmol'
-c$$$ call timer(65)
-c$$$ close (65)
-c$$$ end if
-**********************************************************************
-* *
-* Set default values *
-* *
-**********************************************************************
- iaddfreq=-1 !frequency of molecule addition; <0: no addition
- xadd=-9000.0 !x-coordinate for added molecule; <-5000.0: random
- yadd=-9000.0 !y-coordinate for added molecule; <-5000.0: random
- zadd=-9000.0 !z-coordinate for added molecule; <-5000.0: random
- iveladd=1 !1: random initial velocities; 2: read in velocities
- !from addmol.vel
- addist=-1.00 !Minimum distance between added molecule and rest
- !of system. < 0.0: do not check
- nadattempt=10 !Number of attempts at adding the molecule
- taddmol=-1.0 !Temperature added molecule. <0.0: system temperature
- open (19,file='addmol.bgf',status='old',err=60)
- read (19,'(a40)',end=900,err=900)qromb
- if (qromb(1:6).ne.'BIOGRF') then
- write (*,*)'addmol.bgf should start with BIOGRF'
- stop 'addmol.bgf should start with BIOGRF'
- end if
- naa=0
- iline=0
- 30 read (19,'(a200)',end=900,err=900)qhulp
- irecog=0
- iline=iline+1
-
- if (qhulp(1:6).eq.'DESCRP') then
- irecog=1
- end if
-
- if (qhulp(1:6).eq.'FORMAT') then
- irecog=1
- end if
-
- if (qhulp(1:6).eq.'REMARK') then
- irecog=1
- end if
-
- if (qhulp(1:6).eq.'HETATM') then
- irecog=1
- read (qhulp,'(7x,i5,1x,a5,1x,3x,1x,1x,1x,5x,3f10.5)'
- $,end=900,err=900)
- $ir,qlabhulp,cadd(naa+1,1),cadd(naa+1,2),cadd(naa+1,3)
- if (qlabhulp(1:1).eq.' ') qlabhulp=qlabhulp(2:5)
- if (qlabhulp(1:1).eq.' ') qlabhulp=qlabhulp(2:4)
- if (qlabhulp(1:1).eq.' ') qlabhulp=qlabhulp(2:3)
- if (qlabhulp(1:1).eq.'C ') qadd(naa+1)='C '
- if (qlabhulp(1:2).eq.'Ca') qadd(naa+1)='Ca'
- if (qlabhulp(1:2).eq.'Cl') qadd(naa+1)='Cl'
- if (qlabhulp(1:2).eq.'Cu') qadd(naa+1)='Cu'
- if (qlabhulp(1:2).eq.'Co') qadd(naa+1)='Co'
- if (qlabhulp(1:1).eq.'H ') qadd(naa+1)='H '
- if (qlabhulp(1:2).eq.'He') qadd(naa+1)='He'
- if (qlabhulp(1:1).eq.'N ') qadd(naa+1)='N '
- if (qlabhulp(1:2).eq.'Ni') qadd(naa+1)='Ni'
- if (qlabhulp(1:1).eq.'O ') qadd(naa+1)='O '
- if (qlabhulp(1:1).eq.'B ') qadd(naa+1)='B '
- if (qlabhulp(1:1).eq.'F ') qadd(naa+1)='F '
- if (qlabhulp(1:2).eq.'Fe') qadd(naa+1)='Fe'
- if (qlabhulp(1:1).eq.'P ') qadd(naa+1)='P '
- if (qlabhulp(1:1).eq.'S ') qadd(naa+1)='S '
- if (qlabhulp(1:1).eq.'Y ') qadd(naa+1)='Y '
- if (qlabhulp(1:2).eq.'Al') qadd(naa+1)='Al'
- if (qlabhulp(1:2).eq.'Au') qadd(naa+1)='Au'
- if (qlabhulp(1:2).eq.'Si') qadd(naa+1)='Si'
- if (qlabhulp(1:2).eq.'Pt') qadd(naa+1)='Pt'
- if (qlabhulp(1:2).eq.'Mo') qadd(naa+1)='Mo'
- if (qlabhulp(1:2).eq.'Mg') qadd(naa+1)='Mg'
- if (qlabhulp(1:2).eq.'Ar') qadd(naa+1)='Ar'
- if (qlabhulp(1:2).eq.'Zr') qadd(naa+1)='Zr'
- if (qlabhulp(1:2).eq.'Ba') qadd(naa+1)='Ba'
- if (qlabhulp(1:2).eq.'X ') qadd(naa+1)='X '
- ityadd(naa+1)=0
- do i1=1,nso !Find force field type
- if (qadd(naa+1).eq.qas(i1)) ityadd(naa+1)=i1
- end do
- if (ityadd(naa+1).eq.0) then
- write (*,*) 'Unknown atom type:',qadd(naa+1)
- stop 'Unknown atom type'
- end if
- naa=naa+1
- end if
-
- if (qhulp(1:7).eq.'FREQADD') then
- irecog=1
- read (qhulp,'(8x,i6)',end=900,err=900) iaddfreq
- end if
-
- if (qhulp(1:6).eq.'VELADD') then
- irecog=1
- read (qhulp,'(8x,i6)',end=900,err=900) iveladd
- end if
-
- if (qhulp(1:6).eq.'STARTX') then
- irecog=1
- read (qhulp,'(7x,f8.2)',end=900,err=900) xadd
- end if
-
- if (qhulp(1:6).eq.'STARTY') then
- irecog=1
- read (qhulp,'(7x,f8.2)',end=900,err=900) yadd
- end if
-
- if (qhulp(1:6).eq.'STARTZ') then
- irecog=1
- read (qhulp,'(7x,f8.2)',end=900,err=900) zadd
- end if
-
- if (qhulp(1:6).eq.'ADDIST') then
- irecog=1
- read (qhulp,'(7x,f8.2)',end=900,err=900) addist
- end if
-
- if (qhulp(1:8).eq.'NATTEMPT') then
- irecog=1
- read (qhulp,'(9x,i6)',end=900,err=900) nadattempt
- end if
-
- if (qhulp(1:7).eq.'TADDMOL') then
- irecog=1
- read (qhulp,'(8x,f8.2)',end=900,err=900) taddmol
- end if
-
- if (qhulp(1:6).eq.'FFIELD') goto 30
- if (qhulp(1:6).eq.'CONECT') goto 30
- if (qhulp(1:5).eq.'ORDER') goto 30
- if (qhulp(1:1).eq.'#') goto 30
- if (qhulp(1:3).eq.'END') goto 45
-
- if (irecog.eq.0) then
- write (*,*)'Warning: ignored line starting with: ',qhulp(1:10)
- end if
-
- goto 30
-
- 45 continue
- close (19)
- if (iveladd.eq.2) then
- open (19,file='addmol.vel',status='old',err=800)
- read (19,*)
- read (19,'(3d24.15)',err=850,end=850)
- $((veladd(j,i),j=1,3),i=1,naa)
- close (19)
- end if
-************************************************************************
-* *
-* Place molecule at origin *
-* *
-************************************************************************
- ccx=0.0
- ccy=0.0
- ccz=0.0
- do i1=1,naa
- ccx=ccx+cadd(i1,1)/float(naa)
- ccy=ccy+cadd(i1,2)/float(naa)
- ccz=ccz+cadd(i1,3)/float(naa)
- end do
- do i1=1,naa
- cadd(i1,1)=cadd(i1,1)-ccx
- cadd(i1,2)=cadd(i1,2)-ccy
- cadd(i1,3)=cadd(i1,3)-ccz
- end do
-
- 60 continue
- return
- 800 stop 'Error opening addmol.vel'
- 850 stop 'Error or end of file reading addmol.vel'
- 900 write (*,*)'Error or end-of-file reading addmol.bgf on line:',
- $iline
- return
- end
-************************************************************************
-**********************************************************************
-
- subroutine writegeo(nunit1)
-
-**********************************************************************
-#include "cbka.blk"
-#include "cbkc.blk"
-#include "cbkconst.blk"
-#include "cbkqa.blk"
-#include "cbkrestr.blk"
-#include "cbktregime.blk"
-#include "cellcoord.blk"
-#include "control.blk"
-#include "opt.blk"
-#include "small.blk"
-#include "cbksrtbon1.blk"
-#include "cbkinit.blk"
-**********************************************************************
-* *
-* Copy new geometries to unit nunit1 *
-* *
-**********************************************************************
-c$$$ if (ndebug.eq.1) then
-c$$$C open (65,file='fort.65',status='unknown',access='append')
-c$$$ write (65,*) 'In writegeo'
-c$$$ call timer(65)
-c$$$ close (65)
-c$$$ end if
- if (axiss(1).lt.zero) then
- if (nrestra.eq.0.and.nrestrat.eq.0.and.
- $nrestrav.eq.0)
- $write (nunit1,300)qr,qmol
- if (nrestra.gt.0) write (nunit1,301)qr,
- $rrstra(1),qmol
- if (nrestrav.gt.0) write (nunit1,301)qr,
- $vrstra(1),qmol
- if (nrestrat.gt.0) write (nunit1,301)qr,
- $trstra(1),qmol
- else
- write (nunit1,310)qr,qmol
- write (nunit1,320)axiss(1),axiss(2),axiss(3)
- write (nunit1,320)angles(1),angles(2),angles(3)
- end if
- do i1=1,na
- if (nbiolab.ne.1) write (nunit1,400)i1,qa(i1),(c(i1,i2),i2=1,3)
- if (nbiolab.eq.1) write (nunit1,401)i1,qa(i1),(c(i1,i2),i2=1,3) !Delphi-format
- end do
- if (nbiolab.ne.1) write (nunit1,*)
-
- return
-
- 300 format (2x,a1,1x,a60)
- 301 format (2x,a1,1x,f6.2,a60)
- 310 format (2x,a1,1x,a60)
- 320 format (3f10.4)
- 400 format (i4,1x,a2,3x,3(d21.14,1x),1x,a5,1x,i5)
- 401 format (i3,2x,a2,3x,3(d21.14,1x),1x,a5,1x,i5)
- end
-**********************************************************************
-**********************************************************************
-
- subroutine writebgf(nunit1)
-
-**********************************************************************
-#include "cbka.blk"
-#include "cbkc.blk"
-#include "cbkcha.blk"
-#include "cbkcharmol.blk"
-#include "cbkconst.blk"
-#include "cbkenergies.blk"
-#include "cbkia.blk"
-#include "cbkimove.blk"
-#include "cbkinit.blk"
-#include "cbkqa.blk"
-#include "cbkrestr.blk"
-#include "cbktregime.blk"
-#include "cellcoord.blk"
-#include "control.blk"
-#include "opt.blk"
-#include "cbksrtbon1.blk"
-#include "small.blk"
-
- dimension qdir(3)
- character*2 qt
- character*1 qdir
-**********************************************************************
-* *
-* Copy new Biograf-geometries to unit nunit1 *
-* *
-**********************************************************************
-c$$$ if (ndebug.eq.1) then
-c$$$C open (65,file='fort.65',status='unknown',access='append')
-c$$$ write (65,*) 'In newbgf'
-c$$$ call timer(65)
-c$$$ close (65)
-c$$$ end if
- irom=1
- qdir(1)='x'
- qdir(2)='y'
- qdir(3)='z'
- ibgfversion=200
- if (ibity.eq.1) write (nunit1,1500)ibgfversion
- if (ibity.eq.2) write (nunit1,1600)ibgfversion
-* if (qr.ne.'F'.and.qr.ne.'5'.and.qr.ne.'Y')
-* $write (nunit1,1500)ibgfversion
-* if (qr.eq.'F'.or.qr.eq.'5'.or.qr.eq.'Y')
-* $write (nunit1,1600)ibgfversion
- write (nunit1,1700)qmol
-* write (nunit1,1700)qkeyw(nprob)
- do i1=1,iremark
- write (nunit1,1800)qremark(i1)
- end do
- qruid='NORMAL RUN'
- if (iruid.eq.0) then
- write (nunit1,2000)
- else
- if (abs(endpo-endpoold).gt.1e-5) write (nunit1,2010)endpo
- if (nmmax.ne.nmmaxold) write (nunit1,2020)nmmax
- if (nfc.ne.nfcold) write (nunit1,2030)nfc
- if (ncha.ne.nchaold) write (nunit1,2036)ncha
- if (iredo.gt.1) write (nunit1,2035)iredo
- if (icell.ne.icellold) then
- if (icell.eq.0) write (nunit1,2033)
- if (icell.gt.0) write (nunit1,2034)ncellopt
- end if
- end if
- if (iexco.ne.0.and.nsurp.gt.0) then
- write (nunit1,2040)vvol
- write (nunit1,3500)
- write (nunit1,*)
- return
- end if
- if (nmcharge.gt.0) then
- do i3=1,nmcharge
- write (nunit1,2050)iat1mc(i3),iat2mc(i3),vmcha(i3)
- end do
- end if
-
- ims=0
- do i1=1,na
- if (ims.eq.0.and.imove(i1).eq.0) then
- if1=i1
- ims=1
- end if
- if (ims.eq.1.and.imove(i1).eq.1) then
- write (nunit1,2060)if1,i1-1
- ims=0
- end if
- end do
- if (ims.eq.1) then
- write (nunit1,2060)if1,na
- end if
-
-* if (qr.eq.'F'.or.qr.eq.'5'.or.qr.eq.'Y')
- if (ibity.eq.2)
- $write (nunit1,2100)axiss(1),axiss(2),axiss(3),angles(1),
- $angles(2),angles(3)
-
- if (nrestra.gt.0) write (nunit1,2300)
- do i2=1,nrestra
- write (nunit1,2400)
- $irstra(i2,1),irstra(i2,2),rrstra(i2),
- $vkrstr(i2),vkrst2(i2),rrcha(i2),itstart(i2),itend(i2)
- end do
-
- if (nrestrav.gt.0) write (nunit1,2500)
- do i2=1,nrestrav
- write (nunit1,2600)
- $irstrav(i2,1),irstrav(i2,2),irstrav(i2,3),
- $vrstra(i2),vkrv(i2),vkr2v(i2),zero
- end do
-
- if (nrestrat.gt.0) write (nunit1,2700)
- do i2=1,nrestrat
- write (nunit1,2800)
- $irstrat(i2,1),irstrat(i2,2),irstrat(i2,3),
- $irstrat(i2,4),trstra(i2),vkrt(i2),
- $vkr2t(i2),zero
- end do
-
- if (nrestram.gt.0) write (nunit1,2810)
- do i2=1,nrestram
- write (nunit1,2820)
- $qdir(irstram(i2,1)),irstram(i2,2),irstram(i2,3),
- $rmstra1(i2),irstram(i2,4),irstram(i2,5),rmstra2(i2),
- $rmstra3(i2),rmcha(i2)
- end do
-
- if (icgeo.eq.0.and.ingeo.eq.0) write (nunit1,2830)
- if (icgeo.eq.1.and.ingeo.eq.1) write (nunit1,2840)
- if (ifreq.eq.1) write (nunit1,2850)
- write (nunit1,2900)
- do i2=1,na
- write (nunit1,3000)i2,qa(i2),c(i2,1),c(i2,2),c(i2,3),
- $qa(i2),irom,irom,chgbgf(i2)
- end do
- write (nunit1,3100)
- if (nsurp.lt.2) then
- do i1=1,na
- write (nunit1,3200)i1,(iag(i1,2+i2),i2=1,iag(i1,2))
- end do
- write (nunit1,3300)
- write (nunit1,3400)estrc
- end if
-
- write (nunit1,3500)
- write (nunit1,*)
-
- return
- 1500 format ('BIOGRF',i4)
- 1600 format ('XTLGRF',i4)
- 1700 format ('DESCRP ',a60)
- 1800 format ('REMARK ',a60)
- 1900 format ('FFIELD ',a40)
- 2000 format ('RUTYPE NORMAL RUN')
- 2010 format ('RUTYPE ENDPO',f6.3)
- 2020 format ('RUTYPE MAXIT',i6)
- 2030 format ('RUTYPE MAXMOV',i6)
- 2033 format ('RUTYPE NO CELL OPT')
- 2034 format ('RUTYPE CELL OPT',i6)
- 2035 format ('RUTYPE REDO',i6)
- 2036 format ('RUTYPE CHARGEMET',i6)
- 2040 format ('VCHANGE',f8.4)
- 2050 format ('MOLCHARGE',2i4,f6.2)
- 2060 format ('FIXATOMS',2i6)
- 2100 format ('CRYSTX ',6f11.5)
- 2200 format ('CELLS ',6i5)
- 2300 format ('# At1 At2 R12 Force1 Force2 ',
- $'dR12/dIter(MD) Start (MD) End (MD)')
- 2400 format ('BOND RESTRAINT ',2i4,f8.4,f8.2,f8.4,1x,f10.7,2i8)
- 2500 format ('# At1 At2 At3 Angle Force1 Force2',
- $' dAngle/dIteration (MD only)')
- 2600 format ('ANGLE RESTRAINT ',3i4,2f8.2,f8.4,f9.6)
- 2700 format ('# At1 At2 At3 At3 Angle Force1 ',
- $'Force2 dAngle/dIteration (MD only)')
- 2800 format ('TORSION RESTRAINT ',4i4,2f8.2,f8.4,f9.6)
- 2810 format ('# x/y/z At1 At2 R At3 At4 Force1',
- $' Force2 dR/dIteration (MD only)')
- 2820 format ('MASCEN RESTRAINT ',a1,1x,2i4,f8.2,2i4,2f8.2,f9.6)
- 2830 format ('GEOUPD')
- 2840 format ('NO GEOUPD')
- 2850 format ('FREQUENCY')
- 2900 format ('FORMAT ATOM (a6,1x,i5,1x,a5,1x,a3,1x,a1,1x,a5,',
- $'3f10.5,1x,a5,i3,i2,1x,f8.5)')
- 3000 format ('HETATM',1x,i5,1x,a2,3x,1x,3x,1x,1x,1x,5x,3f10.5,1x,
- $a5,i3,i2,1x,f8.5)
- 3100 format ('FORMAT CONECT (a6,12i6)')
- 3200 format ('CONECT',12i6)
- 3300 format ('UNIT ENERGY kcal')
- 3400 format ('ENERGY',5x,f14.6)
- 3500 format ('END')
-
- end
-**********************************************************************
-**********************************************************************
-
- subroutine writeen(tottime,sum1,sdev,sdeva,sum12,sumt,sump,
- $sumtt,tmax,eaver,eav2,eav3,etot2,ediff)
-**********************************************************************
-#include "cbka.blk"
-#include "cbkcha.blk"
-#include "cbkenergies.blk"
-#include "cbkrestr.blk"
-#include "cbktorang.blk"
-#include "cbktorsion.blk"
-#include "cbktregime.blk"
-#include "control.blk"
-#include "small.blk"
-
- dimension disres(mrestra)
-**********************************************************************
-* *
-* Write out MD statistics to units 71,73 and 76 *
-* *
-**********************************************************************
-c$$$ if (ndebug.eq.1) then
-c$$$C open (65,file='fort.65',status='unknown',access='append')
-c$$$ write (65,*) 'In writeen'
-c$$$ call timer(65)
-c$$$ close (65)
-c$$$ end if
-
- if (nrep1.gt.1)
- $sdev=sqrt((sum12-sum1*sum1/float(nrep1))/float(nrep1-1))
- eavn=eaver/float(mdstep)
- if (mdstep.gt.1)
- $sdeva=sqrt((eav3-eav2*eav2/float(mdstep))/float(mdstep-1))
-C open (71,file='fort.71',status='unknown',access='append')
-C open (73,file='fort.73',status='unknown',access='append')
- write (71,'(i8,2i4,1x,19(f10.2,1x))')mdstep+nprevrun,nmolo,
- $nmolo5,estrc,ekin,estrc+ekin,tempmd,sum1/float(nrep1),eavn,
- $sumt/float(nrep1),tmax,sump/float(nrep1),sdev,sdeva,tset,
- $tstep*1d+15,rmsg,tottime
- write (73,'(i8,1x,14(f10.2,1x))')mdstep+nprevrun,eb,ea,elp,
- $emol,ev,ecoa,ehb,et,eco,ew,ep,ech,efi
- close (71)
- close (73)
-
- if ((sumt/float(nrep1)).gt.tset) then
- if (invt.eq.0) write (*,*)'Switched to NVT in iteration',mdstep
- invt=1
- end if
-
-C if (nrestra.gt.0.or.nrestrat.gt.0)
-C $open (76,file='fort.76',status='unknown',access='append')
-
- if (nrestra.gt.0) then
- do i2=1,nrestra
- call dista2(irstra(i2,1),irstra(i2,2),disres(i2),dx,dy,dz)
- end do
-C open (76,file='fort.76',status='unknown',access='append')
- write (76,'(i8,1x,40f12.4)')mdstep,eres,estrc,
- $(rrstra(i2),disres(i2),i2=1,nrestra)
- end if
-
- if (nrestrat.gt.0) then
-C open (76,file='fort.76',status='unknown',access='append')
- do i2=1,nrestrat
- do i3=1,ntor
- ih1=irstrat(i2,1)
- ih2=irstrat(i2,2)
- ih3=irstrat(i2,3)
- ih4=irstrat(i2,4)
- if (ih1.eq.it(i3,2).and.ih2.eq.it(i3,3).and.ih3.eq.it(i3,4)
- $.and.ih4.eq.it(i3,5)) ittr=i3
- end do
- write (76,'(i8,1x,40f12.4)')mdstep,eres,
- $trstra(i2),thg(ittr)
- end do
- end if
-
- if (nrestra.gt.0.or.nrestrat.gt.0) close(76)
-
- if (nrestram.gt.0) then
-C open (76,file='fort.76',status='unknown',access='append')
- do i2=1,nrestram
- write (76,'(2i8,1x,20f12.4)')mdstep,i2,eres,rmstra1(i2),
- $dismacen(i2)
- end do
- close (76)
- end if
-
- return
- end
-**********************************************************************
-************************************************************************
-
- subroutine molanal
-
-************************************************************************
-#include "cbka.blk"
-#include "cbkbo.blk"
-#include "cbkconst.blk"
-#include "cbkdcell.blk"
-#include "cbkff.blk"
-#include "cbkia.blk"
-#include "cbkrbo.blk"
-#include "control.blk"
-#include "opt.blk"
-#include "small.blk"
-#include "cbksrtbon1.blk"
- dimension iam(nat,mbond+3),nmolata(nmolmax,nat)
- dimension molfra(nmolmax,nsort),ndup(nmolmax)
- character*40 qmolan1
- character*100 qmolan
- logical found
-************************************************************************
-* *
-* Analyse and output molecular fragments *
-* *
-************************************************************************
-c$$$ if (ndebug.eq.1) then
-c$$$C open (65,file='fort.65',status='unknown',access='append')
-c$$$ write (65,*) 'In molanal'
-c$$$ call timer(65)
-c$$$ close (65)
-c$$$ end if
-
- do i1=1,nmolmax
- do i2=1,nsort
- molfra(i1,i2)=0
- end do
- ndup(i1)=1
- end do
-
- do i1=1,na
- do i2=1,mbond+3
- iam(i1,i2)=0
- end do
- end do
-************************************************************************
-* *
-* Create connection table based on corrected bond orders *
-* *
-************************************************************************
- do i1=1,nbon
- if (bo(i1).gt.cutof3) then
- j1=ib(i1,2)
- j2=ib(i1,3)
- iam(j1,2)=iam(j1,2)+1
- iam(j1,2+iam(j1,2))=j2
- iam(j2,2)=iam(j2,2)+1
- iam(j2,2+iam(j2,2))=j1
- end if
- end do
-**********************************************************************
-* *
-* Find molecules *
-* *
-**********************************************************************
- nmolo6=0
- found=.FALSE.
- DO 61 k1=1,na
- IF (iam(K1,3+mbond).EQ.0) found=.TRUE.
- 61 IF (iam(K1,3+mbond).GT.nmolo6) nmolo6=iam(K1,3+mbond)
- IF (.NOT.FOUND) GOTO 62
-************************************************************************
-* *
-* Molecule numbers are assigned. No restrictions are made for the *
-* sequence of the numbers in the connection table. *
-* *
-************************************************************************
- N3=1
- 64 N2=N3
- nmolo6=nmolo6+1
- if (nmolo6.gt.nmolmax) stop 'Too many molecules in system'
- iam(N2,3+mbond)=nmolo6
- 67 FOUND=.FALSE.
- DO 66 N1=N2+1,na
- IF (iam(N1,3+mbond).NE.0) GOTO 66
- DO 65 L=1,mbond
- IF (iam(N1,l+2).EQ.0) GOTO 66
- IF (iam(iam(N1,l+2),3+mbond).EQ.nmolo6) THEN
- FOUND=.TRUE.
- iam(N1,3+mbond)=nmolo6
- GOTO 66
- ENDIF
- 65 CONTINUE
- 66 CONTINUE
- IF (FOUND) GOTO 67
- DO 63 N3=N2+1,NA
- 63 if (iam(N3,3+mbond).eq.0) goto 64
-************************************************************************
-* *
-* The assigned or input molecule numbers are checked for their *
-* consistency. *
-* *
-************************************************************************
- 62 FOUND=.FALSE.
- DO 72 N1=1,NA
- DO 71 L=1,mbond
- IF (iam(N1,L+2).EQ.0) GOTO 72
- IF (iam(iam(N1,L+2),3+mbond).NE.iam(N1,3+mbond)) THEN
- FOUND=.TRUE.
- ENDIF
- 71 CONTINUE
- 72 CONTINUE
- IF (FOUND) THEN
- write (7,'(i4,a40)')na,qmol
- do i1=1,na
- write (7,'(40i4)')i1,iam(i1,1),(iam(i1,2+i2),i2=1,nsbmax),
- $iam(i1,3+mbond)
- end do
- STOP' Mol.nrs. not consistent; maybe wrong cell parameters'
- ENDIF
-
- do i1=1,nmolo6
- natmol=0
- do i2=1,na
- if (iam(i2,3+mbond).eq.i1) then
- natmol=natmol+1
- nmolata(i1,natmol+1)=i2
- end if
- end do
- nmolata(i1,1)=natmol
- end do
-************************************************************************
-* *
-* Analyze molecules *
-* *
-************************************************************************
- do i1=1,nmolo6
- do i2=1,nmolata(i1,1)
- i3=nmolata(i1,1+i2)
- ityp=ia(i3,1)
- molfra(i1,ityp)=molfra(i1,ityp)+1
- end do
- end do
-
- do i1=1,nmolo6
- isee=0
- do i2=1,nmolo6
- isee2=1
- do i3=1,nso
- if (molfra(i1,i3).ne.molfra(i2,i3)) isee2=0
- end do
- if (isee2.eq.1.and.i1.gt.i2.and.isee.eq.0) then !molecule type already exists
- ndup(i2)=ndup(i2)+1
- ndup(i1)=0
- isee=1
- end if
-
- end do
- end do
-
-C open (45,file='molfra.out',status='unknown',access='append')
- if (mdstep.eq.0) write (45,100)cutof3
- write (45,110)
- ntotmol=0
- ntotat=0
- vtotmass=zero
- do i1=1,nmolo6
- if (ndup(i1).gt.0) then
-* write (45,110)i1,(molfra(i1,i2),i2=1,nso),ndup(i1)
- ntotmol=ntotmol+ndup(i1)
- qmolan=' '
- qmolan1=' '
- istart=-4
- ihulp=0
- vmass=zero
- do i2=1,nso
- vmass=vmass+molfra(i1,i2)*amas(i2)
- ntotat=ntotat+molfra(i1,i2)*ndup(i1)
- if (molfra(i1,i2).gt.0) then
- istart=istart+6
- iend=istart+5
- if (molfra(i1,i2).gt.1) then
- write (qmolan(istart:iend),'(a2,i3)')qas(i2),molfra(i1,i2)
- else
- write (qmolan(istart:iend-2),'(a2)')qas(i2)
- end if
- end if
- end do
- ihulp=1
- do i2=1,iend
- if (qmolan(i2:i2).ne.' ') then
- qmolan1(ihulp:ihulp)=qmolan(i2:i2)
- ihulp=ihulp+1
- end if
- end do
-
-* write (45,120)ndup(i1),qmolan(1:iend),vmass
- write (45,120)mdstep,ndup(i1),qmolan1,vmass
- vtotmass=vtotmass+ndup(i1)*vmass
- end if
- end do
- write (45,*)'Total number of molecules:',ntotmol
- write (45,*)'Total number of atoms:',ntotat
- write (45,*)'Total system mass:',vtotmass
- close (45)
- return
- 100 format('Bond order cutoff:',f6.4)
- 110 format('Iteration Freq. Molecular formula',15x,'Molecular mass')
- 120 format(i8,i4,' x ',a35,f10.4)
- end
-************************************************************************
-************************************************************************
-
- subroutine stranal(istart,iend,vout,iout,icheck)
-
-************************************************************************
-#include "cbka.blk"
-#include "cbkconst.blk"
-#include "opt.blk"
-
- character*1 qchar
- dimension qchar(5)
-**********************************************************************
-* *
-* Analyze string for special characters; find words in string *
-* *
-**********************************************************************
- qchar(1)=' '
- qchar(2)='/'
-
- ifound1=0
- do i1=istart,200
- ifound2=0
- do i2=1,icheck
-
- if (qstrana1(i1:i1).eq.qchar(i2)) then
- ifound2=1
- if (ifound1.eq.1) then !End of word
- iend=i1
- goto 10
- end if
-
- end if
-
- end do
-
- if (ifound2.eq.0.and.ifound1.eq.0) then !Start of word
- istart2=i1
- ifound1=1
- end if
-
- end do
-
- 10 continue
- qstrana2=' '
- vout=zero
- iout=0
-
- if (ifound1.eq.1) then
- qstrana2=qstrana1(istart2:iend-1)
- istart=istart2
- vout=zero
- read (qstrana2,*,end=20,err=20) vout
- 20 iout=int(vout)
- end if
-
- return
- end
-************************************************************************
-**********************************************************************
-
- subroutine dipmom(naold,dpmm,xdip,ydip,zdip,xdir,ydir,zdir)
-
-**********************************************************************
-#include "cbka.blk"
-#include "cbkc.blk"
-#include "cbkch.blk"
-#include "cbkconst.blk"
-#include "control.blk"
-#include "small.blk"
-**********************************************************************
-* *
-* Calculate and output dipole moment *
-* *
-**********************************************************************
-c$$$ if (ndebug.eq.1) then
-c$$$C open (65,file='fort.65',status='unknown',access='append')
-c$$$ write (65,*) 'In dipmom'
-c$$$ call timer(65)
-c$$$ close (65)
-c$$$ end if
-************************************************************************
-* *
-* CONVERSION FACTOR TO DEBYE UNITS IS CALCULATED *
-* THE CALCULATION IS INITIALIZED *
-* *
-************************************************************************
-
- ELCHG=1.60217733D-19 ! [C] = [As]
- CLIGHT=2.99792458D8 ! [m/s]
- DBCONV=ONE/(CLIGHT*ELCHG*1.0D11)
-
- CHCPX=ZERO
- CHCPY=ZERO
- CHCPZ=ZERO
- CHCMX=ZERO
- CHCMY=ZERO
- CHCMZ=ZERO
- XDIP=ZERO
- YDIP=ZERO
- ZDIP=ZERO
- XGRD=ZERO
- YGRD=ZERO
- ZGRD=ZERO
-************************************************************************
-* *
-* CALCULATION OF MAGNITUDE AND CENTRES OF POSITIVE AND NEGATIVE *
-* CHARGES *
-* *
-************************************************************************
-
- if (na.eq.0) na=naold
- CHRG=ZERO
- DO 4 K1=1,NA
- CHK1=CH(K1)
- IF (CHK1.EQ.ZERO) GOTO 4
- IF (CHK1.LT.ZERO) GOTO 3
- CHRG=CHRG+CHK1
- CHCPX=CHCPX+CHK1*C(K1,1)
- CHCPY=CHCPY+CHK1*C(K1,2)
- CHCPZ=CHCPZ+CHK1*C(K1,3)
- GOTO 4
- 3 CHCMX=CHCMX-CHK1*C(K1,1)
- CHCMY=CHCMY-CHK1*C(K1,2)
- CHCMZ=CHCMZ-CHK1*C(K1,3)
- 4 CONTINUE
-
-************************************************************************
-* *
-* CALCULATION OF DISTANCE BETWEEN CENTRES AND OF DIPOLE MOMENT *
-* IN DEBIJE UNITS *
-* *
-************************************************************************
-
- CHDSTX=CHCPX-CHCMX
- CHDSTY=CHCPY-CHCMY
- CHDSTZ=CHCPZ-CHCMZ
- DPMM=SQRT(CHDSTX*CHDSTX+CHDSTY*CHDSTY+CHDSTZ*CHDSTZ)/DBCONV
- IF(DPMM.LT.1.0D-4)RETURN
- XDIP=HALF*(CHCPX+CHCMX)/CHRG
- YDIP=HALF*(CHCPY+CHCMY)/CHRG
- ZDIP=HALF*(CHCPZ+CHCMZ)/CHRG
- GRTST=MAX(CHDSTX,CHDSTY,CHDSTZ)
- XDIR=-CHDSTX/GRTST
- YDIR=-CHDSTY/GRTST
- ZDIR=-CHDSTZ/GRTST
- open (64,file='dipole.out',status='unknown')
- write (64,100)dpmm,xdip,ydip,zdip,xdir,ydir,zdir
- close (64)
-
- 100 format ('Dipole moment (Debye):',f12.4,' Location:',3f12.4,
- $' Direction (-side):',3f12.4)
- return
- end
-************************************************************************
-**********************************************************************
-
- subroutine readtraj(ivels)
-
-**********************************************************************
-#include "cbka.blk"
-#include "cbkatomcoord.blk"
-#include "cbkc.blk"
-#include "cbkconst.blk"
-#include "cbkdistan.blk"
-#include "cbktregime.blk"
-#include "cellcoord.blk"
-#include "control.blk"
-#include "small.blk"
-#include "cbkinit.blk"
-**********************************************************************
-* *
-* Read in trajectory file *
-* *
-**********************************************************************
-c$$$ if (ndebug.eq.1) then
-c$$$C open (65,file='fort.65',status='unknown',access='append')
-c$$$ write (65,*) 'In readtraj'
-c$$$ call timer(65)
-c$$$ close (65)
-c$$$ end if
-
- open(unit=66,file='moldyn.vel',status='old',err=10)
- ivels=1
- read (66,*)
- read (66,100)aaxis,baxis,caxis
- read (66,100)angles(1),angles(2),angles(3)
- if (qr.eq.'F'.or.qr.eq.'P'.or.ngeofor.eq.1) then
- axis(1)=aaxis
- axis(2)=baxis
- axis(3)=caxis
- axiss(1)=axis(1)
- axiss(2)=axis(2)
- axiss(3)=axis(3)
- angle(1)=angles(1)
- angle(2)=angles(2)
- angle(3)=angles(3)
- halfa=angle(1)*dgrrdn
- hbeta=angle(2)*dgrrdn
- hgamma=angle(3)*dgrrdn
- sinalf=sin(halfa)
- cosalf=cos(halfa)
- sinbet=sin(hbeta)
- cosbet=cos(hbeta)
- cosphi=(cos(hgamma)-cosalf*cosbet)/(sinalf*sinbet)
- if (cosphi.gt.1.0) cosphi=1.0
- sinphi=sqrt(one-cosphi*cosphi)
- tm11=axis(1)*sinbet*sinphi
- tm21=axis(1)*sinbet*cosphi
- tm31=axis(1)*cosbet
- tm22=axis(2)*sinalf
- tm32=axis(2)*cosalf
- tm33=axis(3)
- end if
- if (aaxis.ne.axis(1).or.baxis.ne.axis(2).or.caxis.ne.axis(3))
- $stop 'Wrong cell parameters in moldyn.vel'
- read (66,200)nan
- if (nan.ne.na) stop 'Wrong number of atoms in moldyn.vel-file'
- if (nbiolab.eq.1) write (*,*)'Warning: using labels in vels-file'
- read (66,250)((c(i,j),j=1,3),qlabel(i),i=1,na)
- read (66,*)
- read (66,300)((vel(j,i),j=1,3),i=1,na)
- read (66,*)
- read (66,300)((accel(j,i),j=1,3),i=1,na)
- read (66,*)
- read (66,300,end=10,err=10)((aold(j,i),j=1,3),i=1,na)
- read (66,*)
- read (66,300,end=10,err=10)tempmd
- read (66,*)
- read (66,350,end=10,err=10)nsbma2
- 10 continue
-**********************************************************************
-* *
-* Format part *
-* *
-**********************************************************************
- 100 format(3d15.8)
- 200 format(i4)
- 250 format(3d24.15,1x,a5)
- 300 format(3d24.15)
- 350 format(i3)
- 400 format (8i3,8f8.4)
- return
- end
-**********************************************************************
diff --git a/lib/reax/reax_lammps.F b/lib/reax/reax_lammps.F
deleted file mode 100644
index 116e88827db47e697ba72b507c9c5c2dfbb801fd..0000000000000000000000000000000000000000
--- a/lib/reax/reax_lammps.F
+++ /dev/null
@@ -1,392 +0,0 @@
-**********************************************************************
-* *
-* REAXFF Reactive force field program *
-* *
-* Developed and written by Adri van Duin, duin@wag.caltech.edu *
-* *
-* Copyright (c) 2001-2010 California Institute of Technology *
-* *
-* This is an open-source program. Feel free to modify its *
-* contents. Please keep me informed of any useful modification *
-* or addition that you made. Please do not distribute this *
-* program to others; if people are interested in obtaining *
-* a copy of this program let them contact me first. *
-* *
-**********************************************************************
-**********************************************************************
-
- subroutine getswb(swb_tmp)
-
-**********************************************************************
-#include "cbka.blk"
-#include "cbkff.blk"
- real*8 swb_tmp
-
-**********************************************************************
-* *
-* Report the value of swb *
-* *
-**********************************************************************
-
- swb_tmp = swb
-
- return
- end
-
-**********************************************************************
-
- subroutine getswa(swa_tmp)
-
-**********************************************************************
-#include "cbka.blk"
-#include "cbkff.blk"
- real*8 swa_tmp
-
-**********************************************************************
-* *
-* Report the value of swa *
-* *
-**********************************************************************
-
- swa_tmp = swa
-
- return
- end
-
-**********************************************************************
-
- subroutine getvrange(vrange_tmp)
-
-**********************************************************************
-#include "cbka.blk"
-#include "control.blk"
- real*8 vrange_tmp
-
-**********************************************************************
-* *
-* Report the value of vrange *
-* *
-**********************************************************************
-
- vrange_tmp = vrange
-
- return
- end
-
-**********************************************************************
-
- subroutine getnvlist(nvlist_tmp)
-
-**********************************************************************
-#include "cbka.blk"
- integer nvlist_tmp
-
-**********************************************************************
-* *
-* Report the value of nvlist *
-* *
-**********************************************************************
-
- nvlist_tmp = nvlist
-
- return
- end
-
-**********************************************************************
-
- subroutine getvlbora(vlbora_tmp)
-
-**********************************************************************
-#include "cbka.blk"
-#include "control.blk"
- real*8 vlbora_tmp
-
-**********************************************************************
-* *
-* Report the value of vlbora *
-* *
-**********************************************************************
-
- vlbora_tmp = vlbora
-
- return
- end
-
-**********************************************************************
-
- subroutine getnval(nval_tmp)
-
-**********************************************************************
-#include "cbka.blk"
-#include "cbkvalence.blk"
- integer nval_tmp
-
-**********************************************************************
-* *
-* Report the value of nval *
-* *
-**********************************************************************
-
- nval_tmp = nval
-
- return
- end
-
-**********************************************************************
-
- subroutine getntor(ntor_tmp)
-
-**********************************************************************
-#include "cbka.blk"
-#include "cbktorsion.blk"
- integer ntor_tmp
-
-**********************************************************************
-* *
-* Report the value of ntor *
-* *
-**********************************************************************
-
- ntor_tmp = ntor
-
- return
- end
-
-
-**********************************************************************
-
- subroutine getnhb(nhb_tmp)
-
-**********************************************************************
-#include "cbka.blk"
-#include "cbksrthb.blk"
- integer nhb_tmp
-
-**********************************************************************
-* *
-* Report the value of nhb *
-* *
-**********************************************************************
-
- nhb_tmp = nhb
-
- return
- end
-
-
-**********************************************************************
-
- subroutine getnbonall(nbonall_tmp)
-
-**********************************************************************
-#include "cbka.blk"
-#include "cbksrtbon1.blk"
- integer nbonall_tmp
-
-**********************************************************************
-* *
-* Report the value of nbonall *
-* *
-**********************************************************************
-
- nbonall_tmp = nbonall
-
- return
- end
-
-
-**********************************************************************
-
- subroutine getnneighmax(nneighmax_tmp)
-
-**********************************************************************
-#include "cbka.blk"
- integer nneighmax_tmp
-
-**********************************************************************
-* *
-* Report the value of nneighmax *
-* *
-**********************************************************************
-
- nneighmax_tmp = nneighmax
-
- return
- end
-
-**********************************************************************
-
- subroutine getnat(nat_tmp)
-
-**********************************************************************
-#include "cbka.blk"
- integer nat_tmp
-
-**********************************************************************
-* *
-* Report the value of nat *
-* *
-**********************************************************************
-
- nat_tmp = nat
-
- return
- end
-
-**********************************************************************
-
- subroutine getnattot(nattot_tmp)
-
-**********************************************************************
-#include "cbka.blk"
- integer nattot_tmp
-
-**********************************************************************
-* *
-* Report the value of nattot *
-* *
-**********************************************************************
-
- nattot_tmp = nattot
-
- return
- end
-
-**********************************************************************
-
- subroutine getnsort(nsort_tmp)
-
-**********************************************************************
-#include "cbka.blk"
- integer nsort_tmp
-
-**********************************************************************
-* *
-* Report the value of nsort *
-* *
-**********************************************************************
-
- nsort_tmp = nsort
-
- return
- end
-
-**********************************************************************
-
- subroutine getmbond(mbond_tmp)
-
-**********************************************************************
-#include "cbka.blk"
- integer mbond_tmp
-
-**********************************************************************
-* *
-* Report the value of mbond *
-* *
-**********************************************************************
-
- mbond_tmp = mbond
-
- return
- end
-
-**********************************************************************
-
- subroutine getnso(nso_tmp)
-
-**********************************************************************
-#include "cbka.blk"
-#include "cbkff.blk"
- integer nso_tmp
-
-**********************************************************************
-* *
-* Report the value of nso *
-* *
-**********************************************************************
-
- nso_tmp = nso
-
- return
- end
-
-
-**********************************************************************
-
- subroutine setngeofor(ngeofor_tmp)
-
-**********************************************************************
-#include "cbka.blk"
-#include "control.blk"
- integer ngeofor_tmp
-
-**********************************************************************
-* *
-* Set value of ngeofor
-* *
-**********************************************************************
-
- ngeofor = ngeofor_tmp
- return
- end
-
-**********************************************************************
-
- subroutine getnsbmax(nsbmax_tmp)
-
-**********************************************************************
-#include "cbka.blk"
-#include "cbksrtbon1.blk"
- integer nsbmax_tmp
-
-**********************************************************************
-* *
-* Report the value of nsbmax *
-* *
-**********************************************************************
-
- nsbmax_tmp = nsbmax
-
- return
- end
-
-**********************************************************************
-
- subroutine getnsbma2(nsbma2_tmp)
-
-**********************************************************************
-#include "cbka.blk"
-#include "cbksrtbon1.blk"
- integer nsbma2_tmp
-
-**********************************************************************
-* *
-* Report the value of nsbma2 *
-* *
-**********************************************************************
-
- nsbma2_tmp = nsbma2
-
- return
- end
-
-**********************************************************************
-
- subroutine getcutof3(cutof3_tmp)
-
-**********************************************************************
-#include "cbka.blk"
-#include "control.blk"
- real*8 cutof3_tmp
-
-**********************************************************************
-* *
-* Report the value of cutof3 *
-* *
-**********************************************************************
-
- cutof3_tmp = cutof3
-
- return
- end
-
diff --git a/lib/reax/reax_poten.F b/lib/reax/reax_poten.F
deleted file mode 100644
index 2228f8546b659c97cf540946d8ce20abc89bcb6d..0000000000000000000000000000000000000000
--- a/lib/reax/reax_poten.F
+++ /dev/null
@@ -1,3985 +0,0 @@
-**********************************************************************
-* *
-* REAXFF Reactive force field program *
-* *
-* Developed and written by Adri van Duin, duin@wag.caltech.edu *
-* *
-* Copyright (c) 2001-2010 California Institute of Technology *
-* *
-* This is an open-source program. Feel free to modify its *
-* contents. Please keep me informed of any useful modification *
-* or addition that you made. Please do not distribute this *
-* program to others; if people are interested in obtaining *
-* a copy of this program let them contact me first. *
-* *
-**********************************************************************
-********************************************************************
-
- subroutine calval
-
-**********************************************************************
-#include "cbka.blk"
-#include "cbkc.blk"
-#include "cbkdhdc.blk"
-#include "cbkdrdc.blk"
-#include "cbkh.blk"
-#include "cbkrbo.blk"
-#include "cbkvalence.blk"
-#include "cellcoord.blk"
-#include "control.blk"
- dimension a(3),b(3),j(3),dradc(3,3),drbdc(3,3),dtdc(3,3),
- $dargdc(3,3),dndc(3,3),dadc(3),dbdc(3)
-**********************************************************************
-* *
-* Calculate valency angles and their derivatives to cartesian *
-* coordinates *
-* Valency angle energies are calculated in valang *
-* *
-**********************************************************************
-**********************************************************************
-* Description of variables used in this routine.
-*
-* ndebug: stored in cbka.blk; control-parameter
-* third: local variable
-* twothird: local variable
-* dadc(3): local array; stores derivative distance to cartesians
-* dbdc(3): local array; stores derivative distance to cartesians
-* i1: local do-loop counter
-* i2: local do-loop counter
-* k1: local do-loop counter
-* k2: local do-loop counter
-* dradc(3,3): local array; stores derivatives bond lengths to
-* cartesians
-* drbdc(3,3): local array; stores derivatives bond lengths to
-* cartesians
-* nval: stored in cbka.blk; number of valence angles
-* ity: local integer; atom type
-* iv(nvalmax,6): stored in cbka.blk; valence angle identifiers
-* j(3): local integer array; stores valence angle atom numbers
-* la: local integer: stores bond numbers in valence angle
-* lb: local integer: stores bond numbers in valence angle
-* ivl1: local integer; stores symmetric copy number of bond
-* ivl2: local integer; stores symmetric copy number of bond
-* ibsym(nbomax): stored in cbka.blk; symmetric copy number of bond
-* isign1: local integer; -1 or 1
-* isign2: local integer; -1 or 1
-* rla: local variable; stores bond length for bond la
-* rlb: local variable; stores bond length for bond lb
-* rbo(nbomax): stored in cbka.blk; stores bond lengths
-* ix1,iy1,iz1,ix2,iy2,iz2: local integers; periodic cell shifts
-* a(3): local variable; distance in x,y and z-direction between atoms
-* b(3): local variable; distance in x,y and z-direction between atoms
-* c(nat,3): stored in cbka.blk; cartesian coordinate array
-* tm11,tm21,tm22,tm31,tm32,tm33: stored in cbka.blk; periodic cell
-* matrix
-* poem: local variable; product of bond lengths
-* tel: local variable; cross-product of x,y and z-interatomic
-* distances
-* arg: local variable; cosine of angle between bonds a and b
-* arg2: local variable; square of arg
-* s1ma22: local variable; used to check whether angle gets to 180
-* degrees
-* s1ma2: local variable; square root of s1ma22
-* hl: local variable; angle (in radians) between bonds a and b
-* h(nvamax): stored in cbka.blk; angle (in radians) between bonds a
-* and b
-* ib(nbomax,3): stored in cbka.blk: bond distance identifiers
-* drdc(nbomax,3,2): stored in cbka.blk; derivatives bond distances
-* to cartesian coordinates
-* dndc(3,3): local variable; temporary storage for calculating
-* derivatives of valence angle to cartesians
-* dtdc(3,3): local variable; temporary storage for calculating
-* derivatives of valence angle to cartesians
-* dargdc(3,3): local variable; temporary storage for calculating
-* derivatives of valence angle to cartesians
-* dhdc(nvamax,3,3): stored in cbka.blk; derivatives of valence angle
-* to cartesians
-*
-**********************************************************************
-c$$$ if (ndebug.eq.1) then
-c$$$C open (65,file='fort.65',status='unknown',access='append')
-c$$$ write (65,*) 'In calval'
-c$$$ call timer(65)
-c$$$ close (65)
-c$$$ end if
-
- third=1.0/3.0
- twothird=2.0/3.0
- dadc(1)=-1.0
- dadc(2)=1.0
- dadc(3)=0.0
- dbdc(1)=0.0
- dbdc(2)=1.0
- dbdc(3)=-1.0
- do k1=1,3
- do k2=1,3
- dradc(k1,k2)=0.0
- drbdc(k1,k2)=0.0
- end do
- end do
- if (nval.eq.0) return
-
- do 10 i1=1,nval
- ity=iv(i1,1)
- j(1)=iv(i1,2)
- j(2)=iv(i1,3)
- j(3)=iv(i1,4)
-**********************************************************************
-* *
-* Determine valency angle *
-* *
-**********************************************************************
- la=iv(i1,5)
- lb=iv(i1,6)
- ivl1=ibsym(la)
- ivl2=ibsym(lb)
- isign1=1
- isign2=1
- rla=rbo(la)
- rlb=rbo(lb)
-
- call dista2(j(2),j(1),dis,a(1),a(2),a(3))
- call dista2(j(2),j(3),dis,b(1),b(2),b(3))
-
- poem=rla*rlb
- tel=a(1)*b(1)+a(2)*b(2)+a(3)*b(3)
- arg=tel/poem
- arg2=arg*arg
- s1ma22=1.0-arg2
- if (s1ma22.lt.1.0d-10) s1ma22=1.0d-10
- s1ma2=sqrt(s1ma22)
- if (arg.gt.1.0) arg=1.0
- if (arg.lt.-1.0) arg=-1.0
- hl=acos(arg)
- h(i1)=hl
-**********************************************************************
-* *
-* Calculate derivative valency angle to cartesian coordinates *
-* *
-**********************************************************************
- if (j(1).eq.ib(la,2)) then
- do k1=1,3
- dradc(k1,1)=drdc(la,k1,1)
- dradc(k1,2)=drdc(la,k1,2)
- end do
- else
- do k1=1,3
- dradc(k1,1)=drdc(la,k1,2)
- dradc(k1,2)=drdc(la,k1,1)
- end do
- end if
- if (j(2).eq.ib(lb,2)) then
- do k1=1,3
- drbdc(k1,2)=drdc(lb,k1,1)
- drbdc(k1,3)=drdc(lb,k1,2)
- end do
- else
- do k1=1,3
- drbdc(k1,2)=drdc(lb,k1,2)
- drbdc(k1,3)=drdc(lb,k1,1)
- end do
- end if
- do k1=1,3
- do k2=1,3
- dndc(k1,k2)=rla*drbdc(k1,k2)+rlb*dradc(k1,k2)
- dtdc(k1,k2)=a(k1)*dbdc(k2)+b(k1)*dadc(k2)
- dargdc(k1,k2)=(dtdc(k1,k2)-arg*dndc(k1,k2))/poem
- dhdc(i1,k1,k2)=-dargdc(k1,k2)/s1ma2
- end do
- end do
-
- 10 continue
-
- return
- end
-**********************************************************************
-**********************************************************************
-
- subroutine boncor
-
-**********************************************************************
-#include "cbka.blk"
-#include "cbkabo.blk"
-#include "cbkc.blk"
-#include "cbkbo.blk"
-#include "cbkboncor.blk"
-#include "cbkbosi.blk"
-#include "cbkbopi.blk"
-#include "cbkbopi2.blk"
-#include "cbkconst.blk"
-#include "cbkdbopi2ndc.blk"
-#include "cbkdbopidc.blk"
-#include "cbkdbopindc.blk"
-#include "cbkff.blk"
-#include "cbkia.blk"
-#include "cbkidbo.blk"
-#include "cbknubon2.blk"
-#include "cbkrbo.blk"
-#include "control.blk"
-#include "small.blk"
-#include "cbkdbodc.blk"
-c$$$ if (ndebug.eq.1) then
-c$$$C open (65,file='fort.65',status='unknown',access='append')
-c$$$ write (65,*) 'In boncor'
-c$$$ call timer(65)
-c$$$ close (65)
-c$$$ end if
-**********************************************************************
-* *
-* Correction for overcoordination and 1-3 bond orders *
-* *
-**********************************************************************
-**********************************************************************
-* Description of variables used in this routine.
-*
-* ndebug: stored in cbka.blk; control-parameter
-* i1: local do-loop counter
-* i2: local do-loop counter
-* k1: local do-loop counter
-* k2: local do-loop counter
-* nbon: stored in cbka.blk; number of bonds in system
-* ibt: local integer; stores bond type
-* ib(nbomax,3): stored in cbka.blk: bond distance identifiers
-* j1: local integer; stores atom number 1st atom in bond
-* j2: local integer; stores atom number 2nd atom in bond
-* ovc(nbotym): stored in cbka.blk: force field parameter for
-* overcoordination correction
-* v13cor(nbotym): stored in cbka.blk: force field parameter for
-* 1-3 bond order correction
-* idbo1(nbomax): stored in cbka.blk; number of atoms in the
-* derivative of the bond order
-* idbo(nbomax,2*mbond): stored in cbka.blk; atom numbers of the
-* atoms in the derivative of the bond order
-* dbondc(nbomax,3,2*mbond): stored in cbka.blk; derivative of
-* corrected total bond orders to cartesians
-* dbosindc(nbomax,3,2*mbond): stored in cbka.blk; derivative of
-* corrected sigma bond orders to cartesians
-* dbopindc(nbomax,3,2*mbond): stored in cbka.blk; derivative of
-* corrected pi bond orders to cartesians
-* dbopi2ndc(nbomax,3,2*mbond): stored in cbka.blk; derivative of
-* corrected double pi bond orders to cartesians
-* dbodc(nbomax,3,2): stored in cbka.blk; derivative of
-* uncorrected total bond orders to cartesians
-* dbosidc(nbomax,3,2): stored in cbka.blk; derivative of
-* uncorrected sigma bond orders to cartesians
-* dbopidc(nbomax,3,2): stored in cbka.blk; derivative of
-* uncorrected pi bond orders to cartesians
-* dbopi2dc(nbomax,3,2): stored in cbka.blk; derivative of
-* uncorrected double pi bond orders to cartesians
-* boo: local variable; storage of uncorrected total bond order
-* bo(nbomax): stored in cbka.blk; total bond order
-* bopi(nbomax): stored in cbka.blk; pi bond order
-* bopi2(nbomax): stored in cbka.blk; double pi bond order
-* bopio: local variable; storage of uncorrected pi bond order
-* bopi2o: local variable; storage of uncorrected double pi bond order
-* iti: local integer; atom type first atom in bond
-* itj: local integer; atom type second atom in bond
-* ia(nat,mbond+3): stored in cbka.blk; connection table without bond
-* order cutoff
-* aboi: local variable: total bond order around atom i
-* aboj: local variable: total bond order around atom j
-* abo(nat): stored in cbka.blk; total bond order around atoms
-* vp131: local variable; force field cross-term
-* vp132: local variable; force field cross-term
-* vp133: local variable; force field cross-term
-* bo131(nsort): stored in cbka.blk; force field parameter for 1-3
-* bond order correction
-* bo132(nsort): stored in cbka.blk; force field parameter for 1-3
-* bond order correction
-* bo133(nsort): stored in cbka.blk; force field parameter for 1-3
-* bond order correction
-* corrtot:local variable; total correction on bond order
-* dbodsboi1: local variable; derivative of bond order to sum of bond
-* orders around atom i
-* dbodsboj1: local variable; derivative of bond order to sum of bond
-* orders around atom j
-* ovi: local variable; overcoordination on atom i
-* ovj: local variable; overcoordination on atom j
-* aval(nat): stored in cbka.blk; nr. of valence electrons on atom
-* exphu1: local variable; stores exponential
-* exphu2: local variable; stores exponential
-* exp11: local variable; stores exponential
-* exp21: local variable; stores exponential
-* vpar(npamax): stored in cbka.blk: general parameters
-* exphu12: local variable; stores sum of exponential
-* ovcor: local variable; temporary storage for BO/ovcor corr.
-* huli: local variable; temporary storage for BO/ovcor corr.
-* hulj: local variable; temporary storage for BO/ovcor corr.
-* corr1: local variable; temporary storage for BO/ovcor corr.
-* corr2: local variable; temporary storage for BO/ovcor corr.
-* dbodsboi2: local variable; derivative of 1-3 BO correction to sum
-* of bond orders around atom i
-* dbodsboj2: local variable; derivative of 1-3 BO correction to sum
-* of bond orders around atom i
-* bocor1: local variable; 1-3 bond order correction
-* bocor2: local variable; 1-3 bond order correction
-* ovi2: local variable; overcoordination on atom i with reference to
-* total number of electrons on atom i, including lone
-* pairs
-* ovj2: local variable; overcoordination on atom j with reference to
-* total number of electrons on atom j, including lone
-* pairs
-* valf(nsort): stored in cbka.blk; total number of electrons on
-* atom, including lone pairs
-* cor1: local variable; temporary storage for BO/1-3 bond corr.
-* cor2: local variable; temporary storage for BO/1-3 bond corr.
-* exphu3: local variable; storage exponential
-* exphu4: local variable; storage exponential
-* corrtot2: local variable; square of corrtot
-* dbodboo: local variable; derivative of corrected total bond order to
-* uncorrected bond order
-* dbopidbopio: local variable; derivative of corrected pi bond order
-* to uncorrected pi bond order
-* dbopidboo: local variable; derivative of corrected pi bond order
-* to uncorrected total bond order
-* dbopi2dbopi2o: local variable; derivative of corrected double pi bond order
-* to uncorrected double pi bond order
-* dbopi2dboo: local variable; derivative of corrected double pi bond order
-* to uncorrected total bond order
-* dbodsboit: local variable; derivative of total bond order to sum
-* of bond orders around atom i
-* dbodsbojt: local variable; derivative of total bond order to sum
-* of bond orders around atom j
-* vhui: local variable; temporary storage
-* vhuj: local variable; temporary storage
-* dbopidsboit: local variable; derivative of pi bond order to sum
-* of bond orders around atom i
-* dbopidsbojt: local variable; derivative of pi bond order to sum
-* of bond orders around atom j
-* dbopi2dsboit: local variable; derivative of pi bond order to sum
-* of bond orders around atom i
-* dbopi2dsbojt: local variable; derivative of pi bond order to sum
-* of bond orders around atom j
-* nco: local integer; counter for number of atoms in derivative
-* ihl: local integer; helps to access right dbodc-term
-* nubon2(nat,mbond): stored in cbka.blk; stored bond number as a
-* function of atom number and connection number
-* iob: local integer; atom number of second atom in bond
-* ncubo: local integer; stores number of current bond
-* na: stored in cbka.blk: number of atoms in system
-* zero: stored in cbka.blk: value 0.00
-*
-**********************************************************************
- do 10 i1=1,nbon
- ibt=ib(i1,1)
- j1=ib(i1,2)
- j2=ib(i1,3)
- if (ovc(ibt).lt.0.001.and.v13cor(ibt).lt.0.001) then
- idbo1(i1)=2
- idbo(i1,1)=j1
- idbo(i1,2)=j2
- do k1=1,3
- dbondc(i1,k1,1)=dbodc(i1,k1,1)
- dbondc(i1,k1,2)=dbodc(i1,k1,2)
- dbosindc(i1,k1,1)=dbosidc(i1,k1,1)
- dbosindc(i1,k1,2)=dbosidc(i1,k1,2)
- dbopindc(i1,k1,1)=dbopidc(i1,k1,1)
- dbopindc(i1,k1,2)=dbopidc(i1,k1,2)
- dbopi2ndc(i1,k1,1)=dbopi2dc(i1,k1,1)
- dbopi2ndc(i1,k1,2)=dbopi2dc(i1,k1,2)
- end do
- goto 10
- end if
- boo=bo(i1)
- bopio=bopi(i1)
- bopi2o=bopi2(i1)
- iti=ia(j1,1)
- itj=ia(j2,1)
- aboi=abo(j1)
- aboj=abo(j2)
- vp131=sqrt(bo131(iti)*bo131(itj))
- vp132=sqrt(bo132(iti)*bo132(itj))
- vp133=sqrt(bo133(iti)*bo133(itj))
- corrtot=1.0
- dbodsboi1=zero
- dbodsboj1=zero
- if (ovc(ibt).gt.0.001) then
- ovi=aboi-aval(iti)
- ovj=aboj-aval(itj)
-
-**********************************************************************
-* *
-* Correction for overcoordination *
-* *
-**********************************************************************
- exphu1=exp(-vpar(2)*ovi)
- exphu2=exp(-vpar(2)*ovj)
- exp11=exp(-vpar(1)*ovi)
- exp21=exp(-vpar(1)*ovj)
- exphu12=(exphu1+exphu2)
- ovcor=-(1.0/vpar(2))*log(0.50*exphu12)
-* huli=((1.0/ovc(ibt))*aval(iti)+exp11+exp21)
-* hulj=((1.0/ovc(ibt))*aval(itj)+exp11+exp21)
- huli=aval(iti)+exp11+exp21
- hulj=aval(itj)+exp11+exp21
- corr1=huli/(huli+ovcor)
- corr2=hulj/(hulj+ovcor)
- corrtot=0.50*(corr1+corr2)
-
- dbodsboi1=0.50*(-vpar(1)*exp11/(huli+ovcor)-
- $(corr1/(huli+ovcor))*
- $(-vpar(1)*exp11+exphu1/exphu12)-vpar(1)*exp11/(hulj+ovcor)-
- $(corr2/(hulj+ovcor))*(-vpar(1)*exp11+exphu1/exphu12))
- dbodsboj1=0.50*(-vpar(1)*exp21/(huli+ovcor)-
- $(corr1/(huli+ovcor))*
- $(-vpar(1)*exp21+exphu2/exphu12)-vpar(1)*exp21/(hulj+ovcor)-
- $(corr2/(hulj+ovcor))*(-vpar(1)*exp21+exphu2/exphu12))
- end if
-**********************************************************************
-* *
-* Correction for 1-3 bond orders *
-* *
-**********************************************************************
- dbodsboi2=zero
- dbodsboj2=zero
- bocor1=1.0
- bocor2=1.0
- if (v13cor(ibt).gt.0.001) then
- ovi2=aboi-vval3(iti) !Modification for metal surfaces
- ovj2=aboj-vval3(itj)
-* ovi2=aboi-valf(iti)
-* ovj2=aboj-valf(itj)
-* ovi2=aboi-aval(iti)
-* ovj2=aboj-aval(itj)
- cor1=vp131*boo*boo-ovi2
- cor2=vp131*boo*boo-ovj2
-* exphu3=v13cor(ibt)*exp(-vp132*cor1+vp133)
-* exphu4=v13cor(ibt)*exp(-vp132*cor2+vp133)
- exphu3=exp(-vp132*cor1+vp133)
- exphu4=exp(-vp132*cor2+vp133)
- bocor1=1.0/(1.0+exphu3)
- bocor2=1.0/(1.0+exphu4)
- dbodsboi2=-bocor1*bocor1*bocor2*vp132*exphu3
- dbodsboj2=-bocor1*bocor2*bocor2*vp132*exphu4
- end if
-
- bo(i1)=boo*corrtot*bocor1*bocor2
- if (bo(i1).lt.1e-10) bo(i1)=zero
- corrtot2=corrtot*corrtot
- bopi(i1)=bopio*corrtot2*bocor1*bocor2
- bopi2(i1)=bopi2o*corrtot2*bocor1*bocor2
- if (bopi(i1).lt.1e-10) bopi(i1)=zero
- if (bopi2(i1).lt.1e-10) bopi2(i1)=zero
-
- dbodboo=corrtot*bocor1*bocor2+corrtot*
- $bocor1*bocor1*bocor2*boo*vp132*vp131*2.0*boo*exphu3+
- $corrtot*bocor1*bocor2*bocor2*boo*
- $vp132*vp131*exphu4*2.0*boo
-
- dbopidbopio=corrtot2*bocor1*bocor2
-
- dbopidboo=corrtot2*
- $bocor1*bocor1*bocor2*boo*vp132*vp131*2.0*bopio*exphu3+
- $corrtot2*bocor1*bocor2*bocor2*boo*
- $vp132*vp131*exphu4*2.0*bopio
-
- dbopi2dbopi2o=corrtot2*bocor1*bocor2
-
- dbopi2dboo=corrtot2*
- $bocor1*bocor1*bocor2*boo*vp132*vp131*2.0*bopi2o*exphu3+
- $corrtot2*bocor1*bocor2*bocor2*boo*
- $vp132*vp131*exphu4*2.0*bopi2o
-
- dbodsboit=boo*dbodsboi1*bocor1*bocor2+boo*corrtot*dbodsboi2
- dbodsbojt=boo*dbodsboj1*bocor1*bocor2+boo*corrtot*dbodsboj2
-
- vhui=2.0*corrtot*dbodsboi1*bocor1*bocor2+corrtot2*dbodsboi2
- vhuj=2.0*corrtot*dbodsboj1*bocor1*bocor2+corrtot2*dbodsboj2
- dbopidsboit=bopio*vhui
- dbopidsbojt=bopio*vhuj
-
- dbopi2dsboit=bopi2o*vhui
- dbopi2dsbojt=bopi2o*vhuj
-
-**********************************************************************
-* *
-* Calculate bond order derivatives *
-* *
-**********************************************************************
- idbo1(i1)=2+ia(j1,2)+ia(j2,2)
- idbo(i1,1)=j1
- idbo(i1,2)=j2
- nco=0
- do k1=1,3
- dbondc(i1,k1,1)=dbodc(i1,k1,1)*dbodboo
- dbondc(i1,k1,2)=dbodc(i1,k1,2)*dbodboo
-* dbosindc(i1,k1,1)=dbosidc(i1,k1,1)*dbosidboo
-* dbosindc(i1,k1,2)=dbosidc(i1,k1,2)*dbosidboo
- dbopindc(i1,k1,1)=dbopidc(i1,k1,1)*dbopidbopio+
- $dbodc(i1,k1,1)*dbopidboo
- dbopindc(i1,k1,2)=dbopidc(i1,k1,2)*dbopidbopio+
- $dbodc(i1,k1,2)*dbopidboo
- dbopi2ndc(i1,k1,1)=dbopi2dc(i1,k1,1)*dbopi2dbopi2o+
- $dbodc(i1,k1,1)*dbopi2dboo
- dbopi2ndc(i1,k1,2)=dbopi2dc(i1,k1,2)*dbopi2dbopi2o+
- $dbodc(i1,k1,2)*dbopi2dboo
- end do
- do i2=1,ia(j1,2)
- ihl=0
- iob=ia(j1,2+i2)
- if (iob.lt.j1) ihl=1
- ncubo=nubon2(j1,i2)
- idbo(i1,2+nco+1)=iob
- do k1=1,3
- dbondc(i1,k1,1)=dbondc(i1,k1,1)+dbodc(ncubo,k1,1+ihl)*dbodsboit
- dbondc(i1,k1,2+nco+1)=dbodc(ncubo,k1,2-ihl)*dbodsboit
-
-* dbosindc(i1,k1,1)=dbosindc(i1,k1,1)+
-* $dbodc(ncubo,k1,1+ihl)*dbosidsboit
-* dbosindc(i1,k1,2+nco+1)=dbodc(ncubo,k1,2-ihl)*dbosidsboit
-
- dbopindc(i1,k1,1)=dbopindc(i1,k1,1)+
- $dbodc(ncubo,k1,1+ihl)*dbopidsboit
- dbopindc(i1,k1,2+nco+1)=dbodc(ncubo,k1,2-ihl)*dbopidsboit
-
- dbopi2ndc(i1,k1,1)=dbopi2ndc(i1,k1,1)+
- $dbodc(ncubo,k1,1+ihl)*dbopi2dsboit
- dbopi2ndc(i1,k1,2+nco+1)=dbodc(ncubo,k1,2-ihl)*dbopi2dsboit
-
- end do
- nco=nco+1
- end do
- do i2=1,ia(j2,2)
- ihl=0
- iob=ia(j2,2+i2)
- if (iob.lt.j2) ihl=1
- ncubo=nubon2(j2,i2)
- idbo(i1,2+nco+1)=iob
- do k1=1,3
-
- dbondc(i1,k1,2)=dbondc(i1,k1,2)+dbodc(ncubo,k1,1+ihl)*dbodsbojt
- dbondc(i1,k1,2+nco+1)=dbodc(ncubo,k1,2-ihl)*dbodsbojt
-
-* dbosindc(i1,k1,2)=dbosindc(i1,k1,2)+
-* $dbodc(ncubo,k1,1+ihl)*dbosidsbojt
-* dbosindc(i1,k1,2+nco+1)=dbodc(ncubo,k1,2-ihl)*dbosidsbojt
-
- dbopindc(i1,k1,2)=dbopindc(i1,k1,2)+
- $dbodc(ncubo,k1,1+ihl)*dbopidsbojt
- dbopindc(i1,k1,2+nco+1)=dbodc(ncubo,k1,2-ihl)*dbopidsbojt
-
- dbopi2ndc(i1,k1,2)=dbopi2ndc(i1,k1,2)+
- $dbodc(ncubo,k1,1+ihl)*dbopi2dsbojt
- dbopi2ndc(i1,k1,2+nco+1)=dbodc(ncubo,k1,2-ihl)*dbopi2dsbojt
-
- end do
- nco=nco+1
- end do
-
- 10 continue
-
- do i1=1,na
- abo(i1)=zero
- end do
-* do i1=1,na
-* do i2=1,ia(i1,2)
-* iob=ia(i1,2+i2)
-* ncubo=nubon2(i1,i2)
-* abo(i1)=abo(i1)+bo(ncubo)
-* end do
-* end do
- do i1=1,nbon
- j1=ib(i1,2)
- j2=ib(i1,3)
- abo(j1)=abo(j1)+bo(i1)
- if (j1.ne.j2) abo(j2)=abo(j2)+bo(i1)
- end do
-
- 15 continue
- return
- end
-**********************************************************************
-**********************************************************************
-
- subroutine lonpar
-
-**********************************************************************
-#include "cbka.blk"
-#include "cbkabo.blk"
-#include "cbkconst.blk"
-#include "cbkc.blk"
-#include "cbkd.blk"
-#include "cbkdcell.blk"
-#include "cbkenergies.blk"
-#include "cbkff.blk"
-#include "cbkia.blk"
-#include "cbkidbo.blk"
-#include "cbklonpar.blk"
-#include "cbknubon2.blk"
-#include "control.blk"
-#include "small.blk"
- dimension virial_tmp(3,3),virialsym(6)
-c$$$ if (ndebug.eq.1) then
-c$$$C open (65,file='fort.65',status='unknown',access='append')
-c$$$ write (65,*) 'In lonpar'
-c$$$ call timer(65)
-c$$$ close (65)
-c$$$ end if
-**********************************************************************
-* *
-* Calculate lone pair energy and first derivatives *
-* *
-**********************************************************************
- elp=zero
- do i1=1,na
-**********************************************************************
-* *
-* Determine number of lone pairs on atoms
-* *
-**********************************************************************
- ity=ia(i1,1)
- voptlp=0.50*(stlp(ity)-aval(ity))
- vlp(i1)=zero
- vund=abo(i1)-stlp(ity)
- vlph=2.0*int(vund/2.0)
- vlpex=vund-vlph
- vp16h=vpar(16)-1.0
-
- expvlp=exp(-vpar(16)*(2.0+vlpex)*(2.0+vlpex))
- dvlpdsbo(i1)=-vpar(16)*2.0*(2.0+vlpex)*expvlp
- vlp(i1)=expvlp-int(vund/2.0)
-* expvlp=exp(-vpar(16)*(2.0+vlpex))
-* dvlpdsbo(i1)=-vpar(16)*expvlp
-* expvlp=exp(-6.0*((-0.50*vlpex)**vpar(16)))
-* vlp(i1)=(1.0-expvlp)-int(vund/2.0)
-* dvlpdsbo(i1)=-0.5*6.0*vpar(16)*((-0.5*vlpex)**vp16h)*
-* $expvlp
-**********************************************************************
-* *
-* Calculate lone pair energy *
-* *
-**********************************************************************
- if (i1 .le. na_local) then
-
- diffvlp=voptlp-vlp(i1)
- exphu1=exp(-75.0*diffvlp)
- hulp1=1.0/(1.0+exphu1)
- elph=vlp1(ity)*diffvlp*hulp1
-* elph=vlp1(ity)*diffvlp
- delpdvlp=-vlp1(ity)*hulp1-vlp1(ity)*diffvlp*hulp1*hulp1*
- $75.0*exphu1
-
- elp=elp+elph
- estrain(i1)=estrain(i1)+elph !atom energy
-
- delpdsbo=delpdvlp*dvlpdsbo(i1)
-**********************************************************************
-* *
-* Calculate first derivative of lone pair energy to *
-* cartesian coordinates *
-* *
-**********************************************************************
- do i3=1,ia(i1,2)
- iob=ia(i1,2+i3)
- ncubo=nubon2(i1,i3)
-
- if (Lvirial.eq.1) then
- do k1=1,3
- do k2=1,3
- virial_tmp(k1,k2) = 0.0
- end do
- end do
- endif
-
- do i4=1,idbo1(ncubo)
- ihu=idbo(ncubo,i4)
- do k1=1,3
- ftmp = delpdsbo*dbondc(ncubo,k1,i4)
- d(k1,ihu)=d(k1,ihu)+ftmp
-
- if (Lvirial.eq.1) then
- do k1p=1,3
- virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p)
- end do
- endif
-
- end do
- end do
- if (Lvirial.eq.1) then
- virialsym(1) = virial_tmp(1,1)
- virialsym(2) = virial_tmp(2,2)
- virialsym(3) = virial_tmp(3,3)
- virialsym(4) = virial_tmp(1,2)
- virialsym(5) = virial_tmp(1,3)
- virialsym(6) = virial_tmp(2,3)
- do k1 = 1,6
- virial(k1) = virial(k1) + virialsym(k1)
- end do
-
- if (Latomvirial.eq.1) then
- frac = 1.0d0/idbo1(ncubo)
- do k1 = 1,6
- vtmp = virialsym(k1)*frac
- do i4=1,idbo1(ncubo)
- ihu=idbo(ncubo,i4)
- atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp
- end do
- end do
- endif
- endif
-
- end do
- endif
-
- end do
-
- return
- end
-**********************************************************************
-**********************************************************************
-
- subroutine covbon
-
-**********************************************************************
-#include "cbka.blk"
-#include "cbkc.blk"
-#include "cbkabo.blk"
-#include "cbkbo.blk"
-#include "cbkbosi.blk"
-#include "cbkbopi.blk"
-#include "cbkbopi2.blk"
-#include "cbkconst.blk"
-#include "cbkcovbon.blk"
-#include "cbkd.blk"
-#include "cbkdbopi2ndc.blk"
-#include "cbkdbopindc.blk"
-#include "cbkdcell.blk"
-#include "cbkenergies.blk"
-#include "cbkff.blk"
-#include "cbkia.blk"
-#include "cbkidbo.blk"
-#include "cbknubon2.blk"
-#include "cbkqa.blk"
-#include "cbkrbo.blk"
-#include "control.blk"
-#include "small.blk"
- dimension virial_tmp(3,3),virialsym(6)
-**********************************************************************
-* *
-* Calculate bond energy and first derivatives *
-* *
-**********************************************************************
-c$$$ if (ndebug.eq.1) then
-c$$$C open (65,file='fort.65',status='unknown',access='append')
-c$$$ write (65,*) 'In covbon'
-c$$$ call timer(65)
-c$$$ close (65)
-c$$$ end if
- eb=0.0d0
- if (nbon.eq.0) return
-**********************************************************************
-* *
-* Calculate bond energies *
-* *
-**********************************************************************
-c$$$ if (ndebug.eq.1) then
-c$$$C open (65,file='fort.65',status='unknown',access='append')
-c$$$ write(65,*) 'Bond forces'
-c$$$ write(65,*) 'nbon = ',nbon
-c$$$ endif
-
- do 20 i1=1,nbon
-
- boa=bo(i1)
-* if (boa.lt.cutof2) goto 20
- j1=ib(i1,2)
- j2=ib(i1,3)
-
-c Only compute interaction if both atoms
-c are local or else flip a coin
- if (j1 .gt. na_local) go to 20
- if (j2 .gt. na_local) then
- if (itag(j1) .lt. itag(j2)) go to 20
- if (itag(j1) .eq. itag(j2)) then
- if(c(j1,3) .gt. c(j2,3)) go to 20
- if(c(j1,3) .eq. c(j2,3) .and.
- $ c(j1,2) .gt. c(j2,2)) go to 20
- if(c(j1,3) .eq. c(j2,3) .and.
- $ c(j1,2) .eq. c(j2,2) .and.
- $ c(j1,1) .gt. c(j2,1)) go to 20
- endif
- endif
- vsymm=1.0
- if (j1.eq.j2) vsymm=0.5
-
- bopia=bopi(i1)
- bopi2a=bopi2(i1)
- bosia=boa-bopia-bopi2a
- if (bosia.lt.zero) bosia=zero
- it1=ia(j1,1)
- it2=ia(j2,1)
- ibt=ib(i1,1)
- de1h=vsymm*de1(ibt)
- de2h=vsymm*de2(ibt)
- de3h=vsymm*de3(ibt)
-
- bopo1=bosia**psp(ibt)
- exphu1=exp(psi(ibt)*(1.0-bopo1))
- ebh=-de1h*bosia*exphu1-de2h*bopia-de3h*bopi2a
-
- debdbo=-de1h*exphu1+de1h*exphu1*psp(ibt)*psi(ibt)*bopo1
- debdbopi=-de2h
- debdbopi2=-de3h
-
- eb=eb+ebh
- estrain(j1)=estrain(j1)+0.50*ebh !1st atom energy
- estrain(j2)=estrain(j2)+0.50*ebh !2nd atom energy
-
- if (Lvirial.eq.1) then
- do k1=1,3
- do k2=1,3
- virial_tmp(k1,k2) = 0.0
- end do
- end do
- endif
-
- do i2=1,idbo1(i1)
- ihu=idbo(i1,i2)
- do k1=1,3
- ftmp = debdbo*(dbondc(i1,k1,i2)-dbopindc(i1,k1,i2)-
- $dbopi2ndc(i1,k1,i2))+
- $debdbopi*dbopindc(i1,k1,i2)+
- $debdbopi2*dbopi2ndc(i1,k1,i2)
- d(k1,ihu)=d(k1,ihu)+ftmp
-
- if (Lvirial.eq.1) then
- do k1p=1,3
- virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p)
- end do
- endif
-
- end do
- end do
- if (Lvirial.eq.1) then
- virialsym(1) = virial_tmp(1,1)
- virialsym(2) = virial_tmp(2,2)
- virialsym(3) = virial_tmp(3,3)
- virialsym(4) = virial_tmp(1,2)
- virialsym(5) = virial_tmp(1,3)
- virialsym(6) = virial_tmp(2,3)
- do k1 = 1,6
- virial(k1) = virial(k1) + virialsym(k1)
- end do
-
- if (Latomvirial.eq.1) then
- frac = 1.0d0/idbo1(i1)
- do k1 = 1,6
- vtmp = virialsym(k1)*frac
- do i2=1,idbo1(i1)
- ihu=idbo(i1,i2)
- atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp
- end do
- end do
- endif
-
- endif
-
-**********************************************************************
-* *
-* Stabilisation terminal triple bond in CO *
-* *
-**********************************************************************
- if (boa.lt.1.00) goto 20
-* Stabilization for all triple bonds (not just for CO) in ReaxFF combustion FF
- if (ltripstaball.eq.1 .or.
- $ (qa(j1).eq.'C '.and.qa(j2).eq.'O ').or.
- $ (qa(j1).eq.'O '.and.qa(j2).eq.'C ')) then
-
- ba=(boa-2.50)*(boa-2.50)
- exphu=exp(-vpar(8)*ba)
- oboa=abo(j1)-boa
- obob=abo(j2)-boa
- exphua1=exp(-vpar(4)*oboa)
- exphub1=exp(-vpar(4)*obob)
- ovoab=abo(j1)-aval(it1)+abo(j2)-aval(it2)
- exphuov=exp(vpar(5)*ovoab)
- hulpov=1.0/(1.0+25.0*exphuov)
-
- estriph=vpar(11)*exphu*hulpov*(exphua1+exphub1)
-
- eb=eb+estriph
- estrain(j1)=estrain(j1)+0.50*estriph !1st atom energy
- estrain(j2)=estrain(j2)+0.50*estriph !2nd atom energy
-
- decobdbo=vpar(4)*vpar(11)*exphu*hulpov*(exphua1+exphub1)
- $-2.0*vpar(11)*vpar(8)*(boa-2.50)*hulpov*exphu*
- $(exphua1+exphub1)
- decobdboua=-25.0*vpar(5)*vpar(11)*exphu*exphuov*hulpov*hulpov*
- $(exphua1+exphub1)-vpar(11)*exphu*vpar(4)*hulpov*exphua1
- decobdboub=-25.0*vpar(5)*vpar(11)*exphu*exphuov*hulpov*hulpov*
- $(exphua1+exphub1)-vpar(11)*exphu*vpar(4)*hulpov*exphub1
-
- if (Lvirial.eq.1) then
- do k1=1,3
- do k2=1,3
- virial_tmp(k1,k2) = 0.0
- end do
- end do
- endif
-
- do i2=1,idbo1(i1)
- ihu=idbo(i1,i2)
- do k1=1,3
- ftmp = decobdbo*dbondc(i1,k1,i2)
- d(k1,ihu)=d(k1,ihu)+ftmp
-
- if (Lvirial.eq.1) then
- do k1p=1,3
- virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p)
- end do
- endif
-
- end do
- end do
- if (Lvirial.eq.1) then
- virialsym(1) = virial_tmp(1,1)
- virialsym(2) = virial_tmp(2,2)
- virialsym(3) = virial_tmp(3,3)
- virialsym(4) = virial_tmp(1,2)
- virialsym(5) = virial_tmp(1,3)
- virialsym(6) = virial_tmp(2,3)
- do k1 = 1,6
- virial(k1) = virial(k1) + virialsym(k1)
- end do
-
- if (Latomvirial.eq.1) then
- frac = 1.0d0/idbo1(i1)
- do k1 = 1,6
- vtmp = virialsym(k1)*frac
- do i2=1,idbo1(i1)
- ihu=idbo(i1,i2)
- atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp
- end do
- end do
- endif
-
- endif
-
- do i3=1,ia(j1,2)
- iob=ia(j1,2+i3)
- ncubo=nubon2(j1,i3)
-
- if (Lvirial.eq.1) then
- do k1=1,3
- do k2=1,3
- virial_tmp(k1,k2) = 0.0
- end do
- end do
- endif
-
- do i4=1,idbo1(ncubo)
- ihu=idbo(ncubo,i4)
- do k1=1,3
- ftmp = decobdboua*dbondc(ncubo,k1,i4)
- d(k1,ihu)=d(k1,ihu)+ftmp
-
- if (Lvirial.eq.1) then
- do k1p=1,3
- virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p)
- end do
- endif
-
- end do
- end do
- if (Lvirial.eq.1) then
- virialsym(1) = virial_tmp(1,1)
- virialsym(2) = virial_tmp(2,2)
- virialsym(3) = virial_tmp(3,3)
- virialsym(4) = virial_tmp(1,2)
- virialsym(5) = virial_tmp(1,3)
- virialsym(6) = virial_tmp(2,3)
- do k1 = 1,6
- virial(k1) = virial(k1) + virialsym(k1)
- end do
-
- if (Latomvirial.eq.1) then
- frac = 1.0d0/idbo1(ncubo)
- do k1 = 1,6
- vtmp = virialsym(k1)*frac
- do i4=1,idbo1(ncubo)
- ihu=idbo(ncubo,i4)
- atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp
- end do
- end do
- endif
-
- endif
-
- end do
-
- do i3=1,ia(j2,2)
- iob=ia(j2,2+i3)
- ncubo=nubon2(j2,i3)
- if (Lvirial.eq.1) then
- do k1=1,3
- do k2=1,3
- virial_tmp(k1,k2) = 0.0
- end do
- end do
- endif
- do i4=1,idbo1(ncubo)
- ihu=idbo(ncubo,i4)
- do k1=1,3
- ftmp = decobdboub*dbondc(ncubo,k1,i4)
- d(k1,ihu)=d(k1,ihu)+ftmp
-
- if (Lvirial.eq.1) then
- do k1p=1,3
- virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p)
- end do
- endif
-
- end do
- end do
- if (Lvirial.eq.1) then
- virialsym(1) = virial_tmp(1,1)
- virialsym(2) = virial_tmp(2,2)
- virialsym(3) = virial_tmp(3,3)
- virialsym(4) = virial_tmp(1,2)
- virialsym(5) = virial_tmp(1,3)
- virialsym(6) = virial_tmp(2,3)
- do k1 = 1,6
- virial(k1) = virial(k1) + virialsym(k1)
- end do
-
- if (Latomvirial.eq.1) then
- frac = 1.0d0/idbo1(ncubo)
- do k1 = 1,6
- vtmp = virialsym(k1)*frac
- do i4=1,idbo1(ncubo)
- ihu=idbo(ncubo,i4)
- atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp
- end do
- end do
- endif
-
- endif
-
- end do
-
- endif
-
- 20 continue
-
- return
- end
-**********************************************************************
-**********************************************************************
-
- subroutine ovcor
-
-**********************************************************************
-#include "cbka.blk"
-#include "cbkc.blk"
-#include "cbkabo.blk"
-#include "cbkbo.blk"
-#include "cbkbopi.blk"
-#include "cbkbopi2.blk"
-#include "cbkconst.blk"
-#include "cbkd.blk"
-#include "cbkdbopi2ndc.blk"
-#include "cbkdbopindc.blk"
-#include "cbkdcell.blk"
-#include "cbkenergies.blk"
-#include "cbkff.blk"
-#include "cbkia.blk"
-#include "cbkidbo.blk"
-#include "cbklonpar.blk"
-#include "cbknubon2.blk"
-#include "cbkrbo.blk"
-#include "control.blk"
-#include "small.blk"
-**********************************************************************
-* *
-* Calculate atom energy *
-* Correction for over- and undercoordinated atoms *
-* *
-**********************************************************************
- dimension vlptemp(nat)
- dimension virial_tmp(3,3),virialsym(6)
-c$$$ if (ndebug.eq.1) then
-c$$$C open (65,file='fort.65',status='unknown',access='append')
-c$$$ write (65,*) 'In ovcor'
-c$$$ call timer(65)
-c$$$ close (65)
-c$$$ end if
- do i1=1,na
- ity1=ia(i1,1)
- vlptemp(i1)=vlp(i1)
- if (amas(ity1).gt.21.0) vlptemp(i1)=0.50*(stlp(ity1)-aval(ity1)) !Only for 1st-row elements
- end do
- 25 ea=zero
- eaot=zero
- eaut=zero
- epen=0.0
-
- do 30 i1=1,na_local
- ity1=ia(i1,1)
- dfvl=1.0
- if (amas(ity1).gt.21.0) dfvl=0.0 !Only for 1st-row elements
-**********************************************************************
-* *
-* Calculate overcoordination energy *
-* Valency is corrected for lone pairs *
-* *
-**********************************************************************
-
- voptlp=0.50*(stlp(ity1)-aval(ity1))
- diffvlph=dfvl*(voptlp-vlptemp(i1))
-**********************************************************************
-* *
-* Determine coordination neighboring atoms *
-* *
-**********************************************************************
- sumov=0.0
- sumov2=0.0
- do i3=1,ia(i1,2)
- iat2=ia(i1,2+i3)
- ity2=ia(iat2,1)
- ncubo=nubon2(i1,i3)
- if (bo(ncubo).gt.0.0) then
- ibt=ib(ncubo,1)
- voptlp2=0.50*(stlp(ity2)-aval(ity2))
- diffvlp2=dfvl*(voptlp2-vlptemp(iat2))
- sumov=sumov+(bopi(ncubo)+bopi2(ncubo))*
- $(abo(iat2)-aval(ity2)-diffvlp2)
- sumov2=sumov2+vover(ibt)*de1(ibt)*bo(ncubo)
- endif
- end do
-
- exphu1=exp(vpar(32)*sumov)
- vho=1.0/(1.0+vpar(33)*exphu1)
- diffvlp=diffvlph*vho
-
- vov1=abo(i1)-aval(ity1)-diffvlp
- dvov1dsumov=diffvlph*vpar(32)*vpar(33)*vho*vho*exphu1
- exphuo=exp(vovun(ity1)*vov1)
- hulpo=1.0/(1.0+exphuo)
-
- hulpp=(1.0/(vov1+aval(ity1)+1e-8))
-
- eah=sumov2*hulpp*hulpo*vov1
- deadvov1=-sumov2*hulpp*hulpp*vov1*hulpo+
- $sumov2*hulpp*hulpo-sumov2*hulpp*vov1*vovun(ity1)*
- $hulpo*hulpo*exphuo
-
- ea=ea+eah
- estrain(i1)=estrain(i1)+eah !atom energy
-**********************************************************************
-* *
-* Calculate first derivative of overcoordination energy to *
-* cartesian coordinates *
-* *
-**********************************************************************
- do i3=1,ia(i1,2)
- iob=ia(i1,2+i3)
- ncubo=nubon2(i1,i3)
- if (bo(ncubo).gt.0.0) then
- ibt=ib(ncubo,1)
- deadbo=vover(ibt)*de1(ibt)*hulpp*hulpo*vov1
-
- if (Lvirial.eq.1) then
- do k1=1,3
- do k2=1,3
- virial_tmp(k1,k2) = 0.0
- end do
- end do
- endif
-
- do i4=1,idbo1(ncubo)
- ihu=idbo(ncubo,i4)
- do k1=1,3
- ftmp = deadvov1*(1.0+dfvl*vho*dvlpdsbo(i1))*
- $dbondc(ncubo,k1,i4)+deadbo*dbondc(ncubo,k1,i4)
- d(k1,ihu)=d(k1,ihu)+ftmp
-
- if (Lvirial.eq.1) then
- do k1p=1,3
- virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p)
- end do
- endif
-
- end do
- end do
- if (Lvirial.eq.1) then
- virialsym(1) = virial_tmp(1,1)
- virialsym(2) = virial_tmp(2,2)
- virialsym(3) = virial_tmp(3,3)
- virialsym(4) = virial_tmp(1,2)
- virialsym(5) = virial_tmp(1,3)
- virialsym(6) = virial_tmp(2,3)
- do k1 = 1,6
- virial(k1) = virial(k1) + virialsym(k1)
- end do
-
- if (Latomvirial.eq.1) then
- frac = 1.0d0/idbo1(ncubo)
- do k1 = 1,6
- vtmp = virialsym(k1)*frac
- do i4=1,idbo1(ncubo)
- ihu=idbo(ncubo,i4)
- atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp
- end do
- end do
- endif
-
- endif
-
- endif
- end do
-
- do i2=1,ia(i1,2)
-
- iat2=ia(i1,2+i2)
- ity2=ia(iat2,1)
- nbosa=nubon2(i1,i2)
- if (bo(nbosa).gt.0.0) then
- deadvov2=deadvov1*dvov1dsumov*(bopi(nbosa)+bopi2(nbosa))
-
- voptlp2=0.50*(stlp(ity2)-aval(ity2))
- diffvlp2=dfvl*(voptlp2-vlptemp(iat2))
- deadpibo=deadvov1*dvov1dsumov*(abo(iat2)-aval(ity2)-diffvlp2)
-
- if (Lvirial.eq.1) then
- do k1=1,3
- do k2=1,3
- virial_tmp(k1,k2) = 0.0
- end do
- end do
- endif
-
- do i4=1,idbo1(nbosa)
- ihu=idbo(nbosa,i4)
- do k1=1,3
- ftmp = deadpibo*(dbopindc(nbosa,k1,i4)+
- $dbopi2ndc(nbosa,k1,i4))
- d(k1,ihu)=d(k1,ihu)+ftmp
-
- if (Lvirial.eq.1) then
- do k1p=1,3
- virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p)
- end do
- endif
-
- end do
- end do
- if (Lvirial.eq.1) then
- virialsym(1) = virial_tmp(1,1)
- virialsym(2) = virial_tmp(2,2)
- virialsym(3) = virial_tmp(3,3)
- virialsym(4) = virial_tmp(1,2)
- virialsym(5) = virial_tmp(1,3)
- virialsym(6) = virial_tmp(2,3)
- do k1 = 1,6
- virial(k1) = virial(k1) + virialsym(k1)
- end do
-
- if (Latomvirial.eq.1) then
- frac = 1.0d0/idbo1(nbosa)
- do k1 = 1,6
- vtmp = virialsym(k1)*frac
- do i4=1,idbo1(nbosa)
- ihu=idbo(nbosa,i4)
- atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp
- end do
- end do
- endif
- endif
-
- do i3=1,ia(iat2,2)
- iob=ia(iat2,2+i3)
- ncubo=nubon2(iat2,i3)
- if (bo(ncubo).gt.0.0) then
-
- if (Lvirial.eq.1) then
- do k1=1,3
- do k2=1,3
- virial_tmp(k1,k2) = 0.0
- end do
- end do
- endif
-
- do i4=1,idbo1(ncubo)
- ihu=idbo(ncubo,i4)
- do k1=1,3
- ftmp = deadvov2*(1.0+dfvl*dvlpdsbo(iat2))*
- $dbondc(ncubo,k1,i4)
- d(k1,ihu)=d(k1,ihu)+ftmp
-
- if (Lvirial.eq.1) then
- do k1p=1,3
- virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p)
- end do
- endif
-
- end do
- end do
- if (Lvirial.eq.1) then
- virialsym(1) = virial_tmp(1,1)
- virialsym(2) = virial_tmp(2,2)
- virialsym(3) = virial_tmp(3,3)
- virialsym(4) = virial_tmp(1,2)
- virialsym(5) = virial_tmp(1,3)
- virialsym(6) = virial_tmp(2,3)
- do k1 = 1,6
- virial(k1) = virial(k1) + virialsym(k1)
- end do
-
- if (Latomvirial.eq.1) then
- frac = 1.0d0/idbo1(ncubo)
- do k1 = 1,6
- vtmp = virialsym(k1)*frac
- do i4=1,idbo1(ncubo)
- ihu=idbo(ncubo,i4)
- atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp
- end do
- end do
- endif
-
- endif
-
- endif
- end do
-
- endif
-
- end do
-
-**********************************************************************
-* *
-* Calculate undercoordination energy *
-* *
-**********************************************************************
- if (valp1(ity1).lt.zero) goto 30 !skip undercoordination
- exphu2=exp(vpar(10)*sumov)
- vuhu1=1.0+vpar(9)*exphu2
- hulpu2=1.0/vuhu1
-
- exphu3=-exp(vpar(7)*vov1)
- hulpu3=-(1.0+exphu3)
-
- dise2=valp1(ity1)
- exphuu=exp(-vovun(ity1)*vov1)
- hulpu=1.0/(1.0+exphuu)
- eahu=dise2*hulpu*hulpu2*hulpu3
- deaudvov1=dise2*hulpu2*vovun(ity1)*hulpu*hulpu*exphuu*hulpu3-
- $dise2*hulpu*hulpu2*vpar(7)*exphu3
-
- ea=ea+eahu
- estrain(i1)=estrain(i1)+eahu !atom energy
-
- deaudsumov=-dise2*hulpu*vpar(9)*vpar(10)*hulpu3*exphu2*
- $hulpu2*hulpu2
-
-**********************************************************************
-* *
-* Calculate first derivative of atom energy to cartesian *
-* coordinates *
-* *
-**********************************************************************
-
- do i3=1,ia(i1,2)
- iob=ia(i1,2+i3)
- ncubo=nubon2(i1,i3)
- if (bo(ncubo).gt.0.0) then
-
- if (Lvirial.eq.1) then
- do k1=1,3
- do k2=1,3
- virial_tmp(k1,k2) = 0.0
- end do
- end do
- endif
-
- do i4=1,idbo1(ncubo)
- ihu=idbo(ncubo,i4)
- do k1=1,3
- ftmp = deaudvov1*(1.0+dfvl*vho*dvlpdsbo(i1))*
- $dbondc(ncubo,k1,i4)
- d(k1,ihu)=d(k1,ihu)+ftmp
-
- if (Lvirial.eq.1) then
- do k1p=1,3
- virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p)
- end do
- endif
-
- end do
- end do
- if (Lvirial.eq.1) then
- virialsym(1) = virial_tmp(1,1)
- virialsym(2) = virial_tmp(2,2)
- virialsym(3) = virial_tmp(3,3)
- virialsym(4) = virial_tmp(1,2)
- virialsym(5) = virial_tmp(1,3)
- virialsym(6) = virial_tmp(2,3)
- do k1 = 1,6
- virial(k1) = virial(k1) + virialsym(k1)
- end do
-
- if (Latomvirial.eq.1) then
- frac = 1.0d0/idbo1(ncubo)
- do k1 = 1,6
- vtmp = virialsym(k1)*frac
- do i4=1,idbo1(ncubo)
- ihu=idbo(ncubo,i4)
- atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp
- end do
- end do
- endif
-
- endif
-
- endif
- end do
-
- do i2=1,ia(i1,2)
-
- iat2=ia(i1,2+i2)
- ity2=ia(iat2,1)
- nbosa=nubon2(i1,i2)
- if (bo(nbosa).gt.0.0) then
- deadvov2=(deaudsumov+dvov1dsumov*deaudvov1)*
- $(bopi(nbosa)+bopi2(nbosa))
-
- voptlp2=0.50*(stlp(ity2)-aval(ity2))
- diffvlp2=dfvl*(voptlp2-vlptemp(iat2))
- deadpibo1=(dvov1dsumov*deaudvov1+deaudsumov)*
- $(abo(iat2)-aval(ity2)-diffvlp2)
-
- if (Lvirial.eq.1) then
- do k1=1,3
- do k2=1,3
- virial_tmp(k1,k2) = 0.0
- end do
- end do
- endif
-
- do i4=1,idbo1(nbosa)
- ihu=idbo(nbosa,i4)
- do k1=1,3
- ftmp = deadpibo1*
- $(dbopindc(nbosa,k1,i4)+dbopi2ndc(nbosa,k1,i4))
- d(k1,ihu)=d(k1,ihu)+ftmp
-
- if (Lvirial.eq.1) then
- do k1p=1,3
- virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p)
- end do
- endif
-
- end do
- end do
- if (Lvirial.eq.1) then
- virialsym(1) = virial_tmp(1,1)
- virialsym(2) = virial_tmp(2,2)
- virialsym(3) = virial_tmp(3,3)
- virialsym(4) = virial_tmp(1,2)
- virialsym(5) = virial_tmp(1,3)
- virialsym(6) = virial_tmp(2,3)
- do k1 = 1,6
- virial(k1) = virial(k1) + virialsym(k1)
- end do
-
- if (Latomvirial.eq.1) then
- frac = 1.0d0/idbo1(nbosa)
- do k1 = 1,6
- vtmp = virialsym(k1)*frac
- do i4=1,idbo1(nbosa)
- ihu=idbo(nbosa,i4)
- atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp
- end do
- end do
- endif
-
- endif
-
- do i3=1,ia(iat2,2)
- iob=ia(iat2,2+i3)
- ncubo=nubon2(iat2,i3)
- if (bo(ncubo).gt.0.0) then
-
- if (Lvirial.eq.1) then
- do k1=1,3
- do k2=1,3
- virial_tmp(k1,k2) = 0.0
- end do
- end do
- endif
-
- do i4=1,idbo1(ncubo)
- ihu=idbo(ncubo,i4)
- do k1=1,3
- ftmp = deadvov2*(1.0+dfvl*dvlpdsbo(iat2))*
- $dbondc(ncubo,k1,i4)
- d(k1,ihu)=d(k1,ihu)+ftmp
-
- if (Lvirial.eq.1) then
- do k1p=1,3
- virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p)
- end do
- endif
-
- end do
- end do
- if (Lvirial.eq.1) then
- virialsym(1) = virial_tmp(1,1)
- virialsym(2) = virial_tmp(2,2)
- virialsym(3) = virial_tmp(3,3)
- virialsym(4) = virial_tmp(1,2)
- virialsym(5) = virial_tmp(1,3)
- virialsym(6) = virial_tmp(2,3)
- do k1 = 1,6
- virial(k1) = virial(k1) + virialsym(k1)
- end do
-
- if (Latomvirial.eq.1) then
- frac = 1.0d0/idbo1(ncubo)
- do k1 = 1,6
- vtmp = virialsym(k1)*frac
- do i4=1,idbo1(ncubo)
- ihu=idbo(ncubo,i4)
- atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp
- end do
- end do
- endif
-
- endif
-
- endif
- end do
-
- endif
-
- end do
-
-
- 30 continue
-
-**********************************************************************
-* *
-* Calculate correction for C2 *
-* *
-**********************************************************************
- if (abs(vpar(6)).gt.0.001) then
- do 40 i1=1,na_local
- ity1=ia(i1,1)
- vov4=abo(i1)-aval(ity1)
-
- do i2=1,ia(i1,2)
- iat2=ia(i1,2+i2)
- nbohu=nubon2(i1,i2)
- if (bo(nbohu).gt.0.0) then
-
- ibt=ib(nbohu,1)
- elph=zero
- deahu2dbo=zero
- deahu2dsbo=zero
- vov3=bo(nbohu)-vov4-0.040*(vov4**4)
- if (vov3.gt.3.0) then
- elph=vpar(6)*(vov3-3.0)*(vov3-3.0)
- deahu2dbo=2.0*vpar(6)*(vov3-3.0)
- deahu2dsbo=2.0*vpar(6)*(vov3-3.0)*(-1.0-
- $0.16*(vov4**3))
- end if
-
- elp=elp+elph
- estrain(i1)=estrain(i1)+elph !atom energy
-
- if (Lvirial.eq.1) then
- do k1=1,3
- do k2=1,3
- virial_tmp(k1,k2) = 0.0
- end do
- end do
- endif
-
- do i3=1,idbo1(nbohu)
- ihu=idbo(nbohu,i3)
- do k1=1,3
- ftmp = deahu2dbo*dbondc(nbohu,k1,i3)
- d(k1,ihu)=d(k1,ihu)+ftmp
-
- if (Lvirial.eq.1) then
- do k1p=1,3
- virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p)
- end do
- endif
-
- end do
- end do
- if (Lvirial.eq.1) then
- virialsym(1) = virial_tmp(1,1)
- virialsym(2) = virial_tmp(2,2)
- virialsym(3) = virial_tmp(3,3)
- virialsym(4) = virial_tmp(1,2)
- virialsym(5) = virial_tmp(1,3)
- virialsym(6) = virial_tmp(2,3)
- do k1 = 1,6
- virial(k1) = virial(k1) + virialsym(k1)
- end do
-
- if (Latomvirial.eq.1) then
- frac = 1.0d0/idbo1(nbohu)
- do k1 = 1,6
- vtmp = virialsym(k1)*frac
- do i3=1,idbo1(nbohu)
- ihu=idbo(nbohu,i3)
- atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp
- end do
- end do
- endif
-
- endif
-
- do i3=1,ia(i1,2)
- iob=ia(i1,2+i3)
- ncubo=nubon2(i1,i3)
- if (bo(ncubo).gt.0.0) then
-
- if (Lvirial.eq.1) then
- do k1=1,3
- do k2=1,3
- virial_tmp(k1,k2) = 0.0
- end do
- end do
- endif
-
- do i4=1,idbo1(ncubo)
- ihu=idbo(ncubo,i4)
- do k1=1,3
- ftmp = deahu2dsbo*dbondc(ncubo,k1,i4)
- d(k1,ihu)=d(k1,ihu)+ftmp
-
- if (Lvirial.eq.1) then
- do k1p=1,3
- virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p)
- end do
- endif
-
- end do
- end do
- if (Lvirial.eq.1) then
- virialsym(1) = virial_tmp(1,1)
- virialsym(2) = virial_tmp(2,2)
- virialsym(3) = virial_tmp(3,3)
- virialsym(4) = virial_tmp(1,2)
- virialsym(5) = virial_tmp(1,3)
- virialsym(6) = virial_tmp(2,3)
- do k1 = 1,6
- virial(k1) = virial(k1) + virialsym(k1)
- end do
-
- if (Latomvirial.eq.1) then
- frac = 1.0d0/idbo1(ncubo)
- do k1 = 1,6
- vtmp = virialsym(k1)*frac
- do i4=1,idbo1(ncubo)
- ihu=idbo(ncubo,i4)
- atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp
- end do
- end do
- endif
-
- endif
-
- end if
- end do
-
- end if
- end do
-
- 40 continue
- end if
-
- return
- end
-**********************************************************************
-**********************************************************************
-
- subroutine molen
-
-**********************************************************************
-#include "cbka.blk"
-#include "cbkbo.blk"
-#include "cbkconst.blk"
-#include "cbkc.blk"
-#include "cbkd.blk"
-#include "cbkenergies.blk"
-#include "cbkff.blk"
-#include "cbkia.blk"
-#include "cbkidbo.blk"
-#include "cbknmolat.blk"
-#include "cbknubon2.blk"
-#include "control.blk"
-#include "small.blk"
- dimension virial_tmp(3,3),virialsym(6)
-**********************************************************************
-* *
-* Calculate molecular energy and first derivatives *
-* Only used to prevent creating virtual electrons *
-* *
-**********************************************************************
-c$$$ if (ndebug.eq.1) then
-c$$$C open (65,file='fort.65',status='unknown',access='append')
-c$$$ write (65,*) 'In molen'
-c$$$ call timer(65)
-c$$$ close (65)
-c$$$ end if
- emol=zero
- return
- do i1=1,nmolo
-
- enelm=0.0
- do i2=1,na
- if (ia(i2,3+mbond).eq.i1) then
- it1=ia(i2,1)
- enelm=enelm+aval(it1)
- end if
- end do
-
- na1m=nmolat(i1,1)
-
- enelm=2*int(enelm*0.50)
-* enelm=elmol(i1)
- bomsum=zero
- do i2=1,na1m
- ihu=nmolat(i1,i2+1)
- do i3=1,ia(ihu,2)
- ihu2=nubon2(ihu,i3)
- bomsum=bomsum+bo(ihu2)
- end do
- end do
- diff=(bomsum-enelm)
- exphu=exp(-vpar(37)*diff)
- exphu2=1.0/(1.0+15.0*exphu)
- emolh=zero
- demoldsbo=zero
- emolh=vpar(38)*exphu2
- emol=emol+emolh
- demoldsbo=vpar(38)*vpar(37)*15.0*exphu2*exphu2*exphu
-
- do i2=1,na1m
- ihu1=nmolat(i1,i2+1)
- do i3=1,ia(ihu1,2)
- iob=ia(ihu1,2+i3)
- ncubo=nubon2(ihu1,i3)
-
- if (Lvirial.eq.1) then
- do k1=1,3
- do k2=1,3
- virial_tmp(k1,k2) = 0.0
- end do
- end do
- endif
-
- do i4=1,idbo1(ncubo)
- ihu=idbo(ncubo,i4)
- do k1=1,3
- ftmp = demoldsbo*dbondc(ncubo,k1,i4)
- d(k1,ihu)=d(k1,ihu)+ftmp
-
- if (Lvirial.eq.1) then
- do k1p=1,3
- virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p)
- end do
- endif
-
- end do
- end do
- if (Lvirial.eq.1) then
- virialsym(1) = virial_tmp(1,1)
- virialsym(2) = virial_tmp(2,2)
- virialsym(3) = virial_tmp(3,3)
- virialsym(4) = virial_tmp(1,2)
- virialsym(5) = virial_tmp(1,3)
- virialsym(6) = virial_tmp(2,3)
- do k1 = 1,6
- virial(k1) = virial(k1) + virialsym(k1)
- end do
-
- if (Latomvirial.eq.1) then
- frac = 1.0d0/idbo1(ncubo)
- do k1 = 1,6
- vtmp = virialsym(k1)*frac
- do i4=1,idbo1(ncubo)
- ihu=idbo(ncubo,i4)
- atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp
- end do
- end do
- endif
-
- endif
-
- end do
- end do
-
-
- end do
-
-
- return
- end
-**********************************************************************
-**********************************************************************
-
- subroutine valang
-
-**********************************************************************
-#include "cbka.blk"
-#include "cbkabo.blk"
-#include "cbkbo.blk"
-#include "cbkbopi.blk"
-#include "cbkbopi2.blk"
-#include "cbkconst.blk"
-#include "cbkc.blk"
-#include "cbkd.blk"
-#include "cbkdbopi2ndc.blk"
-#include "cbkdbopindc.blk"
-#include "cbkdcell.blk"
-#include "cbkdhdc.blk"
-#include "cbkenergies.blk"
-#include "cbkff.blk"
-#include "cbkh.blk"
-#include "cbkia.blk"
-#include "cbkidbo.blk"
-#include "cbklonpar.blk"
-#include "cbknubon2.blk"
-#include "cbkvalence.blk"
-#include "control.blk"
-#include "valang.blk"
-#include "small.blk"
- dimension j(3)
- dimension virial_tmp(3,3),virialsym(6)
-**********************************************************************
-* *
-* Calculate valency angle energies and first derivatives *
-* *
-**********************************************************************
-c$$$ if (ndebug.eq.1) then
-c$$$C open (65,file='fort.65',status='unknown',access='append')
-c$$$ write (65,*) 'In valang'
-c$$$ call timer(65)
-c$$$ close (65)
-c$$$ end if
-* eco=0.0
- ev=0.0
- ecoa=0.0
- if (nval.eq.0) return
-
- do 10 i1=1,nval
- ity=iv(i1,1)
- j(1)=iv(i1,2)
- j(2)=iv(i1,3)
- j(3)=iv(i1,4)
-
- if (j(2) .le. na_local) then
-
- la=iv(i1,5)
- lb=iv(i1,6)
- boa=bo(la)-cutof2
- bob=bo(lb)-cutof2
- if (boa.lt.zero.or.bob.lt.zero) goto 10
-
- hl=h(i1) ! Calculated earlier in routine calval
-**********************************************************************
-* *
-* Calculate valency angle energy *
-* *
-**********************************************************************
- nbocen=ia(j(2),2)
- sbo2=0.0
- vmbo=1.0
-
- do i2=1,nbocen
- ibv=nubon2(j(2),i2)
- if (bo(ibv).gt.0.0) then
- vmbo=vmbo*exp(-bo(ibv)**8)
- sbo2=sbo2+bopi(ibv)+bopi2(ibv)
- endif
- end do
-
- ity2=ia(j(2),1)
-* exbo=abo(j(2))-stlp(ia(j(2),1))
- exbo=abo(j(2))-valf(ity2)
-* if (exbo.gt.zero) exbo=zero
-* expov=exp(vka8(ity)*exbo)
-* expov2=exp(-vpar(13)*exbo)
-* htov1=2.0+expov2
-* htov2=1.0+expov+expov2
-* evboadj=htov1/htov2
- evboadj=1.0
- expun=exp(-vkac(ity)*exbo)
- expun2=exp(vpar(15)*exbo)
- htun1=2.0+expun2
- htun2=1.0+expun+expun2
- evboadj2=vval4(ity2)-(vval4(ity2)-1.0)*htun1/htun2
-**********************************************************************
-* *
-* Calculate number of lone pairs *
-* *
-**********************************************************************
- dsbo2dvlp=(1.0-vmbo)
- vlpadj=zero
- exlp1=abo(j(2))-stlp(ia(j(2),1))
- exlp2=2.0*int(exlp1/2.0)
- exlp=exlp1-exlp2
- if (exlp.lt.zero) then
-* expvlp=exp(-vpar(16)*(2.0+exlp)*(2.0+exlp))
-* vlpadj=expvlp-int(exlp1/2.0)
-* dsbo2dvlp=(1.0-vmbo)*(1.0-vpar(34)*2.0*
-* $(2.0+exlp)*vpar(16)*expvlp)
- vlpadj=vlp(j(2))
- dsbo2dvlp=(1.0-vmbo)*(1.0+vpar(34)*dvlpdsbo(j(2)))
- end if
-
- sbo2=sbo2+(1.0-vmbo)*(-exbo-vpar(34)*vlpadj)
- dsbo2dvmbo=exbo+vpar(34)*vlpadj
-
- sbo2h=sbo2
- powv=vpar(17)
- if (sbo2.le.0.0) sbo2h=0.0
- if (sbo2.gt.0.0.and.sbo2.le.1.0) sbo2h=sbo2**powv
- if (sbo2.gt.1.0.and.sbo2.lt.2.0) sbo2h=2.0-(2.0-sbo2)**powv
- if (sbo2.gt.2.0) sbo2h=2.0
- thba=th0(ity)
- expsbo=exp(-vpar(18)*(2.0-sbo2h))
- thetao=180.0-thba*(1.0-expsbo)
-
- thetao=thetao*dgrrdn
- thdif=(thetao-hl)
- thdi2=thdif*thdif
- dthsbo=dgrrdn*thba*vpar(18)*expsbo
- if (sbo2.lt.0.0) dthsbo=zero
- if (sbo2.gt.0.0.and.sbo2.le.1.0)
- $dthsbo=powv*(sbo2**(powv-1.0))*dgrrdn*thba*vpar(18)*expsbo
- if (sbo2.gt.1.0.and.sbo2.lt.2.0)
- $dthsbo=powv*((2.0-sbo2)**(powv-1.0))*dgrrdn*thba*vpar(18)*expsbo
- if (sbo2.gt.2.0) dthsbo=zero
-
- exphu=vka(ity)*exp(-vka3(ity)*thdi2)
- exphu2=vka(ity)-exphu
- if (vka(ity).lt.zero) exphu2=exphu2-vka(ity) !To avoid linear Me-H-Me angles (6/6/06)
- boap=boa**vval2(ity)
- boap2=boa**(vval2(ity)-1.0)
- bobp=bob**vval2(ity)
- bobp2=bob**(vval2(ity)-1.0)
- exa=exp(-vval1(ity2)*boap)
- exb=exp(-vval1(ity2)*bobp)
- dexadboa=vval2(ity)*vval1(ity2)*exa*boap2
- dexbdbob=vval2(ity)*vval1(ity2)*exb*bobp2
- exa2=(1.0-exa)
- exb2=(1.0-exb)
-
- evh=evboadj2*evboadj*exa2*exb2*exphu2
- devdlb=evboadj2*evboadj*dexbdbob*exa2*exphu2
- devdla=evboadj2*evboadj*dexadboa*exb2*exphu2
- devdsbo=2.0*evboadj2*evboadj*dthsbo*exa2*exb2*
- $vka3(ity)*thdif*exphu
- devdh=-2.0*evboadj2*evboadj*exa2*exb2*vka3(ity)*thdif*exphu
-
- devdsbo2=
- $evboadj*exa2*exb2*exphu2*(vval4(ity2)-1.0)*(-vpar(15)*expun2/htun2
- $+htun1*(vpar(15)*expun2-vkac(ity)*expun)/(htun2*htun2))
-
-* devdsbo2=-evboadj2*exa2*exb2*exphu2*(vpar(13)*expov2/htov2+
-* $htov1*(vka8(ity)*expov-vpar(13)*expov2)/(htov2*htov2))+
-* $evboadj*exa2*exb2*exphu2*(vpar(14)-1.0)*(-vpar(15)*expun2/htun2
-* $+htun1*(vpar(15)*expun2-vkac(ity)*expun)/(htun2*htun2))
-
- if (j(2) .le. na_local) then
- ev=ev+evh
- estrain(j(2))=estrain(j(2))+evh !central atom energy
- endif
-
-* write (64,'(4i8,18f8.2)')mdstep,j(1),j(2),j(3),sbo2,sbo2h,
-* $thetao*rdndgr,hl*rdndgr,bo(la),bo(lb),bopi(la),
-* $vlp(j(2)),exbo,vlpadj,vmbo,evh,ev,vka(ity)
-**********************************************************************
-* *
-* Calculate penalty for two double bonds in valency angle *
-* *
-**********************************************************************
- exbo=abo(j(2))-aval(ia(j(2),1))
- expov=exp(vpar(22)*exbo)
- expov2=exp(-vpar(21)*exbo)
- htov1=2.0+expov2
- htov2=1.0+expov+expov2
- ecsboadj=htov1/htov2
- exphu1=exp(-vpar(20)*(boa-2.0)*(boa-2.0))
- exphu2=exp(-vpar(20)*(bob-2.0)*(bob-2.0))
-
- epenh=vkap(ity)*ecsboadj*exphu1*exphu2
- estrain(j(2))=estrain(j(2))+epenh
- epen=epen+epenh
- decoadboa=-2.0*vpar(20)*epenh*(boa-2.0)
- decoadbob=-2.0*vpar(20)*epenh*(bob-2.0)
-
- decdsbo2=-vkap(ity)*exphu1*exphu2*(vpar(21)*expov2/htov2+htov1*
- $(vpar(22)*expov-vpar(21)*expov2)/(htov2*htov2))
-**********************************************************************
-* *
-* Calculate valency angle conjugation energy *
-* *
-**********************************************************************
- unda=abo(j(1))-boa
-* ovb=abo(j(2))-valf(ia(j(2),1))
- ovb=abo(j(2))-vval3(ia(j(2),1)) !Modification for Ru 7/6/2004
-
- undc=abo(j(3))-bob
- ba=(boa-1.50)*(boa-1.50)
- bb=(bob-1.50)*(bob-1.50)
- exphua=exp(-vpar(31)*ba)
- exphub=exp(-vpar(31)*bb)
- exphuua=exp(-vpar(39)*unda*unda)
- exphuob=exp(vpar(3)*ovb)
- exphuuc=exp(-vpar(39)*undc*undc)
- hulpob=1.0/(1.0+exphuob)
- ecoah=vka8(ity)*exphua*exphub*exphuua*exphuuc*hulpob
- decodbola=-2.0*vka8(ity)*(boa-1.50)*vpar(31)*exphua*exphub
- $*exphuua*exphuuc*hulpob+vpar(39)*vka8(ity)*exphua*exphub*
- $exphuua*exphuuc*hulpob*2.0*unda
- decodbolb=-2.0*vka8(ity)*(bob-1.50)*vpar(31)*exphua*exphub
- $*exphuua*exphuuc*hulpob+vpar(39)*vka8(ity)*exphua*exphub*
- $exphuua*exphuuc*hulpob*2.0*undc
- decodboua=-2.0*unda*vka8(ity)*vpar(39)*exphua*exphub
- $*exphuua*exphuuc*hulpob
- decodbouc=-2.0*undc*vka8(ity)*vpar(39)*exphua*exphub
- $*exphuua*exphuuc*hulpob
- decodboob=-vka8(ity)*exphua*exphub*exphuua*exphuuc*hulpob*
- $hulpob*vpar(3)*exphuob
-* decodboob=zero
-* decodboua=zero
-* decodbouc=zero
-
- ecoa=ecoa+ecoah
- estrain(j(2))=estrain(j(2))+ecoah !central atom energy
-
-**********************************************************************
-* *
-* Calculate derivative valency energy to cartesian coordinates *
-* *
-**********************************************************************
- if (Lvirial.eq.1) then
- do k1=1,3
- do k2=1,3
- virial_tmp(k1,k2) = 0.0
- end do
- end do
- endif
-
- do k1=1,3
- do k2=1,3
- ftmp = devdh*dhdc(i1,k1,k2)
- d(k1,j(k2))=d(k1,j(k2))+ftmp
-
- if (Lvirial.eq.1) then
- do k1p=1,3
- virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(j(k2),k1p)
- end do
- endif
-
- end do
- end do
- if (Lvirial.eq.1) then
- virialsym(1) = virial_tmp(1,1)
- virialsym(2) = virial_tmp(2,2)
- virialsym(3) = virial_tmp(3,3)
- virialsym(4) = virial_tmp(1,2)
- virialsym(5) = virial_tmp(1,3)
- virialsym(6) = virial_tmp(2,3)
- do k1 = 1,6
- virial(k1) = virial(k1) + virialsym(k1)
- end do
-
- if (Latomvirial.eq.1) then
- frac = 1.0d0/3
- do k1 = 1,6
- vtmp = virialsym(k1)*frac
- do k2=1,3
- ihu=j(k2)
- atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp
- end do
- end do
- endif
-
- endif
-
- if (Lvirial.eq.1) then
- do k1=1,3
- do k2=1,3
- virial_tmp(k1,k2) = 0.0
- end do
- end do
- endif
-
- do i2=1,idbo1(la)
- ihu=idbo(la,i2)
- do k1=1,3
- ftmp = (devdla+decoadboa+decodbola)*
- $dbondc(la,k1,i2)
- d(k1,ihu)=d(k1,ihu)+ftmp
-
- if (Lvirial.eq.1) then
- do k1p=1,3
- virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p)
- end do
- endif
-
- end do
- end do
- if (Lvirial.eq.1) then
- virialsym(1) = virial_tmp(1,1)
- virialsym(2) = virial_tmp(2,2)
- virialsym(3) = virial_tmp(3,3)
- virialsym(4) = virial_tmp(1,2)
- virialsym(5) = virial_tmp(1,3)
- virialsym(6) = virial_tmp(2,3)
- do k1 = 1,6
- virial(k1) = virial(k1) + virialsym(k1)
- end do
-
- if (Latomvirial.eq.1) then
- frac = 1.0d0/idbo1(la)
- do k1 = 1,6
- vtmp = virialsym(k1)*frac
- do i2=1,idbo1(la)
- ihu=idbo(la,i2)
- atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp
- end do
- end do
- endif
-
- endif
-
- if (Lvirial.eq.1) then
- do k1=1,3
- do k2=1,3
- virial_tmp(k1,k2) = 0.0
- end do
- end do
- endif
-
- do i2=1,idbo1(lb)
- ihu=idbo(lb,i2)
- do k1=1,3
- ftmp = (devdlb+decoadbob+decodbolb)*
- $dbondc(lb,k1,i2)
- d(k1,ihu)=d(k1,ihu)+ftmp
-
- if (Lvirial.eq.1) then
- do k1p=1,3
- virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p)
- end do
- endif
-
- end do
- end do
- if (Lvirial.eq.1) then
- virialsym(1) = virial_tmp(1,1)
- virialsym(2) = virial_tmp(2,2)
- virialsym(3) = virial_tmp(3,3)
- virialsym(4) = virial_tmp(1,2)
- virialsym(5) = virial_tmp(1,3)
- virialsym(6) = virial_tmp(2,3)
- do k1 = 1,6
- virial(k1) = virial(k1) + virialsym(k1)
- end do
-
- if (Latomvirial.eq.1) then
- frac = 1.0d0/idbo1(lb)
- do k1 = 1,6
- vtmp = virialsym(k1)*frac
- do i2=1,idbo1(lb)
- ihu=idbo(lb,i2)
- atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp
- end do
- end do
- endif
-
- endif
-
- do i2=1,nbocen
- j5=ia(j(2),2+i2)
- ibv=nubon2(j(2),i2)
- if (bo(ibv).gt.0.0) then
- dvmbodbo=-vmbo*8.0*bo(ibv)**7
-
- if (Lvirial.eq.1) then
- do k1=1,3
- do k2=1,3
- virial_tmp(k1,k2) = 0.0
- end do
- end do
- endif
-
- do i3=1,idbo1(ibv)
- ihu=idbo(ibv,i3)
- do k1=1,3
- ftmp = (-dsbo2dvlp*devdsbo+devdsbo2+decdsbo2
- $+dvmbodbo*dsbo2dvmbo*devdsbo)*
- $dbondc(ibv,k1,i3)+devdsbo*(dbopindc(ibv,k1,i3)+
- $dbopi2ndc(ibv,k1,i3))
- d(k1,ihu)=d(k1,ihu)+ftmp
-
- if (Lvirial.eq.1) then
- do k1p=1,3
- virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p)
- end do
- endif
-
- end do
- end do
- if (Lvirial.eq.1) then
- virialsym(1) = virial_tmp(1,1)
- virialsym(2) = virial_tmp(2,2)
- virialsym(3) = virial_tmp(3,3)
- virialsym(4) = virial_tmp(1,2)
- virialsym(5) = virial_tmp(1,3)
- virialsym(6) = virial_tmp(2,3)
- do k1 = 1,6
- virial(k1) = virial(k1) + virialsym(k1)
- end do
-
- if (Latomvirial.eq.1) then
- frac = 1.0d0/idbo1(ibv)
- do k1 = 1,6
- vtmp = virialsym(k1)*frac
- do i3=1,idbo1(ibv)
- ihu=idbo(ibv,i3)
- atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp
- end do
- end do
- endif
-
- endif
-
- endif
- end do
-
- do i2=1,ia(j(1),2)
- j5=ia(j(1),2+i2)
- ibv=nubon2(j(1),i2)
- if (bo(ibv).gt.0.0) then
-
- if (Lvirial.eq.1) then
- do k1=1,3
- do k2=1,3
- virial_tmp(k1,k2) = 0.0
- end do
- end do
- endif
-
- do i3=1,idbo1(ibv)
- ihu=idbo(ibv,i3)
- do k1=1,3
- ftmp = decodboua*dbondc(ibv,k1,i3)
- d(k1,ihu)=d(k1,ihu)+ftmp
-
- if (Lvirial.eq.1) then
- do k1p=1,3
- virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p)
- end do
- endif
-
- end do
- end do
- if (Lvirial.eq.1) then
- virialsym(1) = virial_tmp(1,1)
- virialsym(2) = virial_tmp(2,2)
- virialsym(3) = virial_tmp(3,3)
- virialsym(4) = virial_tmp(1,2)
- virialsym(5) = virial_tmp(1,3)
- virialsym(6) = virial_tmp(2,3)
- do k1 = 1,6
- virial(k1) = virial(k1) + virialsym(k1)
- end do
-
- if (Latomvirial.eq.1) then
- frac = 1.0d0/idbo1(ibv)
- do k1 = 1,6
- vtmp = virialsym(k1)*frac
- do i3=1,idbo1(ibv)
- ihu=idbo(ibv,i3)
- atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp
- end do
- end do
- endif
-
- endif
-
- endif
- end do
-
- do i2=1,ia(j(2),2)
- j5=ia(j(2),2+i2)
- ibv=nubon2(j(2),i2)
- if (bo(ibv).gt.0.0) then
-
- if (Lvirial.eq.1) then
- do k1=1,3
- do k2=1,3
- virial_tmp(k1,k2) = 0.0
- end do
- end do
- endif
-
- do i3=1,idbo1(ibv)
- ihu=idbo(ibv,i3)
- do k1=1,3
- ftmp = decodboob*dbondc(ibv,k1,i3)
- d(k1,ihu)=d(k1,ihu)+ftmp
-
- if (Lvirial.eq.1) then
- do k1p=1,3
- virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p)
- end do
- endif
-
- end do
- end do
- if (Lvirial.eq.1) then
- virialsym(1) = virial_tmp(1,1)
- virialsym(2) = virial_tmp(2,2)
- virialsym(3) = virial_tmp(3,3)
- virialsym(4) = virial_tmp(1,2)
- virialsym(5) = virial_tmp(1,3)
- virialsym(6) = virial_tmp(2,3)
- do k1 = 1,6
- virial(k1) = virial(k1) + virialsym(k1)
- end do
-
- if (Latomvirial.eq.1) then
- frac = 1.0d0/idbo1(ibv)
- do k1 = 1,6
- vtmp = virialsym(k1)*frac
- do i3=1,idbo1(ibv)
- ihu=idbo(ibv,i3)
- atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp
- end do
- end do
- endif
-
- endif
-
- endif
- end do
-
- do i2=1,ia(j(3),2)
- j5=ia(j(3),2+i2)
- ibv=nubon2(j(3),i2)
- if (bo(ibv).gt.0.0) then
-
- if (Lvirial.eq.1) then
- do k1=1,3
- do k2=1,3
- virial_tmp(k1,k2) = 0.0
- end do
- end do
- endif
-
- do i3=1,idbo1(ibv)
- ihu=idbo(ibv,i3)
- do k1=1,3
- ftmp = decodbouc*dbondc(ibv,k1,i3)
- d(k1,ihu)=d(k1,ihu)+ftmp
-
- if (Lvirial.eq.1) then
- do k1p=1,3
- virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p)
- end do
- endif
-
- end do
- end do
- if (Lvirial.eq.1) then
- virialsym(1) = virial_tmp(1,1)
- virialsym(2) = virial_tmp(2,2)
- virialsym(3) = virial_tmp(3,3)
- virialsym(4) = virial_tmp(1,2)
- virialsym(5) = virial_tmp(1,3)
- virialsym(6) = virial_tmp(2,3)
- do k1 = 1,6
- virial(k1) = virial(k1) + virialsym(k1)
- end do
-
- if (Latomvirial.eq.1) then
- frac = 1.0d0/idbo1(ibv)
- do k1 = 1,6
- vtmp = virialsym(k1)*frac
- do i3=1,idbo1(ibv)
- ihu=idbo(ibv,i3)
- atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp
- end do
- end do
- endif
-
- endif
-
- endif
- end do
-
- endif
-
- 10 continue
-
- return
- end
-**********************************************************************
-**********************************************************************
-
- subroutine hbond
-
-**********************************************************************
-#include "cbka.blk"
-#include "cbkbo.blk"
-#include "cbkconst.blk"
-#include "cbkc.blk"
-#include "cbkd.blk"
-#include "cbkdcell.blk"
-#include "cbkenergies.blk"
-#include "cbkidbo.blk"
-#include "cbksrthb.blk"
-#include "control.blk"
-#include "cbkhbond.blk"
-#include "small.blk"
- dimension drda(3),j(3),dvdc(3,3),dargdc(3,3)
- dimension virial_tmp(3,3),virialsym(6)
-**********************************************************************
-* *
-* Calculate hydrogen bond energies and first derivatives *
-* *
-**********************************************************************
-c$$$ if (ndebug.eq.1) then
-c$$$C open (65,file='fort.65',status='unknown',access='append')
-c$$$ write (65,*) 'In hbond'
-c$$$ call timer(65)
-c$$$ close (65)
-c$$$ end if
- ehb=zero
- do 10 i1=1,nhb
- ityhb=ihb(i1,1)
- j(1)=ihb(i1,2)
- j(2)=ihb(i1,3)
- j(3)=ihb(i1,4)
- la=ihb(i1,5)
- boa=bo(la)
- call dista2(j(2),j(3),rda,dxm,dym,dzm)
- drda(1)=dxm/rda
- drda(2)=dym/rda
- drda(3)=dzm/rda
- call calvalhb(j(1),j(2),j(3),ix,iy,iz,arg,hhb(i1),dvdc,dargdc)
- rhu1=rhb(ityhb)/rda
- rhu2=rda/rhb(ityhb)
- sinhu=sin(hhb(i1)/2.0)
- sin2=sinhu*sinhu
- exphu1=exp(-vhb1(ityhb)*boa)
- exphu2=exp(-vhb2(ityhb)*(rhu1+rhu2-2.0))
- if (lhbnew .eq. 0) then
- ehbh=(1.0-exphu1)*dehb(ityhb)*exphu2*sin2*sin2*sin2*sin2
- else
- ehbh=(1.0-exphu1)*dehb(ityhb)*exphu2*sin2*sin2
- endif
- ehb=ehb+ehbh
- estrain(j(2))=estrain(j(2))+ehbh !2nd atom energy
-
-**********************************************************************
-* *
-* Calculate first derivatives *
-* *
-**********************************************************************
- if (lhbnew .eq. 0) then
- dehbdbo=vhb1(ityhb)*exphu1*dehb(ityhb)*exphu2*sin2*sin2*
- $ sin2*sin2
- dehbdv=(1.0-exphu1)*dehb(ityhb)*exphu2*
- $ 4.0*sin2*sin2*sin2*sinhu*cos(hhb(i1)/2.0)
- dehbdrda=(1.0-exphu1)*dehb(ityhb)*sin2*sin2*sin2*sin2*
- $ vhb2(ityhb)*(rhb(ityhb)/(rda*rda)-1.0/rhb(ityhb))*exphu2
- else
- dehbdbo=vhb1(ityhb)*exphu1*dehb(ityhb)*exphu2*sin2*sin2
- dehbdv=(1.0-exphu1)*dehb(ityhb)*exphu2*
- $ 2.0*sin2*sinhu*cos(hhb(i1)/2.0)
- dehbdrda=(1.0-exphu1)*dehb(ityhb)*sin2*sin2*
- $ vhb2(ityhb)*(rhb(ityhb)/(rda*rda)-1.0/rhb(ityhb))*exphu2
- endif
-
- if (Lvirial.eq.1) then
- do k1=1,3
- do k2=1,3
- virial_tmp(k1,k2) = 0.0
- end do
- end do
- endif
-
- do k1=1,3
- ftmp = dehbdrda*drda(k1)
- d(k1,j(2))=d(k1,j(2))+ftmp
- d(k1,j(3))=d(k1,j(3))-ftmp
-
- if (Lvirial.eq.1) then
- do k1p=1,3
- virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+
- $ ftmp*c(j(2),k1p)-ftmp*c(j(3),k1p)
- end do
- endif
-
- end do
- if (Lvirial.eq.1) then
- virialsym(1) = virial_tmp(1,1)
- virialsym(2) = virial_tmp(2,2)
- virialsym(3) = virial_tmp(3,3)
- virialsym(4) = virial_tmp(1,2)
- virialsym(5) = virial_tmp(1,3)
- virialsym(6) = virial_tmp(2,3)
- do k1 = 1,6
- virial(k1) = virial(k1) + virialsym(k1)
- end do
-
- if (Latomvirial.eq.1) then
- frac = 1.0d0/2
- do k1 = 1,6
- vtmp = virialsym(k1)*frac
- ihu = j(2)
- atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp
- ihu = j(3)
- atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp
- end do
- endif
-
- endif
-
- if (Lvirial.eq.1) then
- do k1=1,3
- do k2=1,3
- virial_tmp(k1,k2) = 0.0
- end do
- end do
- endif
-
- do k1=1,3
- do k2=1,3
- ftmp = dehbdv*dvdc(k1,k2)
- d(k1,j(k2))=d(k1,j(k2))+ftmp
-
- if (Lvirial.eq.1) then
- do k1p=1,3
- virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(j(k2),k1p)
- end do
- endif
-
- end do
- end do
- if (Lvirial.eq.1) then
- virialsym(1) = virial_tmp(1,1)
- virialsym(2) = virial_tmp(2,2)
- virialsym(3) = virial_tmp(3,3)
- virialsym(4) = virial_tmp(1,2)
- virialsym(5) = virial_tmp(1,3)
- virialsym(6) = virial_tmp(2,3)
- do k1 = 1,6
- virial(k1) = virial(k1) + virialsym(k1)
- end do
-
- if (Latomvirial.eq.1) then
- frac = 1.0d0/3
- do k1 = 1,6
- vtmp = virialsym(k1)*frac
- do k2=1,3
- ihu=j(k2)
- atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp
- end do
- end do
- endif
-
- endif
-
- if (Lvirial.eq.1) then
- do k1=1,3
- do k2=1,3
- virial_tmp(k1,k2) = 0.0
- end do
- end do
- endif
-
- do i2=1,idbo1(la)
- ihu=idbo(la,i2)
- do k1=1,3
- ftmp = dehbdbo*dbondc(la,k1,i2)
- d(k1,ihu)=d(k1,ihu)+ftmp
-
- if (Lvirial.eq.1) then
- do k1p=1,3
- virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p)
- end do
- endif
-
- end do
- end do
- if (Lvirial.eq.1) then
- virialsym(1) = virial_tmp(1,1)
- virialsym(2) = virial_tmp(2,2)
- virialsym(3) = virial_tmp(3,3)
- virialsym(4) = virial_tmp(1,2)
- virialsym(5) = virial_tmp(1,3)
- virialsym(6) = virial_tmp(2,3)
- do k1 = 1,6
- virial(k1) = virial(k1) + virialsym(k1)
- end do
-
- if (Latomvirial.eq.1) then
- frac = 1.0d0/idbo1(la)
- do k1 = 1,6
- vtmp = virialsym(k1)*frac
- do i2=1,idbo1(la)
- ihu=idbo(la,i2)
- atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp
- end do
- end do
- endif
-
- endif
-
- 10 continue
- return
- end
-
-**********************************************************************
-**********************************************************************
-
- subroutine torang
-
-**********************************************************************
-#include "cbka.blk"
-#include "cbkabo.blk"
-#include "cbkbo.blk"
-#include "cbkbopi.blk"
-#include "cbkc.blk"
-#include "cbkconst.blk"
-#include "cbkd.blk"
-#include "cbkdbopindc.blk"
-#include "cbkdcell.blk"
-#include "cbkdhdc.blk"
-#include "cbkdrdc.blk"
-#include "cbkenergies.blk"
-#include "cbkff.blk"
-#include "cbkfftorang.blk"
-#include "cbkh.blk"
-#include "cbkia.blk"
-#include "cbkidbo.blk"
-#include "cbkinit.blk"
-#include "cbknubon2.blk"
-#include "cbkrbo.blk"
-#include "cbktorang.blk"
-#include "cbktorsion.blk"
-#include "cbktregime.blk"
-#include "cbkvalence.blk"
-#include "cellcoord.blk"
-#include "control.blk"
-#include "small.blk"
-
- DIMENSION A(3),DRDA(3),DADC(4),DRADC(3,4),DRBDC(3,4),
- $DRCDC(3,4),DHDDC(3,4),DHEDC(3,4),DRVDC(3,4),DTDC(3,4),
- $DNDC(3,4)
- dimension j(4),dh1rdc(3,3),dh2rdc(3,3),dargdc(3,3)
- dimension virial_tmp(3,3),virialsym(6)
-**********************************************************************
-* *
-* Calculate torsion angle energies and first derivatives *
-* *
-**********************************************************************
-c$$$ if (ndebug.eq.1) then
-c$$$C open (65,file='fort.65',status='unknown',access='append')
-c$$$ write (65,*) 'In torang'
-c$$$ call timer(65)
-c$$$ close (65)
-c$$$ end if
- do k1=1,3
- do k2=1,4
- dhddc(k1,k2)=0.0
- dhedc(k1,k2)=0.0
- dradc(k1,k2)=0.0
- drbdc(k1,k2)=0.0
- drcdc(k1,k2)=0.0
- end do
- end do
- et=0.0
- eth12=0.0
- eco=0.0
- dadc(1)=1.0
- dadc(2)=0.0
- dadc(3)=0.0
- dadc(4)=-1.0
- if (ntor.eq.0) return
-
- do 10 i1=1,ntor
- j(1)=it(i1,2)
- j(2)=it(i1,3)
- j(3)=it(i1,4)
- j(4)=it(i1,5)
-
- ity=it(i1,1)
- la=it(i1,6)
- lb=it(i1,7)
- lc=it(i1,8)
- call calvalres(j(1),j(2),j(3),arg1,ht1,dh1rdc,dargdc)
- call calvalres(j(2),j(3),j(4),arg2,ht2,dh2rdc,dargdc)
- boa=bo(la)-cutof2
- bob=bo(lb)-cutof2
- boc=bo(lc)-cutof2
- if (boa.lt.zero.or.bob.lt.zero.or.boc.lt.zero)
- $goto 10
- r42=0.0
- ivl1=ibsym(la)
- ivl2=ibsym(lb)
- ivl3=ibsym(lc)
- isign1=1
- isign2=1
- isign3=1
- rla=rbo(la)
- rlb=rbo(lb)
-
- call dista2(j(1),j(4),r4,a(1),a(2),a(3))
-**********************************************************************
-* *
-* Determine torsion angle *
-* *
-**********************************************************************
- d142=r4*r4
- rla=rbo(la)
- rlb=rbo(lb)
- rlc=rbo(lc)
- coshd=cos(ht1)
- coshe=cos(ht2)
- sinhd=sin(ht1)
- sinhe=sin(ht2)
- poem=2.0*rla*rlc*sinhd*sinhe
- poem2=poem*poem
- tel=rla*rla+rlb*rlb+rlc*rlc-d142-2.0*(rla*rlb*coshd-rla*rlc*
- $coshd*coshe+rlb*rlc*coshe)
- if (poem.lt.1e-20) poem=1e-20
- arg=tel/poem
- if (arg.gt.1.0) arg=1.0
- if (arg.lt.-1.0) arg=-1.0
- arg2=arg*arg
- thg(i1)=acos(arg)*rdndgr
- k1=j(1)
- k2=j(2)
- k3=j(3)
- k4=j(4)
- call dista2(k3,k2,dis,x3,y3,z3)
- y32z32=y3*y3+z3*z3
- wort1=sqrt(y32z32)+1e-6
- wort2=sqrt(y32z32+x3*x3)+1e-6
-* if (wort1.lt.1e-6) wort1=1e-6
-* if (wort2.lt.1e-6) wort2=1e-6
- sinalf=y3/wort1
- cosalf=z3/wort1
- sinbet=x3/wort2
- cosbet=wort1/wort2
- call dista2(k1,k2,dis,x1,y1,z1)
- x1=x1*cosbet-y1*sinalf*sinbet-z1*cosalf*sinbet
- y1=y1*cosalf-z1*sinalf
- wort3=sqrt(x1*x1+y1*y1)+1e-6
-* if (wort3.lt.1e-6) wort3=1e-6
- singam=y1/wort3
- cosgam=x1/wort3
- call dista2(k4,k2,dis,x4,y4,z4)
- x4=x4*cosbet-y4*sinalf*sinbet-z4*cosalf*sinbet
- y4=y4*cosalf-z4*sinalf
- y4=x4*singam-y4*cosgam
- if (y4.gt.0.0) thg(i1)=-thg(i1)
- if (thg(i1).lt.-179.999999d0) thg(i1)=-179.999999d0
- if (thg(i1).gt.179.999999d0) thg(i1)=179.999999d0
- th2=thg(i1)*dgrrdn
-**********************************************************************
-* *
-* Calculate torsion angle energy *
-* *
-**********************************************************************
- exbo1=abo(j(2))-valf(ia(j(2),1))
- exbo2=abo(j(3))-valf(ia(j(3),1))
- htovt=exbo1+exbo2
- expov=exp(vpar(26)*htovt)
- expov2=exp(-vpar(25)*(htovt))
- htov1=2.0+expov2
- htov2=1.0+expov+expov2
- etboadj=htov1/htov2
-
- btb2=bopi(lb)-1.0+etboadj
- bo2t=1.0-btb2
- bo2p=bo2t*bo2t
- bocor2=exp(v4(ity)*bo2p)
-
- hsin=sinhd*sinhe
- ethhulp=0.50*v1(ity)*(1.0+arg)+v2(ity)*bocor2*(1.0-arg2)+
- $v3(ity)*(0.50+2.0*arg2*arg-1.50*arg)
-
- exphua=exp(-vpar(24)*boa)
- exphub=exp(-vpar(24)*bob)
- exphuc=exp(-vpar(24)*boc)
- bocor4=(1.0-exphua)*(1.0-exphub)*(1.0-exphuc)
- eth=hsin*ethhulp*bocor4
-
- detdar=hsin*bocor4*(0.50*v1(ity)-2.0*v2(ity)*bocor2*arg+
- $v3(ity)*(6.0*arg2-1.5d0))
- detdhd=coshd*sinhe*bocor4*ethhulp
- detdhe=sinhd*coshe*bocor4*ethhulp
-
- detdboa=vpar(24)*exphua*(1.0-exphub)*(1.0-exphuc)*ethhulp*hsin
- detdbopib=-bocor4*2.0*v4(ity)*v2(ity)*
- $bo2t*bocor2*(1.0-arg2)*hsin
- detdbob=vpar(24)*exphub*(1.0-exphua)*
- $(1.0-exphuc)*ethhulp*hsin
- detdboc=vpar(24)*exphuc*(1.0-exphua)*
- $(1.0-exphub)*ethhulp*hsin
-
- detdsbo1=-(detdbopib)*
- $(vpar(25)*expov2/htov2+htov1*
- $(vpar(26)*expov-vpar(25)*expov2)/(htov2*htov2))
-
- et=et+eth
- estrain(j(2))=estrain(j(2))+0.50*eth !2nd atom energy
- estrain(j(3))=estrain(j(3))+0.50*eth !3rd atom energy
-
-**********************************************************************
-* *
-* Calculate conjugation energy *
-* *
-**********************************************************************
- ba=(boa-1.50)*(boa-1.50)
- bb=(bob-1.50)*(bob-1.50)
- bc=(boc-1.50)*(boc-1.50)
- exphua1=exp(-vpar(28)*ba)
- exphub1=exp(-vpar(28)*bb)
- exphuc1=exp(-vpar(28)*bc)
- sbo=exphua1*exphub1*exphuc1
- dbohua=-2.0*(boa-1.50)*vpar(28)*exphua1*exphub1*exphuc1
- dbohub=-2.0*(bob-1.50)*vpar(28)*exphua1*exphub1*exphuc1
- dbohuc=-2.0*(boc-1.50)*vpar(28)*exphua1*exphub1*exphuc1
- arghu0=(arg2-1.0)*sinhd*sinhe
- ehulp=vconj(ity)*(arghu0+1.0)
- ecoh=ehulp*sbo
- decodar=sbo*vconj(ity)*2.0*arg*sinhd*sinhe
- decodbola=dbohua*ehulp
- decodbolb=dbohub*ehulp
- decodbolc=dbohuc*ehulp
- decodhd=coshd*sinhe*vconj(ity)*sbo*(arg2-1.0)
- decodhe=coshe*sinhd*vconj(ity)*sbo*(arg2-1.0)
-
- eco=eco+ecoh
- estrain(j(2))=estrain(j(2))+0.50*ecoh !2nd atom energy
- estrain(j(3))=estrain(j(3))+0.50*ecoh !3rd atom energy
-
- 1 continue
-**********************************************************************
-* *
-* Calculate derivative torsion angle and conjugation energy *
-* to cartesian coordinates *
-* *
-**********************************************************************
- SINTH=SIN(THG(i1)*DGRRDN)
- IF (SINTH.GE.0.0.AND.SINTH.LT.1.0D-10) SINTH=1.0D-10
- IF (SINTH.LT.0.0.AND.SINTH.GT.-1.0D-10) SINTH=-1.0D-10
- IF (j(1).EQ.IB(LA,2)) THEN
- DO K1=1,3
- DRADC(K1,1)=DRDC(LA,K1,1)
- DRADC(K1,2)=DRDC(LA,K1,2)
- end do
- ELSE
- DO K1=1,3
- DRADC(K1,1)=DRDC(LA,K1,2)
- DRADC(K1,2)=DRDC(LA,K1,1)
- end do
- ENDIF
- IF (j(2).EQ.IB(LB,2)) THEN
- DO K1=1,3
- DRBDC(K1,2)=DRDC(LB,K1,1)
- DRBDC(K1,3)=DRDC(LB,K1,2)
- end do
- ELSE
- DO K1=1,3
- DRBDC(K1,2)=DRDC(LB,K1,2)
- DRBDC(K1,3)=DRDC(LB,K1,1)
- end do
- ENDIF
- IF (j(3).EQ.IB(LC,2)) THEN
- DO K1=1,3
- DRCDC(K1,3)=DRDC(LC,K1,1)
- DRCDC(K1,4)=DRDC(LC,K1,2)
- end do
- ELSE
- DO K1=1,3
- DRCDC(K1,3)=DRDC(LC,K1,2)
- DRCDC(K1,4)=DRDC(LC,K1,1)
- end do
- ENDIF
-
- do k1=1,3
- dhddc(1,k1)=dh1rdc(1,k1)
- dhddc(2,k1)=dh1rdc(2,k1)
- dhddc(3,k1)=dh1rdc(3,k1)
- dhedc(1,k1+1)=dh2rdc(1,k1)
- dhedc(2,k1+1)=dh2rdc(2,k1)
- dhedc(3,k1+1)=dh2rdc(3,k1)
- end do
-
-**********************************************************************
-* write (64,*)j(1),j(2),j(3),j(4)
-* do k1=1,3
-* write (64,'(10f12.4)')(dh1rdc(k1,k2),k2=1,3),
-* $(dhdc(ld,k1,k2),k2=1,3),(dhddc(k1,k2),k2=1,4)
-* write (64,'(10f12.4)')(dh2rdc(k1,k2),k2=1,3),
-* $(dhdc(le,k1,k2),k2=1,3),(dhedc(k1,k2),k2=1,4)
-* end do
-* write (64,*)
-**********************************************************************
- HTRA=RLA+COSHD*(RLC*COSHE-RLB)
- HTRB=RLB-RLA*COSHD-RLC*COSHE
- HTRC=RLC+COSHE*(RLA*COSHD-RLB)
- HTHD=RLA*SINHD*(RLB-RLC*COSHE)
- HTHE=RLC*SINHE*(RLB-RLA*COSHD)
- HNRA=RLC*SINHD*SINHE
- HNRC=RLA*SINHD*SINHE
- HNHD=RLA*RLC*COSHD*SINHE
- HNHE=RLA*RLC*SINHD*COSHE
-
- if (Lvirial.eq.1) then
- do k1=1,3
- do k2=1,3
- virial_tmp(k1,k2) = 0.0
- end do
- end do
- endif
-
- DO K1=1,3
- DRDA(K1)=A(K1)/R4
- DO K2=1,4
- DRVDC(K1,K2)=DRDA(K1)*DADC(K2)
- DTDC(K1,K2)=2.0*(DRADC(K1,K2)*HTRA+DRBDC(K1,K2)*HTRB+DRCDC(K1,K2
- $)*HTRC-DRVDC(K1,K2)*R4+DHDDC(K1,K2)*HTHD+DHEDC(K1,K2)*HTHE)
- DNDC(K1,K2)=2.0*(DRADC(K1,K2)*HNRA+DRCDC(K1,K2)*HNRC+DHDDC(K1,K2
- $)*HNHD+DHEDC(K1,K2)*HNHE)
- DARGTDC(i1,K1,K2)=(DTDC(K1,K2)-ARG*DNDC(K1,K2))/POEM
-
- ftmp = DARGTDC(i1,K1,K2)*detdar+
- $dargtdc(i1,k1,k2)*decodar+(detdhd+decodhd)*dhddc(k1,k2)+
- $(detdhe+decodhe)*dhedc(k1,k2)
- D(K1,J(K2))=D(K1,J(K2))+ftmp
-
- if (Lvirial.eq.1) then
- do k1p=1,3
- virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(j(k2),k1p)
- end do
- endif
-
- end do
- end do
- if (Lvirial.eq.1) then
- virialsym(1) = virial_tmp(1,1)
- virialsym(2) = virial_tmp(2,2)
- virialsym(3) = virial_tmp(3,3)
- virialsym(4) = virial_tmp(1,2)
- virialsym(5) = virial_tmp(1,3)
- virialsym(6) = virial_tmp(2,3)
- do k1 = 1,6
- virial(k1) = virial(k1) + virialsym(k1)
- end do
-
- if (Latomvirial.eq.1) then
- frac = 1.0d0/4
- do k1 = 1,6
- vtmp = virialsym(k1)*frac
- do k2=1,4
- ihu=j(k2)
- atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp
- end do
- end do
- endif
-
- endif
-
- if (Lvirial.eq.1) then
- do k1=1,3
- do k2=1,3
- virial_tmp(k1,k2) = 0.0
- end do
- end do
- endif
-
- do i2=1,idbo1(la)
- ihu=idbo(la,i2)
- do k1=1,3
- ftmp = dbondc(la,k1,i2)*(detdboa+decodbola)
- d(k1,ihu)=d(k1,ihu)+ftmp
-
- if (Lvirial.eq.1) then
- do k1p=1,3
- virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p)
- end do
- endif
-
- end do
- end do
- if (Lvirial.eq.1) then
- virialsym(1) = virial_tmp(1,1)
- virialsym(2) = virial_tmp(2,2)
- virialsym(3) = virial_tmp(3,3)
- virialsym(4) = virial_tmp(1,2)
- virialsym(5) = virial_tmp(1,3)
- virialsym(6) = virial_tmp(2,3)
- do k1 = 1,6
- virial(k1) = virial(k1) + virialsym(k1)
- end do
-
- if (Latomvirial.eq.1) then
- frac = 1.0d0/idbo1(la)
- do k1 = 1,6
- vtmp = virialsym(k1)*frac
- do i2=1,idbo1(la)
- ihu=idbo(la,i2)
- atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp
- end do
- end do
- endif
-
- endif
-
- if (Lvirial.eq.1) then
- do k1=1,3
- do k2=1,3
- virial_tmp(k1,k2) = 0.0
- end do
- end do
- endif
-
- do i2=1,idbo1(lb)
- ihu=idbo(lb,i2)
- do k1=1,3
- ftmp = dbondc(lb,k1,i2)*(detdbob+decodbolb)
- $ +dbopindc(lb,k1,i2)*detdbopib
- d(k1,ihu)=d(k1,ihu)+ftmp
-
- if (Lvirial.eq.1) then
- do k1p=1,3
- virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p)
- end do
- endif
-
- end do
- end do
- if (Lvirial.eq.1) then
- virialsym(1) = virial_tmp(1,1)
- virialsym(2) = virial_tmp(2,2)
- virialsym(3) = virial_tmp(3,3)
- virialsym(4) = virial_tmp(1,2)
- virialsym(5) = virial_tmp(1,3)
- virialsym(6) = virial_tmp(2,3)
- do k1 = 1,6
- virial(k1) = virial(k1) + virialsym(k1)
- end do
-
- if (Latomvirial.eq.1) then
- frac = 1.0d0/idbo1(lb)
- do k1 = 1,6
- vtmp = virialsym(k1)*frac
- do i2=1,idbo1(lb)
- ihu=idbo(lb,i2)
- atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp
- end do
- end do
- endif
-
- endif
-
- if (Lvirial.eq.1) then
- do k1=1,3
- do k2=1,3
- virial_tmp(k1,k2) = 0.0
- end do
- end do
- endif
-
- do i2=1,idbo1(lc)
- ihu=idbo(lc,i2)
- do k1=1,3
- ftmp = dbondc(lc,k1,i2)*(detdboc+decodbolc)
- d(k1,ihu)=d(k1,ihu)+ftmp
-
- if (Lvirial.eq.1) then
- do k1p=1,3
- virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p)
- end do
- endif
-
- end do
- end do
- if (Lvirial.eq.1) then
- virialsym(1) = virial_tmp(1,1)
- virialsym(2) = virial_tmp(2,2)
- virialsym(3) = virial_tmp(3,3)
- virialsym(4) = virial_tmp(1,2)
- virialsym(5) = virial_tmp(1,3)
- virialsym(6) = virial_tmp(2,3)
- do k1 = 1,6
- virial(k1) = virial(k1) + virialsym(k1)
- end do
-
- if (Latomvirial.eq.1) then
- frac = 1.0d0/idbo1(lc)
- do k1 = 1,6
- vtmp = virialsym(k1)*frac
- do i2=1,idbo1(lc)
- ihu=idbo(lc,i2)
- atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp
- end do
- end do
- endif
-
- endif
-
- do i2=1,ia(j(2),2)
- iob=ia(j(2),2+i2)
- ncubo=nubon2(j(2),i2)
- if (bo(ncubo).gt.0.0) then
-
- if (Lvirial.eq.1) then
- do k1=1,3
- do k2=1,3
- virial_tmp(k1,k2) = 0.0
- end do
- end do
- endif
-
- do i3=1,idbo1(ncubo)
- ihu=idbo(ncubo,i3)
- do k1=1,3
- ftmp = detdsbo1*dbondc(ncubo,k1,i3)
- d(k1,ihu)=d(k1,ihu)+ftmp
-
- if (Lvirial.eq.1) then
- do k1p=1,3
- virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p)
- end do
- endif
-
- end do
- end do
- if (Lvirial.eq.1) then
- virialsym(1) = virial_tmp(1,1)
- virialsym(2) = virial_tmp(2,2)
- virialsym(3) = virial_tmp(3,3)
- virialsym(4) = virial_tmp(1,2)
- virialsym(5) = virial_tmp(1,3)
- virialsym(6) = virial_tmp(2,3)
- do k1 = 1,6
- virial(k1) = virial(k1) + virialsym(k1)
- end do
-
- if (Latomvirial.eq.1) then
- frac = 1.0d0/idbo1(ncubo)
- do k1 = 1,6
- vtmp = virialsym(k1)*frac
- do i3=1,idbo1(ncubo)
- ihu=idbo(ncubo,i3)
- atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp
- end do
- end do
- endif
-
- endif
-
- endif
- end do
-
- do i2=1,ia(j(3),2)
- iob=ia(j(3),2+i2)
- ncubo=nubon2(j(3),i2)
- if (bo(ncubo).gt.0.0) then
-
- if (Lvirial.eq.1) then
- do k1=1,3
- do k2=1,3
- virial_tmp(k1,k2) = 0.0
- end do
- end do
- endif
-
- do i3=1,idbo1(ncubo)
- ihu=idbo(ncubo,i3)
- do k1=1,3
- ftmp = detdsbo1*dbondc(ncubo,k1,i3)
- d(k1,ihu)=d(k1,ihu)+ftmp
-
- if (Lvirial.eq.1) then
- do k1p=1,3
- virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p)
- end do
- endif
-
- end do
- end do
-
- if (Lvirial.eq.1) then
- virialsym(1) = virial_tmp(1,1)
- virialsym(2) = virial_tmp(2,2)
- virialsym(3) = virial_tmp(3,3)
- virialsym(4) = virial_tmp(1,2)
- virialsym(5) = virial_tmp(1,3)
- virialsym(6) = virial_tmp(2,3)
- do k1 = 1,6
- virial(k1) = virial(k1) + virialsym(k1)
- end do
-
- if (Latomvirial.eq.1) then
- frac = 1.0d0/idbo1(ncubo)
- do k1 = 1,6
- vtmp = virialsym(k1)*frac
- do i3=1,idbo1(ncubo)
- ihu=idbo(ncubo,i3)
- atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp
- end do
- end do
- endif
-
- endif
-
- endif
- end do
-
- 10 continue
-
- return
- end
-**********************************************************************
-**********************************************************************
-
- subroutine nonbon
-
-**********************************************************************
-#include "cbka.blk"
-#include "cbkc.blk"
-#include "cbkch.blk"
-#include "cbkconst.blk"
-#include "cbkd.blk"
-#include "cbkdcell.blk"
-#include "cbkenergies.blk"
-#include "cbkff.blk"
-#include "cbkia.blk"
-#include "cbknonbon.blk"
-#include "cbkpairs.blk"
-#include "cbknvlown.blk"
-#include "cellcoord.blk"
-#include "control.blk"
-#include "small.blk"
-
- dimension a(3),da(6)
- dimension virial_tmp(3,3),virialsym(6)
-**********************************************************************
-* *
-* Calculate vdWaals and Coulomb energies and derivatives *
-* *
-**********************************************************************
-c$$$ if (ndebug.eq.1) then
-c$$$C open (65,file='fort.65',status='unknown',access='append')
-c$$$ write (65,*) 'In nonbon'
-c$$$ call timer(65)
-c$$$ end if
-
- ew=0.0
- ep=0.0
-
- c1c=332.0638
- third=one/three
- fothird=4.0/3.0
- twothird=2.0/3.0
- h15=(vpar(29)-1.0)/vpar(29)
-
- nptmp=0
- nstmp=0
- do 10 ivl=1,nvpair-nvlself
-c Use precomputed midpoint criterion to decide if interaction is owned.
- if (nvlown(ivl).eq.1) then
-
- i1=nvl1(ivl)
- i2=nvl2(ivl)
-
- call dista2(i1,i2,rr,a(1),a(2),a(3))
- if (rr.gt.swb.or.rr.lt.0.001) goto 10
-
- ity1=ia(i1,1)
- ity2=ia(i2,1)
- imol1=iag(i1,3+mbond)
- imol2=iag(i2,3+mbond)
- rr2=rr*rr
-
- sw=1.0
- sw1=0.0
- call taper(rr,rr2)
-**********************************************************************
-* *
-* Calculate vdWaals energy *
-* *
-**********************************************************************
- p1=p1co(ity1,ity2)
- p2=p2co(ity1,ity2)
- p3=p3co(ity1,ity2)
- hulpw=(rr**vpar(29)+gamwco(ity1,ity2))
- rrw=hulpw**(1.0/vpar(29))
- h1=exp(p3*(1.0-rrw/p1))
- h2=exp(0.50*p3*(1.0-rrw/p1))
-
- ewh=p2*(h1-2.0*h2)
- rrhuw=rr**(vpar(29)-1.0)
- dewdr=(p2*p3/p1)*(h2-h1)*rrhuw*(hulpw**(-h15))
-
-**********************************************************************
-* *
-* Calculate Coulomb energy *
-* *
-**********************************************************************
- q1q2=ch(i1)*ch(i2)
- hulp1=(rr2*rr+gamcco(ity1,ity2))
- eph=c1c*q1q2/(hulp1**third)
- depdr=-c1c*q1q2*rr2/(hulp1**fothird)
-**********************************************************************
-* *
-* Taper correction *
-* *
-**********************************************************************
- ephtap=eph*sw
- depdrtap=depdr*sw+eph*sw1
- ewhtap=ewh*sw
- dewdrtap=dewdr*sw+ewh*sw1
-
-* write (64,*)i1,i2,p1,p2,p3,gamwco(ity1,ity2),vpar(29),ewh,ew
- ew=ew+ewhtap
- ep=ep+ephtap
- estrain(i1)=estrain(i1)+0.50*(ewhtap+ephtap) !1st atom energy
- estrain(i2)=estrain(i2)+0.50*(ewhtap+ephtap) !2nd atom energy
-
-**********************************************************************
-* *
-* Calculate derivatives vdWaals energy to cartesian *
-* coordinates *
-* *
-**********************************************************************
-
- if (Lvirial.eq.1) then
- do k1=1,3
- do k2=1,3
- virial_tmp(k1,k2) = 0.0
- end do
- end do
- endif
-
- do k4=1,3
- ftmp = (dewdrtap+depdrtap)*(a(k4)/rr)
- d(k4,i1)=d(k4,i1)+ftmp
- d(k4,i2)=d(k4,i2)-ftmp
- if (Lvirial.eq.1) then
- do k1p=1,3
- virial_tmp(k4,k1p)=virial_tmp(k4,k1p)+
- $ ftmp*c(i1,k1p)-ftmp*c(i2,k1p)
- end do
- endif
- end do
-
- if (Lvirial.eq.1) then
- virialsym(1) = virial_tmp(1,1)
- virialsym(2) = virial_tmp(2,2)
- virialsym(3) = virial_tmp(3,3)
- virialsym(4) = virial_tmp(1,2)
- virialsym(5) = virial_tmp(1,3)
- virialsym(6) = virial_tmp(2,3)
- do k1 = 1,6
- virial(k1) = virial(k1) + virialsym(k1)
- end do
-
- if (Latomvirial.eq.1) then
- frac = 1.0d0/2
- do k1 = 1,6
- vtmp = virialsym(k1)*frac
- ihu=i1
- atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp
- ihu=i2
- atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp
- end do
- endif
-
- endif
-
- endif
-
- 10 continue
-
- return
- end
-
-**********************************************************************
-**********************************************************************
-
- subroutine efield
-
-**********************************************************************
-#include "cbka.blk"
-#include "cbkc.blk"
-#include "cbkch.blk"
-#include "cbkcha.blk"
-#include "cbkd.blk"
-#include "cbkefield.blk"
-#include "cbkenergies.blk"
-#include "cbktregime.blk"
-#include "control.blk"
-#include "small.blk"
-c$$$ if (ndebug.eq.1) then
-c$$$C open (65,file='fort.65',status='unknown',access='append')
-c$$$ write (65,*) 'In efield'
-c$$$ call timer(65)
-c$$$ close (65)
-c$$$ end if
-**********************************************************************
-* *
-* Electric field *
-* *
-**********************************************************************
- efi=0.0
- efix=0.0
- efiy=0.0
- efiz=0.0
- c1c=332.0638 !Coulomb energy conversion
- c1=23.02 !conversion from kcal to eV
-
- if (ifieldx.eq.1) then
- do i1=1,na
- efih=vfieldx*c1*c1c*ch(i1)*c(i1,1)
- efix=efix+efih
- estrain(i1)=estrain(i1)+efih !atom energy
-
- defidc=c1*c1c*vfieldx*ch(i1)
- d(1,i1)=d(1,i1)+defidc
- end do
- end if
-
- if (ifieldy.eq.1) then
- do i1=1,na
- efih=vfieldy*c1*c1c*ch(i1)*c(i1,2)
- efiy=efiy+efih
- estrain(i1)=estrain(i1)+efih !atom energy
-
- defidc=c1*c1c*vfieldy*ch(i1)
- d(2,i1)=d(2,i1)+defidc
- end do
- end if
-
- if (ifieldz.eq.1) then
- do i1=1,na
- efih=vfieldz*c1*c1c*ch(i1)*c(i1,3)
- efiz=efiz+efih
- estrain(i1)=estrain(i1)+efih !atom energy
-
- defidc=c1*c1c*vfieldz*ch(i1)
- d(3,i1)=d(3,i1)+defidc
- end do
- end if
-
- efi=efix+efiy+efiz
- return
- end
-**********************************************************************
-**********************************************************************
-
- subroutine restraint
-
-**********************************************************************
-#include "cbka.blk"
-#include "cbkatomcoord.blk"
-#include "cbkc.blk"
-#include "cbkconst.blk"
-#include "cbkd.blk"
-#include "cbkenergies.blk"
-#include "cbkrestr.blk"
-#include "cbktorang.blk"
-#include "cbktorsion.blk"
-#include "cbktregime.blk"
-#include "control.blk"
-#include "small.blk"
-#include "cbkinit.blk"
- dimension drda(3),j(4),dhrdc(3,3),dargdc(3,3)
-**********************************************************************
-* *
-* Calculate distance restraint energy *
-* *
-**********************************************************************
-c$$$ if (ndebug.eq.1) then
-c$$$C open (65,file='fort.65',status='unknown',access='append')
-c$$$ write (65,*) 'In restraint'
-c$$$ call timer(65)
-c$$$ close (65)
-c$$$ end if
- do i1=1,nrestra
- ih1=irstra(i1,1)
- ih2=irstra(i1,2)
- if (itend(i1).eq.0.or.(mdstep.gt.itstart(i1).and.mdstep.lt.
- $itend(i1))) then
- call dista2(ih1,ih2,rr,dx,dy,dz)
- diffr=rr-rrstra(i1)
-* diffr=rrstra(i1)
- exphu=exp(-vkrst2(i1)*(diffr*diffr))
- erh=vkrstr(i1)*(1.0-exphu)
- deresdr=2.0*vkrst2(i1)*diffr*vkrstr(i1)*exphu
-* deresdr=-2.0*vkrst2(i1)*diffr*vkrstr(i1)*exphu
- eres=eres+erh
- drda(1)=dx/rr
- drda(2)=dy/rr
- drda(3)=dz/rr
- do k1=1,3
- d(k1,ih1)=d(k1,ih1)+deresdr*drda(k1)
- d(k1,ih2)=d(k1,ih2)-deresdr*drda(k1)
- end do
- end if
- end do
-
-**********************************************************************
-* *
-* Calculate angle restraint energy *
-* *
-**********************************************************************
- do i1=1,nrestrav
- j(1)=irstrav(i1,1)
- j(2)=irstrav(i1,2)
- j(3)=irstrav(i1,3)
- ittr=0
-* do i2=1,nval
-* if (j(1).eq.iv(i2,2).and.j(2).eq.iv(i2,3).and.j(3).eq.iv(i2,4))
-* $ittr=i2
-* end do
-* if (ittr.eq.0) stop 'Wrong valence angle restraint'
- call calvalres(j(1),j(2),j(3),arg,hr,dhrdc,dargdc)
- vaval=hr*rdndgr
- diffv=-(vaval-vrstra(i1))*dgrrdn
- exphu=exp(-vkr2v(i1)*(diffv*diffv))
- erh=vkrv(i1)*(1.0-exphu)
- deresdv=-2.0*vkr2v(i1)*diffv*vkrv(i1)*exphu
- eres=eres+erh
- do k1=1,3
- do k2=1,3
- d(k1,j(k2))=d(k1,j(k2))+deresdv*dhrdc(k1,k2)
- end do
- end do
-
- end do
-
-**********************************************************************
-* *
-* Calculate torsion restraint energy *
-* *
-**********************************************************************
- do i1=1,nrestrat
- j(1)=irstrat(i1,1)
- j(2)=irstrat(i1,2)
- j(3)=irstrat(i1,3)
- j(4)=irstrat(i1,4)
- ittr=0
- do i2=1,ntor
- if (j(1).eq.it(i2,2).and.j(2).eq.it(i2,3).and.j(3).eq.it(i2,4)
- $.and.j(4).eq.it(i2,5)) ittr=i2
- if (j(4).eq.it(i2,2).and.j(3).eq.it(i2,3).and.j(2).eq.it(i2,4)
- $.and.j(1).eq.it(i2,5)) ittr=i2
- end do
- if (ittr.eq.0) then
- write (*,*)'Wrong torsion restraint'
- write (*,*)i1,j(1),j(2),j(3),j(4)
- stop 'Wrong torsion restraint'
- end if
- vtor=thg(ittr)
- difft=-(vtor-trstra(i1))*dgrrdn
- exphu=exp(-vkr2t(i1)*(difft*difft))
- erh=vkrt(i1)*(1.0-exphu)
- deresdt=2.0*vkr2t(i1)*difft*vkrt(i1)*exphu
- if (vtor.lt.zero) deresdt=-deresdt
- eres=eres+erh
- do k1=1,3
- do k2=1,4
- d(k1,j(k2))=d(k1,j(k2))+deresdt*dargtdc(ittr,k1,k2)
- end do
- end do
-
- end do
-**********************************************************************
-* *
-* Calculate mass centre restraint energy *
-* *
-**********************************************************************
- do i1=1,nrestram
- j1=irstram(i1,2)
- j2=irstram(i1,3)
- j3=irstram(i1,4)
- j4=irstram(i1,5)
- kdir=irstram(i1,1)
- cmx1=0.0
- cmy1=0.0
- cmz1=0.0
- cmx2=0.0
- cmy2=0.0
- cmz2=0.0
- summas1=0.0
- summas2=0.0
- do i2=j1,j2
- cmx1=cmx1+c(i2,1)*xmasat(i2)
- cmy1=cmy1+c(i2,2)*xmasat(i2)
- cmz1=cmz1+c(i2,3)*xmasat(i2)
- summas1=summas1+xmasat(i2)
- end do
- cmx1=cmx1/summas1
- cmy1=cmy1/summas1
- cmz1=cmz1/summas1
- if (mdstep.lt.2) then
- rmstrax(i1)=cmx1
- rmstray(i1)=cmy1
- rmstraz(i1)=cmz1
- end if
- if (kdir.le.3) then
- do i2=j3,j4
- cmx2=cmx2+c(i2,1)*xmasat(i2)
- cmy2=cmy2+c(i2,2)*xmasat(i2)
- cmz2=cmz2+c(i2,3)*xmasat(i2)
- summas2=summas2+xmasat(i2)
- end do
- cmx2=cmx2/summas2
- cmy2=cmy2/summas2
- cmz2=cmz2/summas2
- end if
- if (kdir.eq.1) dist=cmx1-cmx2
- if (kdir.eq.2) dist=cmy1-cmy2
- if (kdir.eq.3) dist=cmz1-cmz2
- if (kdir.eq.4) then
- distx=cmx1-rmstrax(i1)
- disty=cmy1-rmstray(i1)
- distz=cmz1-rmstraz(i1)
- dist=sqrt(distx*distx+disty*disty+distz*distz)
- end if
- dismacen(i1)=dist
- dist=dist-rmstra1(i1)
- erh=rmstra2(i1)*dist*dist
- deresdr=2.0*dist*rmstra2(i1)
-* exphu=exp(-rmstra3(i1)*(dist*dist))
-* erh=rmstra2(i1)*(1.0-exphu)
-* deresdr=2.0*rmstra3(i1)*dist*rmstra2(i1)*exphu
- eres=eres+erh
- if (kdir.le.3) then
- do i2=j1,j2
- d(kdir,i2)=d(kdir,i2)+deresdr*xmasat(i2)/summas1
- end do
- do i2=j3,j4
- d(kdir,i2)=d(kdir,i2)-deresdr*xmasat(i2)/summas2
- end do
- end if
- if (kdir.eq.4.and.mdstep.gt.5) then
- do i2=j1,j2
- d(1,i2)=d(1,i2)+deresdr*(distx/dist)*(xmasat(i2)/summas1)
- d(2,i2)=d(2,i2)+deresdr*(disty/dist)*(xmasat(i2)/summas1)
- d(3,i2)=d(3,i2)+deresdr*(distz/dist)*(xmasat(i2)/summas1)
- end do
- end if
- end do
-**********************************************************************
-* *
-* Calculate morphing energy *
-* *
-**********************************************************************
- if (imorph.eq.1) then
- distot=zero
- do i1=1,na
- dmx=c(i1,1)-cmo(i1,1)
- dmy=c(i1,2)-cmo(i1,2)
- dmz=c(i1,3)-cmo(i1,3)
- dism=sqrt(dmx*dmx+dmy*dmy+dmz*dmz)
- distot=distot+dism
-* exphu=exp(-vmo2(i1)*(dism*dism))
-* erh=vmo1(i1)*(1.0-exphu)
- erh=vmo1(i1)*dism
- eres=eres+erh
-* deresddis=2.0*vmo2(i1)*dism*vmo1(i1)*exphu
- deresddis=vmo1(i1)
- drda1=dmx/dism
- drda2=dmy/dism
- drda3=dmz/dism
- d(1,i1)=d(1,i1)+deresddis*drda1
- d(2,i1)=d(2,i1)+deresddis*drda2
- d(3,i1)=d(3,i1)+deresddis*drda3
- end do
-
- end if
-
-
- return
- end
-**********************************************************************
-********************************************************************
-
- subroutine calvalres (ja1,ja2,ja3,arg,hr,dhrdc,dargdc)
-
-**********************************************************************
-#include "cbka.blk"
-#include "cbkc.blk"
- dimension a(3),b(3),j(3),dradc(3,3),drbdc(3,3),dtdc(3,3),
- $dargdc(3,3),dndc(3,3),dadc(3),dbdc(3),dhrdc(3,3)
-**********************************************************************
-* *
-* Calculate valency angles and their derivatives to cartesian *
-* coordinates for restraint calculations *
-* *
-**********************************************************************
-c$$$* if (ndebug.eq.1) then
-c$$$C* open (65,file='fort.65',status='unknown',access='append')
-c$$$* write (65,*) 'In calvalres'
-c$$$* call timer(65)
-c$$$* close (65)
-c$$$* end if
-
- dadc(1)=-1.0
- dadc(2)=1.0
- dadc(3)=0.0
- dbdc(1)=0.0
- dbdc(2)=1.0
- dbdc(3)=-1.0
- do k1=1,3
- do k2=1,3
- dradc(k1,k2)=0.0
- drbdc(k1,k2)=0.0
- end do
- end do
-**********************************************************************
-* *
-* Determine valency angle *
-* *
-**********************************************************************
- call dista2(ja1,ja2,rla,dx1,dy1,dz1)
- call dista2(ja2,ja3,rlb,dx2,dy2,dz2)
-
- a(1)=-dx1
- a(2)=-dy1
- a(3)=-dz1
- b(1)=dx2
- b(2)=dy2
- b(3)=dz2
- poem=rla*rlb
- tel=a(1)*b(1)+a(2)*b(2)+a(3)*b(3)
- arg=tel/poem
- arg2=arg*arg
- s1ma22=1.0-arg2
- if (s1ma22.lt.1.0d-10) s1ma22=1.0d-10
- s1ma2=sqrt(s1ma22)
- if (arg.gt.1.0) arg=1.0
- if (arg.lt.-1.0) arg=-1.0
- hr=acos(arg)
-**********************************************************************
-* *
-* Calculate derivative valency angle to cartesian coordinates *
-* *
-**********************************************************************
- do k1=1,3
- dradc(k1,1)=-a(k1)/rla
- dradc(k1,2)=a(k1)/rla
- end do
-
- do k1=1,3
- drbdc(k1,2)=b(k1)/rlb
- drbdc(k1,3)=-b(k1)/rlb
- end do
-
- do k1=1,3
- do k2=1,3
- dndc(k1,k2)=rla*drbdc(k1,k2)+rlb*dradc(k1,k2)
- dtdc(k1,k2)=a(k1)*dbdc(k2)+b(k1)*dadc(k2)
- dargdc(k1,k2)=(dtdc(k1,k2)-arg*dndc(k1,k2))/poem
- dhrdc(k1,k2)=-dargdc(k1,k2)/s1ma2
- end do
- end do
-
- 10 continue
-
- return
- end
-**********************************************************************
-********************************************************************
-
- subroutine calvalhb (ja1,ja2,ja3,ix,iy,iz,arg,hr,dhrdc,dargdc)
-
-**********************************************************************
-#include "cbka.blk"
-#include "cbkc.blk"
- dimension a(3),b(3),j(3),dradc(3,3),drbdc(3,3),dtdc(3,3),
- $dargdc(3,3),dndc(3,3),dadc(3),dbdc(3),dhrdc(3,3)
-**********************************************************************
-* *
-* Calculate valency angles and their derivatives to cartesian *
-* coordinates for hydrogen bond calculations *
-* *
-**********************************************************************
-c$$$* if (ndebug.eq.1) then
-c$$$* open (65,file='fort.65',status='unknown',access='append')
-c$$$* write (65,*) 'In calvalhb'
-c$$$* call timer(65)
-c$$$* close (65)
-c$$$* end if
-
- dadc(1)=-1.0
- dadc(2)=1.0
- dadc(3)=0.0
- dbdc(1)=0.0
- dbdc(2)=1.0
- dbdc(3)=-1.0
- do k1=1,3
- do k2=1,3
- dradc(k1,k2)=0.0
- drbdc(k1,k2)=0.0
- end do
- end do
-**********************************************************************
-* *
-* Determine valency angle *
-* *
-**********************************************************************
- call dista2(ja1,ja2,rla,dx1,dy1,dz1)
- call dista2(ja2,ja3,rlb,dx2,dy2,dz2)
-
- a(1)=-dx1
- a(2)=-dy1
- a(3)=-dz1
- b(1)=dx2
- b(2)=dy2
- b(3)=dz2
- poem=rla*rlb
- tel=a(1)*b(1)+a(2)*b(2)+a(3)*b(3)
- arg=tel/poem
- arg2=arg*arg
- s1ma22=1.0-arg2
- if (s1ma22.lt.1.0d-10) s1ma22=1.0d-10
- s1ma2=sqrt(s1ma22)
- if (arg.gt.1.0) arg=1.0
- if (arg.lt.-1.0) arg=-1.0
- hr=acos(arg)
-**********************************************************************
-* *
-* Calculate derivative valency angle to cartesian coordinates *
-* *
-**********************************************************************
- do k1=1,3
- dradc(k1,1)=-a(k1)/rla
- dradc(k1,2)=a(k1)/rla
- end do
-
- do k1=1,3
- drbdc(k1,2)=b(k1)/rlb
- drbdc(k1,3)=-b(k1)/rlb
- end do
-
- do k1=1,3
- do k2=1,3
- dndc(k1,k2)=rla*drbdc(k1,k2)+rlb*dradc(k1,k2)
- dtdc(k1,k2)=a(k1)*dbdc(k2)+b(k1)*dadc(k2)
- dargdc(k1,k2)=(dtdc(k1,k2)-arg*dndc(k1,k2))/poem
- dhrdc(k1,k2)=-dargdc(k1,k2)/s1ma2
- end do
- end do
-
- 10 continue
-
- return
- end
-**********************************************************************
-**********************************************************************
-
- subroutine caltor(ja1,ja2,ja3,ja4,ht)
-
-**********************************************************************
-#include "cbka.blk"
-#include "cbkenergies.blk"
-#include "cbktregime.blk"
-#include "control.blk"
-#include "cbkinit.blk"
- DIMENSION A(3),DRDA(3),DADC(4),DRADC(3,4),DRBDC(3,4),
- $DRCDC(3,4),DHDDC(3,4),DHEDC(3,4),DRVDC(3,4),DTDC(3,4),
- $DNDC(3,4)
- dimension j(4),dvdc1(3,3),dargdc1(3,3),dvdc2(3,3),dargdc2(3,3)
-**********************************************************************
-* *
-* Calculate torsion angle (for internal coordinates output) *
-* *
-**********************************************************************
-c$$$ if (ndebug.eq.1) then
-c$$$C open (65,file='fort.65',status='unknown',access='append')
-c$$$ write (65,*) 'In caltor'
-c$$$ call timer(65)
-c$$$ close (65)
-c$$$ end if
- do k1=1,3
- do k2=1,4
- dhddc(k1,k2)=0.0
- dhedc(k1,k2)=0.0
- dradc(k1,k2)=0.0
- drbdc(k1,k2)=0.0
- drcdc(k1,k2)=0.0
- end do
- end do
- et=0.0
- eco=0.0
- dadc(1)=1.0
- dadc(2)=0.0
- dadc(3)=0.0
- dadc(4)=-1.0
- call dista2(ja1,ja2,rla,dx1,dy1,dz1)
- call dista2(ja2,ja3,rlb,dx2,dy2,dz2)
- call dista2(ja3,ja4,rlc,dx2,dy2,dz2)
- call dista2(ja1,ja4,r4,dx2,dy2,dz2)
- call calvalres(ja1,ja2,ja3,arg1,h1,dvdc1,dargdc1)
- call calvalres(ja2,ja3,ja4,arg2,h2,dvdc2,dargdc2)
-**********************************************************************
-* *
-* Determine torsion angle *
-* *
-**********************************************************************
- d142=r4*r4
- coshd=cos(h1)
- coshe=cos(h2)
- sinhd=sin(h1)
- sinhe=sin(h2)
- poem=2.0*rla*rlc*sinhd*sinhe
- poem2=poem*poem
- tel=rla*rla+rlb*rlb+rlc*rlc-d142-2.0*(rla*rlb*coshd-rla*rlc*
- $coshd*coshe+rlb*rlc*coshe)
- arg=tel/poem
- if (arg.gt.1.0) arg=1.0
- if (arg.lt.-1.0) arg=-1.0
- arg2=arg*arg
- ht=acos(arg)*rdndgr
- k1=ja1
- k2=ja2
- k3=ja3
- k4=ja4
- call dista2(k3,k2,dis,x3,y3,z3)
- y32z32=y3*y3+z3*z3
- wort1=sqrt(y32z32)+1e-6
- wort2=sqrt(y32z32+x3*x3)+1e-6
- sinalf=y3/wort1
- cosalf=z3/wort1
- sinbet=x3/wort2
- cosbet=wort1/wort2
- call dista2(k1,k2,dis,x1,y1,z1)
- x1=x1*cosbet-y1*sinalf*sinbet-z1*cosalf*sinbet
- y1=y1*cosalf-z1*sinalf
- wort3=sqrt(x1*x1+y1*y1)+1e-6
- singam=y1/wort3
- cosgam=x1/wort3
- call dista2(k4,k2,dis,x4,y4,z4)
- x4=x4*cosbet-y4*sinalf*sinbet-z4*cosalf*sinbet
- y4=y4*cosalf-z4*sinalf
- y4=x4*singam-y4*cosgam
- if (y4.gt.0.0) ht=-ht
- if (ht.lt.-179.999999d0) ht=-179.999999d0
- if (ht.gt.179.999999d0) ht=179.999999d0
-
- return
- end
-**********************************************************************
diff --git a/lib/reax/reax_reac.F b/lib/reax/reax_reac.F
deleted file mode 100644
index 73c625d7f10255c0239a7231f542c3d33d1e435a..0000000000000000000000000000000000000000
--- a/lib/reax/reax_reac.F
+++ /dev/null
@@ -1,312 +0,0 @@
-**********************************************************************
-* *
-* REAXFF Reactive force field program *
-* *
-* Developed and written by Adri van Duin, duin@wag.caltech.edu *
-* *
-* Copyright (c) 2001-2010 California Institute of Technology *
-* *
-* This is an open-source program. Feel free to modify its *
-* contents. Please keep me informed of any useful modification *
-* or addition that you made. Please do not distribute this *
-* program to others; if people are interested in obtaining *
-* a copy of this program let them contact me first. *
-* *
-**********************************************************************
-**********************************************************************
-* *
-* REAXFF Reactive force field program *
-* *
-* Developed and written by Adri van Duin, duin@wag.caltech.edu *
-* *
-* Copyright (c) 2001-2010 California Institute of Technology *
-* *
-* This is an open-source program. Feel free to modify its *
-* contents. Please keep me informed of any useful modification *
-* or addition that you made. Please do not distribute this *
-* program to others; if people are interested in obtaining *
-* a copy of this program let them contact me first. *
-* *
-**********************************************************************
-**********************************************************************
-
- subroutine encalc
-
-**********************************************************************
-#include "cbka.blk"
-#include "cbkc.blk"
-#include "cbkcha.blk"
-#include "cbkconst.blk"
-#include "cbkd.blk"
-#include "cbkdcell.blk"
-#include "cbkenergies.blk"
-#include "cellcoord.blk"
-#include "control.blk"
-#include "small.blk"
-**********************************************************************
-* *
-* Calculate energy and first derivatives *
-* *
-**********************************************************************
-c$$$ if (ndebug.eq.1) then
-c$$$C open (65,file='fort.65',status='unknown',access='append')
-c$$$ write (65,*) 'In encalc'
-c$$$ call timer(65)
-c$$$ close (65)
-c$$$ end if
- estrc=0.0
- do i1=1,na
- do i2=1,3
- d(i2,i1)=0.0
- estrain(i1)=0.0
- end do
- end do
- eb=zero
- ea=zero
- elp=zero
- emol=zero
- ev=zero
- ehb=zero
- ecoa=zero
- epen=zero
- et=zero
- eco=zero
- eres=zero
- eradbo=zero
- efi=zero
-
- if(Lvirial.eq.1) then
- do k1 = 1,6
- virial(k1) = zero
- end do
- endif
-
- if (Latomvirial.eq.1) then
- do i1=1,na
- do i2=1,6
- atomvirial(i2,i1)=0.0
- end do
- end do
- endif
-
- call boncor
- call lonpar
- call covbon
- call ovcor
-
- call srtang !Determine valency angles
- call srttor !Determine torsion angles
-* call srtoop !Determine out of plane angles
- call srthb !Determine hydrogen bonds
-
- call calval
- call valang
-
-* call oopang
-
- call torang
- call hbond
- !print *, 'called hbond'
- !print *, nchaud
-
- call nonbon
- call efield
-
- call restraint
-
-c
-c Use this to print out fort.73-style energies
-c It only works correctly in serial mode
-c
-c write (6,'(i8,1x,14(f21.10,1x))')mdstep+nprevrun,eb,ea,elp,
-c $emol,ev+epen,ecoa,ehb,et,eco,ew,ep,ech,efi
-
- estrc=eb+ea+elp+ev+ecoa+emol+epen+et+ehb+eco+ew+ep+ncha2*ech+efi
- if (estrc.gt.zero) return
- if (estrc.le.zero) then
- goto 10
- else
- write (*,*)mdstep
- write (92,*)eb,ea,elp,ev,ecoa,emol,epen,eoop,et,eco,ew,
- $ep,ech,eres,eradbo
- stop 'Energy not a number'
- end if
-
- 10 continue
- return
- end
-**********************************************************************
-**********************************************************************
-
- subroutine reaxinit
-
-**********************************************************************
-#include "cbka.blk"
-#include "cbkatomcoord.blk"
-#include "cbkc.blk"
-#include "cbkcha.blk"
-#include "cbkconst.blk"
-#include "cbkdcell.blk"
-#include "cbkdistan.blk"
-#include "cbkenergies.blk"
-#include "cbkia.blk"
-#include "cbkimove.blk"
-#include "cbkinit.blk"
-#include "cbktregime.blk"
-#include "cellcoord.blk"
-#include "control.blk"
-#include "opt.blk"
-#include "small.blk"
-**********************************************************************
-c$$$ if (ndebug.eq.1) then
-c$$$C open (65,file='fort.65',status='unknown',access='append')
-c$$$ write (65,*) 'In init'
-c$$$ call timer(65)
-c$$$ close (65)
-c$$$ end if
-**********************************************************************
-* *
-* Initialize variables *
-* *
-**********************************************************************
- convmd=4.184*1.0d26
- pi=3.14159265
- avognr=6.0221367d23
- rdndgr=180.0/pi
- dgrrdn=1.0/rdndgr
- rgasc=8.314510
- caljou=4.184
- xjouca=1.0/caljou
- ech=zero
- zero=0.0
- one=1.0
- two=2.0
- three=3.0
- half=one/two
- nzero=0
- none=1
- ntwo=2
- nthree=3
- invt=0
- ndata2=0
- iheatf=0
- nradcount=0
- itemp=1
- xinh=zero
- ifieldx=0
- ifieldy=0
- ifieldz=0
- mdstep=0
- kx=0
- ky=0
- kz=0
- nit=0
- nbon=0
- angle(1)=90.0
- angle(2)=90.0
- angle(3)=90.0
- axiss(1)=zero
- axiss(2)=zero
- axiss(3)=zero
- do i1=1,nat
- id(i1,1)=0
- id(i1,2)=0
- id(i1,3)=0
- end do
- icgeo=0
- sumhe=zero
- ustime=zero
- systime=zero
- vpmax=zero
- vpmin=zero
- dseed=0
- iagain=0
- do i1=1,nat
- do i2=1,mbond+3
- ia(i1,i2)=0
- iag(i1,i2)=0
- end do
- end do
-
- ioldchg=0
- na=0
- nrestra=0
- nrestrav=0
- nrestrat=0
- nrestram=0
- tset=tsetor
- tm11=axis(1)
- tm21=zero
- tm31=zero
- tm22=axis(2)
- tm32=zero
- tm33=axis(3)
- qruid='NORMAL RUN'
-c$$$ do i1=1,nat
-c$$$ imove(i1)=1
-c$$$ end do
-
-**********************************************************************
-* *
-* Write file headers *
-* *
-**********************************************************************
-Cc open (71,file='fort.71',status='unknown',access='append')
-c write (71,10)
-c close (71)
-Cc open (73,file='fort.73',status='unknown',access='append')
-c write (73,20)
-c close (73)
-c if (ntrc.gt.0) then
-Cc open (75,file='fort.75',status='unknown',access='append')
-c write (75,30)
-c close (75)
-c end if
-c if (nmethod.eq.4) then
-Cc open (59,file='fort.59',status='unknown',access='append')
-c write (59,40)
-c close (59)
-c end if
-
- return
-**********************************************************************
-* *
-* Format part *
-* *
-**********************************************************************
- 10 format (' Iter. Nmol Epot Ekin Etot ',
- $' T(K) Eaver(block) Eaver(total) Taver Tmax ',
- $' Pres(MPa) sdev(Epot) sdev(Eaver) Tset Timestep',
- $' RMSG Totaltime')
- 20 format (' Iter. Ebond Eatom Elp Emol',
- $' Eval Ecoa Ehbo Etors Econj',
- $' Evdw Ecoul Echarge Efield')
- 30 format (' Iter. Tsys Tzone1 Tset1 Tzone2 Tset2')
- 40 format (' Iter. a b c px',
- $'(MPa) py(MPa) pz(MPa) pset(MPa) Volume ')
- end
-**********************************************************************
-************************************************************************
-
-c subroutine timer(nunit)
-
-************************************************************************
-c#include "cbka.blk"
-c#include "cbkinit.blk"
-c real timear
-c real tarray(2)
-c#ifdef _IBM
-c call dtime_(tarray,timear)
-c#else
-c call dtime(tarray,timear)
-c#endif
-
-c ustime=ustime+tarray(1)
-c systime=systime+tarray(2)
-c write (nunit,100)ustime,systime,ustime+systime
-c return
-c 100 format ('User time:',f20.4,' System time:',f20.4,
-c $' Total time:',f20.4)
-c end
-************************************************************************
-************************************************************************
diff --git a/lib/reax/small.blk b/lib/reax/small.blk
deleted file mode 100644
index 9ec66b6e17205c8f53899b2cba247b540207027f..0000000000000000000000000000000000000000
--- a/lib/reax/small.blk
+++ /dev/null
@@ -1,5 +0,0 @@
- common
- $/rsmall/ tset,dseed,tempmd,ts2,ts22,nmolo,nmolo5,nbon,na,namov,
- $ na_local
-
-
diff --git a/lib/reax/valang.blk b/lib/reax/valang.blk
deleted file mode 100644
index c4b0027b8af9f7f597682e741b4f7a0c247fc5e7..0000000000000000000000000000000000000000
--- a/lib/reax/valang.blk
+++ /dev/null
@@ -1,9 +0,0 @@
-
-
-
- common
- $/cbkvalang/ vval1(nsort),vval2(nvatym),
- $ vval4(nsort),vkac(nvatym),vkap(nvatym),
- $ vka3(nvatym),vka8(nvatym),th0(nvatym)
-
-
diff --git a/src/.gitignore b/src/.gitignore
index 13aeee4d6e8309ed9e23698efe8eb8b14fdec172..9670d1ca20af2ba29b5428a9e12c0547b75f7707 100644
--- a/src/.gitignore
+++ b/src/.gitignore
@@ -583,8 +583,6 @@
/fix_qeq_reax.h
/fix_qmmm.cpp
/fix_qmmm.h
-/fix_reax_bonds.cpp
-/fix_reax_bonds.h
/fix_reaxc.cpp
/fix_reaxc.h
/fix_reaxc_bonds.cpp
@@ -930,9 +928,6 @@
/pair_peri_ves.h
/pair_quip.cpp
/pair_quip.h
-/pair_reax.cpp
-/pair_reax.h
-/pair_reax_fortran.h
/pair_reaxc.cpp
/pair_reaxc.h
/pair_rebo.cpp
diff --git a/src/MEAM/Install.sh b/src/MEAM/Install.sh
deleted file mode 100755
index 7bfc76c0e2ed72390f980347ea1130e8d5850c82..0000000000000000000000000000000000000000
--- a/src/MEAM/Install.sh
+++ /dev/null
@@ -1,67 +0,0 @@
-# Install/unInstall package files in LAMMPS
-# mode = 0/1/2 for uninstall/install/update
-
-mode=$1
-
-# enforce using portable C locale
-LC_ALL=C
-export LC_ALL
-
-# arg1 = file, arg2 = file it depends on
-
-action () {
- if (test $mode = 0) then
- rm -f ../$1
- elif (! cmp -s $1 ../$1) then
- if (test -z "$2" || test -e ../$2) then
- cp $1 ..
- if (test $mode = 2) then
- echo " updating src/$1"
- fi
- fi
- elif (test -n "$2") then
- if (test ! -e ../$2) then
- rm -f ../$1
- fi
- fi
-}
-
-# all package files with no dependencies
-
-for file in *.cpp *.h; do
- test -f ${file} && action $file
-done
-
-# edit 2 Makefile.package files to include/exclude package info
-
-if (test $1 = 1) then
-
- if (test -e ../Makefile.package) then
- sed -i -e 's/[^ \t]*meam[^ \t]* //' ../Makefile.package
- sed -i -e 's|^PKG_INC =[ \t]*|&-I../../lib/meam |' ../Makefile.package
- sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/meam |' ../Makefile.package
- sed -i -e 's|^PKG_LIB =[ \t]*|&-lmeam |' ../Makefile.package
- sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(meam_SYSINC) |' ../Makefile.package
- sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(meam_SYSLIB) |' ../Makefile.package
- sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(meam_SYSPATH) |' ../Makefile.package
- fi
-
- if (test -e ../Makefile.package.settings) then
- sed -i -e '/^include.*meam.*$/d' ../Makefile.package.settings
- # multiline form needed for BSD sed on Macs
- sed -i -e '4 i \
-include ..\/..\/lib\/meam\/Makefile.lammps
-' ../Makefile.package.settings
- fi
-
-elif (test $1 = 0) then
-
- if (test -e ../Makefile.package) then
- sed -i -e 's/[^ \t]*meam[^ \t]* //' ../Makefile.package
- fi
-
- if (test -e ../Makefile.package.settings) then
- sed -i -e '/^include.*meam.*$/d' ../Makefile.package.settings
- fi
-
-fi
diff --git a/src/MEAM/README b/src/MEAM/README
deleted file mode 100644
index 2f2bf275fb92ffcca01c794d11626b8e46c8b628..0000000000000000000000000000000000000000
--- a/src/MEAM/README
+++ /dev/null
@@ -1,11 +0,0 @@
-This package implements the MEAM potential as a LAMMPS pair style.
-
-This package uses an external library in lib/meam which must be
-compiled before making LAMMPS. See the lib/meam/README file and the
-LAMMPS manual for information on building LAMMPS with external
-libraries. The settings in the Makefile.lammps file in that directory
-must be correct for LAMMPS to build correctly with this package
-installed.
-
-The person who created the MEAM library and this pair style is Greg
-Wagner (while at Sandia, now at Northwestern U).
diff --git a/src/MEAM/pair_meam.cpp b/src/MEAM/pair_meam.cpp
deleted file mode 100644
index 38e8e97810790ac81ab20b7555fb97d94a59f6e4..0000000000000000000000000000000000000000
--- a/src/MEAM/pair_meam.cpp
+++ /dev/null
@@ -1,949 +0,0 @@
-/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
- http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
-
- Copyright (2003) Sandia Corporation. Under the terms of Contract
- DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
- the GNU General Public License.
-
- See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-/* ----------------------------------------------------------------------
- Contributing author: Greg Wagner (SNL)
-------------------------------------------------------------------------- */
-
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
-#include "pair_meam.h"
-#include "atom.h"
-#include "force.h"
-#include "comm.h"
-#include "memory.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "neigh_request.h"
-#include "memory.h"
-#include "error.h"
-
-using namespace LAMMPS_NS;
-
-#define MAXLINE 1024
-
-enum{FCC,BCC,HCP,DIM,DIAMOND,B1,C11,L12,B2};
-static const int nkeywords = 21;
-static const char *keywords[] = {
- "Ec","alpha","rho0","delta","lattce",
- "attrac","repuls","nn2","Cmin","Cmax","rc","delr",
- "augt1","gsmooth_factor","re","ialloy",
- "mixture_ref_t","erose_form","zbl",
- "emb_lin_neg","bkgd_dyn"};
-
-/* ---------------------------------------------------------------------- */
-
-PairMEAM::PairMEAM(LAMMPS *lmp) : Pair(lmp)
-{
- if (comm->me == 0)
- error->warning(FLERR,"THE pair_style meam COMMAND IS OBSOLETE AND "
- "WILL BE REMOVED VERY SOON. PLEASE USE meam/c");
-
- single_enable = 0;
- restartinfo = 0;
- one_coeff = 1;
- manybody_flag = 1;
-
- nmax = 0;
- rho = rho0 = rho1 = rho2 = rho3 = frhop = NULL;
- gamma = dgamma1 = dgamma2 = dgamma3 = arho2b = NULL;
- arho1 = arho2 = arho3 = arho3b = t_ave = tsq_ave = NULL;
-
- maxneigh = 0;
- allocated = 0;
- scrfcn = dscrfcn = fcpair = NULL;
-
- nelements = 0;
- elements = NULL;
- mass = NULL;
-
- // set comm size needed by this Pair
-
- comm_forward = 38;
- comm_reverse = 30;
-}
-
-/* ----------------------------------------------------------------------
- free all arrays
- check if allocated, since class can be destructed when incomplete
-------------------------------------------------------------------------- */
-
-PairMEAM::~PairMEAM()
-{
- meam_cleanup_();
-
- memory->destroy(rho);
- memory->destroy(rho0);
- memory->destroy(rho1);
- memory->destroy(rho2);
- memory->destroy(rho3);
- memory->destroy(frhop);
- memory->destroy(gamma);
- memory->destroy(dgamma1);
- memory->destroy(dgamma2);
- memory->destroy(dgamma3);
- memory->destroy(arho2b);
-
- memory->destroy(arho1);
- memory->destroy(arho2);
- memory->destroy(arho3);
- memory->destroy(arho3b);
- memory->destroy(t_ave);
- memory->destroy(tsq_ave);
-
- memory->destroy(scrfcn);
- memory->destroy(dscrfcn);
- memory->destroy(fcpair);
-
- for (int i = 0; i < nelements; i++) delete [] elements[i];
- delete [] elements;
- delete [] mass;
-
- if (allocated) {
- memory->destroy(setflag);
- memory->destroy(cutsq);
- delete [] map;
- delete [] fmap;
- }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void PairMEAM::compute(int eflag, int vflag)
-{
- int i,j,ii,n,inum_half,errorflag;
- int *ilist_half,*numneigh_half,**firstneigh_half;
- int *numneigh_full,**firstneigh_full;
-
- if (eflag || vflag) ev_setup(eflag,vflag);
- else evflag = vflag_fdotr = eflag_global = vflag_global =
- eflag_atom = vflag_atom = 0;
-
- // grow local arrays if necessary
-
- if (atom->nmax > nmax) {
- memory->destroy(rho);
- memory->destroy(rho0);
- memory->destroy(rho1);
- memory->destroy(rho2);
- memory->destroy(rho3);
- memory->destroy(frhop);
- memory->destroy(gamma);
- memory->destroy(dgamma1);
- memory->destroy(dgamma2);
- memory->destroy(dgamma3);
- memory->destroy(arho2b);
- memory->destroy(arho1);
- memory->destroy(arho2);
- memory->destroy(arho3);
- memory->destroy(arho3b);
- memory->destroy(t_ave);
- memory->destroy(tsq_ave);
-
- nmax = atom->nmax;
-
- memory->create(rho,nmax,"pair:rho");
- memory->create(rho0,nmax,"pair:rho0");
- memory->create(rho1,nmax,"pair:rho1");
- memory->create(rho2,nmax,"pair:rho2");
- memory->create(rho3,nmax,"pair:rho3");
- memory->create(frhop,nmax,"pair:frhop");
- memory->create(gamma,nmax,"pair:gamma");
- memory->create(dgamma1,nmax,"pair:dgamma1");
- memory->create(dgamma2,nmax,"pair:dgamma2");
- memory->create(dgamma3,nmax,"pair:dgamma3");
- memory->create(arho2b,nmax,"pair:arho2b");
- memory->create(arho1,nmax,3,"pair:arho1");
- memory->create(arho2,nmax,6,"pair:arho2");
- memory->create(arho3,nmax,10,"pair:arho3");
- memory->create(arho3b,nmax,3,"pair:arho3b");
- memory->create(t_ave,nmax,3,"pair:t_ave");
- memory->create(tsq_ave,nmax,3,"pair:tsq_ave");
- }
-
- // neighbor list info
-
- inum_half = listhalf->inum;
- ilist_half = listhalf->ilist;
- numneigh_half = listhalf->numneigh;
- firstneigh_half = listhalf->firstneigh;
- numneigh_full = listfull->numneigh;
- firstneigh_full = listfull->firstneigh;
-
- // strip neighbor lists of any special bond flags before using with MEAM
- // necessary before doing neigh_f2c and neigh_c2f conversions each step
-
- if (neighbor->ago == 0) {
- neigh_strip(inum_half,ilist_half,numneigh_half,firstneigh_half);
- neigh_strip(inum_half,ilist_half,numneigh_full,firstneigh_full);
- }
-
- // check size of scrfcn based on half neighbor list
-
- int nlocal = atom->nlocal;
- int nall = nlocal + atom->nghost;
-
- n = 0;
- for (ii = 0; ii < inum_half; ii++) n += numneigh_half[ilist_half[ii]];
-
- if (n > maxneigh) {
- memory->destroy(scrfcn);
- memory->destroy(dscrfcn);
- memory->destroy(fcpair);
- maxneigh = n;
- memory->create(scrfcn,maxneigh,"pair:scrfcn");
- memory->create(dscrfcn,maxneigh,"pair:dscrfcn");
- memory->create(fcpair,maxneigh,"pair:fcpair");
- }
-
- // zero out local arrays
-
- for (i = 0; i < nall; i++) {
- rho0[i] = 0.0;
- arho2b[i] = 0.0;
- arho1[i][0] = arho1[i][1] = arho1[i][2] = 0.0;
- for (j = 0; j < 6; j++) arho2[i][j] = 0.0;
- for (j = 0; j < 10; j++) arho3[i][j] = 0.0;
- arho3b[i][0] = arho3b[i][1] = arho3b[i][2] = 0.0;
- t_ave[i][0] = t_ave[i][1] = t_ave[i][2] = 0.0;
- tsq_ave[i][0] = tsq_ave[i][1] = tsq_ave[i][2] = 0.0;
- }
-
- double **x = atom->x;
- double **f = atom->f;
- int *type = atom->type;
- int ntype = atom->ntypes;
-
- // change neighbor list indices to Fortran indexing
-
- neigh_c2f(inum_half,ilist_half,numneigh_half,firstneigh_half);
- neigh_c2f(inum_half,ilist_half,numneigh_full,firstneigh_full);
-
- // 3 stages of MEAM calculation
- // loop over my atoms followed by communication
-
- int ifort;
- int offset = 0;
- errorflag = 0;
-
- for (ii = 0; ii < inum_half; ii++) {
- i = ilist_half[ii];
- ifort = i+1;
- meam_dens_init_(&ifort,&nmax,&ntype,type,fmap,&x[0][0],
- &numneigh_half[i],firstneigh_half[i],
- &numneigh_full[i],firstneigh_full[i],
- &scrfcn[offset],&dscrfcn[offset],&fcpair[offset],
- rho0,&arho1[0][0],&arho2[0][0],arho2b,
- &arho3[0][0],&arho3b[0][0],&t_ave[0][0],&tsq_ave[0][0],
- &errorflag);
- if (errorflag) {
- char str[128];
- sprintf(str,"MEAM library error %d",errorflag);
- error->one(FLERR,str);
- }
- offset += numneigh_half[i];
- }
-
- comm->reverse_comm_pair(this);
-
- meam_dens_final_(&nlocal,&nmax,&eflag_either,&eflag_global,&eflag_atom,
- &eng_vdwl,eatom,&ntype,type,fmap,
- &arho1[0][0],&arho2[0][0],arho2b,&arho3[0][0],
- &arho3b[0][0],&t_ave[0][0],&tsq_ave[0][0],gamma,dgamma1,
- dgamma2,dgamma3,rho,rho0,rho1,rho2,rho3,frhop,&errorflag);
- if (errorflag) {
- char str[128];
- sprintf(str,"MEAM library error %d",errorflag);
- error->one(FLERR,str);
- }
-
- comm->forward_comm_pair(this);
-
- offset = 0;
-
- // vptr is first value in vatom if it will be used by meam_force()
- // else vatom may not exist, so pass dummy ptr
-
- double *vptr;
- if (vflag_atom) vptr = &vatom[0][0];
- else vptr = &cutmax;
-
- for (ii = 0; ii < inum_half; ii++) {
- i = ilist_half[ii];
- ifort = i+1;
- meam_force_(&ifort,&nmax,&eflag_either,&eflag_global,&eflag_atom,
- &vflag_atom,&eng_vdwl,eatom,&ntype,type,fmap,&x[0][0],
- &numneigh_half[i],firstneigh_half[i],
- &numneigh_full[i],firstneigh_full[i],
- &scrfcn[offset],&dscrfcn[offset],&fcpair[offset],
- dgamma1,dgamma2,dgamma3,rho0,rho1,rho2,rho3,frhop,
- &arho1[0][0],&arho2[0][0],arho2b,&arho3[0][0],&arho3b[0][0],
- &t_ave[0][0],&tsq_ave[0][0],&f[0][0],vptr,&errorflag);
- if (errorflag) {
- char str[128];
- sprintf(str,"MEAM library error %d",errorflag);
- error->one(FLERR,str);
- }
- offset += numneigh_half[i];
- }
-
- // change neighbor list indices back to C indexing
-
- neigh_f2c(inum_half,ilist_half,numneigh_half,firstneigh_half);
- neigh_f2c(inum_half,ilist_half,numneigh_full,firstneigh_full);
-
- if (vflag_fdotr) virial_fdotr_compute();
-}
-
-/* ---------------------------------------------------------------------- */
-
-void PairMEAM::allocate()
-{
- allocated = 1;
- int n = atom->ntypes;
-
- memory->create(setflag,n+1,n+1,"pair:setflag");
- memory->create(cutsq,n+1,n+1,"pair:cutsq");
-
- map = new int[n+1];
- fmap = new int[n];
-}
-
-/* ----------------------------------------------------------------------
- global settings
-------------------------------------------------------------------------- */
-
-void PairMEAM::settings(int narg, char **/*arg*/)
-{
- if (narg != 0) error->all(FLERR,"Illegal pair_style command");
-}
-
-/* ----------------------------------------------------------------------
- set coeffs for one or more type pairs
-------------------------------------------------------------------------- */
-
-void PairMEAM::coeff(int narg, char **arg)
-{
- int i,j,m,n;
-
- if (!allocated) allocate();
-
- if (narg < 6) error->all(FLERR,"Incorrect args for pair coefficients");
-
- // insure I,J args are * *
-
- if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
- error->all(FLERR,"Incorrect args for pair coefficients");
-
- // read MEAM element names between 2 filenames
- // nelements = # of MEAM elements
- // elements = list of unique element names
-
- if (nelements) {
- for (i = 0; i < nelements; i++) delete [] elements[i];
- delete [] elements;
- delete [] mass;
- }
- nelements = narg - 4 - atom->ntypes;
- if (nelements < 1) error->all(FLERR,"Incorrect args for pair coefficients");
- elements = new char*[nelements];
- mass = new double[nelements];
-
- for (i = 0; i < nelements; i++) {
- n = strlen(arg[i+3]) + 1;
- elements[i] = new char[n];
- strcpy(elements[i],arg[i+3]);
- }
-
- // read MEAM library and parameter files
- // pass all parameters to MEAM package
- // tell MEAM package that setup is done
-
- read_files(arg[2],arg[2+nelements+1]);
- meam_setup_done_(&cutmax);
-
- // read args that map atom types to MEAM elements
- // map[i] = which element the Ith atom type is, -1 if not mapped
-
- for (i = 4 + nelements; i < narg; i++) {
- m = i - (4+nelements) + 1;
- for (j = 0; j < nelements; j++)
- if (strcmp(arg[i],elements[j]) == 0) break;
- if (j < nelements) map[m] = j;
- else if (strcmp(arg[i],"NULL") == 0) map[m] = -1;
- else error->all(FLERR,"Incorrect args for pair coefficients");
- }
-
- // clear setflag since coeff() called once with I,J = * *
-
- n = atom->ntypes;
- for (int i = 1; i <= n; i++)
- for (int j = i; j <= n; j++)
- setflag[i][j] = 0;
-
- // set setflag i,j for type pairs where both are mapped to elements
- // set mass for i,i in atom class
-
- int count = 0;
- for (int i = 1; i <= n; i++)
- for (int j = i; j <= n; j++)
- if (map[i] >= 0 && map[j] >= 0) {
- setflag[i][j] = 1;
- if (i == j) atom->set_mass(FLERR,i,mass[map[i]]);
- count++;
- }
-
- if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
-}
-
-/* ----------------------------------------------------------------------
- init specific to this pair style
-------------------------------------------------------------------------- */
-
-void PairMEAM::init_style()
-{
- if (force->newton_pair == 0)
- error->all(FLERR,"Pair style MEAM requires newton pair on");
-
- // need full and half neighbor list
-
- int irequest_full = neighbor->request(this,instance_me);
- neighbor->requests[irequest_full]->id = 1;
- neighbor->requests[irequest_full]->half = 0;
- neighbor->requests[irequest_full]->full = 1;
- int irequest_half = neighbor->request(this,instance_me);
- neighbor->requests[irequest_half]->id = 2;
-
- // setup Fortran-style mapping array needed by MEAM package
- // fmap is indexed from 1:ntypes by Fortran and stores a Fortran index
- // if type I is not a MEAM atom, fmap stores a 0
-
- for (int i = 1; i <= atom->ntypes; i++) fmap[i-1] = map[i] + 1;
-}
-
-/* ----------------------------------------------------------------------
- neighbor callback to inform pair style of neighbor list to use
- half or full
-------------------------------------------------------------------------- */
-
-void PairMEAM::init_list(int id, NeighList *ptr)
-{
- if (id == 1) listfull = ptr;
- else if (id == 2) listhalf = ptr;
-}
-
-/* ----------------------------------------------------------------------
- init for one type pair i,j and corresponding j,i
-------------------------------------------------------------------------- */
-
-double PairMEAM::init_one(int /*i*/, int /*j*/)
-{
- return cutmax;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void PairMEAM::read_files(char *globalfile, char *userfile)
-{
- // open global meamf file on proc 0
-
- FILE *fp;
- if (comm->me == 0) {
- fp = force->open_potential(globalfile);
- if (fp == NULL) {
- char str[128];
- snprintf(str,128,"Cannot open MEAM potential file %s",globalfile);
- error->one(FLERR,str);
- }
- }
-
- // allocate parameter arrays
-
- int params_per_line = 19;
-
- int *lat = new int[nelements];
- int *ielement = new int[nelements];
- int *ibar = new int[nelements];
- double *z = new double[nelements];
- double *atwt = new double[nelements];
- double *alpha = new double[nelements];
- double *b0 = new double[nelements];
- double *b1 = new double[nelements];
- double *b2 = new double[nelements];
- double *b3 = new double[nelements];
- double *alat = new double[nelements];
- double *esub = new double[nelements];
- double *asub = new double[nelements];
- double *t0 = new double[nelements];
- double *t1 = new double[nelements];
- double *t2 = new double[nelements];
- double *t3 = new double[nelements];
- double *rozero = new double[nelements];
-
- bool *found = new bool[nelements];
- for (int i = 0; i < nelements; i++) found[i] = false;
-
- // read each set of params from global MEAM file
- // one set of params can span multiple lines
- // store params if element name is in element list
- // if element name appears multiple times, only store 1st entry
-
- int i,n,nwords;
- char **words = new char*[params_per_line+1];
- char line[MAXLINE],*ptr;
- int eof = 0;
-
- int nset = 0;
- while (1) {
- if (comm->me == 0) {
- ptr = fgets(line,MAXLINE,fp);
- if (ptr == NULL) {
- eof = 1;
- fclose(fp);
- } else n = strlen(line) + 1;
- }
- MPI_Bcast(&eof,1,MPI_INT,0,world);
- if (eof) break;
- MPI_Bcast(&n,1,MPI_INT,0,world);
- MPI_Bcast(line,n,MPI_CHAR,0,world);
-
- // strip comment, skip line if blank
-
- if ((ptr = strchr(line,'#'))) *ptr = '\0';
- nwords = atom->count_words(line);
- if (nwords == 0) continue;
-
- // concatenate additional lines until have params_per_line words
-
- while (nwords < params_per_line) {
- n = strlen(line);
- if (comm->me == 0) {
- ptr = fgets(&line[n],MAXLINE-n,fp);
- if (ptr == NULL) {
- eof = 1;
- fclose(fp);
- } else n = strlen(line) + 1;
- }
- MPI_Bcast(&eof,1,MPI_INT,0,world);
- if (eof) break;
- MPI_Bcast(&n,1,MPI_INT,0,world);
- MPI_Bcast(line,n,MPI_CHAR,0,world);
- if ((ptr = strchr(line,'#'))) *ptr = '\0';
- nwords = atom->count_words(line);
- }
-
- if (nwords != params_per_line)
- error->all(FLERR,"Incorrect format in MEAM potential file");
-
- // words = ptrs to all words in line
- // strip single and double quotes from words
-
- nwords = 0;
- words[nwords++] = strtok(line,"' \t\n\r\f");
- while ((words[nwords++] = strtok(NULL,"' \t\n\r\f"))) continue;
-
- // skip if element name isn't in element list
-
- for (i = 0; i < nelements; i++)
- if (strcmp(words[0],elements[i]) == 0) break;
- if (i >= nelements) continue;
-
- // skip if element already appeared
-
- if (found[i] == true) continue;
- found[i] = true;
-
- // map lat string to an integer
-
- if (strcmp(words[1],"fcc") == 0) lat[i] = FCC;
- else if (strcmp(words[1],"bcc") == 0) lat[i] = BCC;
- else if (strcmp(words[1],"hcp") == 0) lat[i] = HCP;
- else if (strcmp(words[1],"dim") == 0) lat[i] = DIM;
- else if (strcmp(words[1],"dia") == 0) lat[i] = DIAMOND;
- else error->all(FLERR,"Unrecognized lattice type in MEAM file 1");
-
- // store parameters
-
- z[i] = atof(words[2]);
- ielement[i] = atoi(words[3]);
- atwt[i] = atof(words[4]);
- alpha[i] = atof(words[5]);
- b0[i] = atof(words[6]);
- b1[i] = atof(words[7]);
- b2[i] = atof(words[8]);
- b3[i] = atof(words[9]);
- alat[i] = atof(words[10]);
- esub[i] = atof(words[11]);
- asub[i] = atof(words[12]);
- t0[i] = atof(words[13]);
- t1[i] = atof(words[14]);
- t2[i] = atof(words[15]);
- t3[i] = atof(words[16]);
- rozero[i] = atof(words[17]);
- ibar[i] = atoi(words[18]);
-
- nset++;
- }
-
- // error if didn't find all elements in file
-
- if (nset != nelements)
- error->all(FLERR,"Did not find all elements in MEAM library file");
-
- // pass element parameters to MEAM package
-
- meam_setup_global_(&nelements,lat,z,ielement,atwt,alpha,b0,b1,b2,b3,
- alat,esub,asub,t0,t1,t2,t3,rozero,ibar);
-
- // set element masses
-
- for (i = 0; i < nelements; i++) mass[i] = atwt[i];
-
- // clean-up memory
-
- delete [] words;
-
- delete [] lat;
- delete [] ielement;
- delete [] ibar;
- delete [] z;
- delete [] atwt;
- delete [] alpha;
- delete [] b0;
- delete [] b1;
- delete [] b2;
- delete [] b3;
- delete [] alat;
- delete [] esub;
- delete [] asub;
- delete [] t0;
- delete [] t1;
- delete [] t2;
- delete [] t3;
- delete [] rozero;
- delete [] found;
-
- // done if user param file is NULL
-
- if (strcmp(userfile,"NULL") == 0) return;
-
- // open user param file on proc 0
-
- if (comm->me == 0) {
- fp = force->open_potential(userfile);
- if (fp == NULL) {
- char str[128];
- snprintf(str,128,"Cannot open MEAM potential file %s",userfile);
- error->one(FLERR,str);
- }
- }
-
- // read settings
- // pass them one at a time to MEAM package
- // match strings to list of corresponding ints
-
- int which;
- double value;
- int nindex,index[3];
- int maxparams = 6;
- char **params = new char*[maxparams];
- int nparams;
-
- eof = 0;
- while (1) {
- if (comm->me == 0) {
- ptr = fgets(line,MAXLINE,fp);
- if (ptr == NULL) {
- eof = 1;
- fclose(fp);
- } else n = strlen(line) + 1;
- }
- MPI_Bcast(&eof,1,MPI_INT,0,world);
- if (eof) break;
- MPI_Bcast(&n,1,MPI_INT,0,world);
- MPI_Bcast(line,n,MPI_CHAR,0,world);
-
- // strip comment, skip line if blank
-
- if ((ptr = strchr(line,'#'))) *ptr = '\0';
- nparams = atom->count_words(line);
- if (nparams == 0) continue;
-
- // words = ptrs to all words in line
-
- nparams = 0;
- params[nparams++] = strtok(line,"=(), '\t\n\r\f");
- while (nparams < maxparams &&
- (params[nparams++] = strtok(NULL,"=(), '\t\n\r\f")))
- continue;
- nparams--;
-
- for (which = 0; which < nkeywords; which++)
- if (strcmp(params[0],keywords[which]) == 0) break;
- if (which == nkeywords) {
- char str[128];
- snprintf(str,128,"Keyword %s in MEAM parameter file not recognized",
- params[0]);
- error->all(FLERR,str);
- }
- nindex = nparams - 2;
- for (i = 0; i < nindex; i++) index[i] = atoi(params[i+1]);
-
- // map lattce_meam value to an integer
-
- if (which == 4) {
- if (strcmp(params[nparams-1],"fcc") == 0) value = FCC;
- else if (strcmp(params[nparams-1],"bcc") == 0) value = BCC;
- else if (strcmp(params[nparams-1],"hcp") == 0) value = HCP;
- else if (strcmp(params[nparams-1],"dim") == 0) value = DIM;
- else if (strcmp(params[nparams-1],"dia") == 0) value = DIAMOND;
- else if (strcmp(params[nparams-1],"b1") == 0) value = B1;
- else if (strcmp(params[nparams-1],"c11") == 0) value = C11;
- else if (strcmp(params[nparams-1],"l12") == 0) value = L12;
- else if (strcmp(params[nparams-1],"b2") == 0) value = B2;
- else error->all(FLERR,"Unrecognized lattice type in MEAM file 2");
- }
- else value = atof(params[nparams-1]);
-
- // pass single setting to MEAM package
-
- int errorflag = 0;
- meam_setup_param_(&which,&value,&nindex,index,&errorflag);
- if (errorflag) {
- char str[128];
- sprintf(str,"MEAM library error %d",errorflag);
- error->all(FLERR,str);
- }
- }
-
- delete [] params;
-}
-
-/* ---------------------------------------------------------------------- */
-
-int PairMEAM::pack_forward_comm(int n, int *list, double *buf,
- int /*pbc_flag*/, int * /*pbc*/)
-{
- int i,j,k,m;
-
- m = 0;
- for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = rho0[j];
- buf[m++] = rho1[j];
- buf[m++] = rho2[j];
- buf[m++] = rho3[j];
- buf[m++] = frhop[j];
- buf[m++] = gamma[j];
- buf[m++] = dgamma1[j];
- buf[m++] = dgamma2[j];
- buf[m++] = dgamma3[j];
- buf[m++] = arho2b[j];
- buf[m++] = arho1[j][0];
- buf[m++] = arho1[j][1];
- buf[m++] = arho1[j][2];
- buf[m++] = arho2[j][0];
- buf[m++] = arho2[j][1];
- buf[m++] = arho2[j][2];
- buf[m++] = arho2[j][3];
- buf[m++] = arho2[j][4];
- buf[m++] = arho2[j][5];
- for (k = 0; k < 10; k++) buf[m++] = arho3[j][k];
- buf[m++] = arho3b[j][0];
- buf[m++] = arho3b[j][1];
- buf[m++] = arho3b[j][2];
- buf[m++] = t_ave[j][0];
- buf[m++] = t_ave[j][1];
- buf[m++] = t_ave[j][2];
- buf[m++] = tsq_ave[j][0];
- buf[m++] = tsq_ave[j][1];
- buf[m++] = tsq_ave[j][2];
- }
-
- return m;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void PairMEAM::unpack_forward_comm(int n, int first, double *buf)
-{
- int i,k,m,last;
-
- m = 0;
- last = first + n;
- for (i = first; i < last; i++) {
- rho0[i] = buf[m++];
- rho1[i] = buf[m++];
- rho2[i] = buf[m++];
- rho3[i] = buf[m++];
- frhop[i] = buf[m++];
- gamma[i] = buf[m++];
- dgamma1[i] = buf[m++];
- dgamma2[i] = buf[m++];
- dgamma3[i] = buf[m++];
- arho2b[i] = buf[m++];
- arho1[i][0] = buf[m++];
- arho1[i][1] = buf[m++];
- arho1[i][2] = buf[m++];
- arho2[i][0] = buf[m++];
- arho2[i][1] = buf[m++];
- arho2[i][2] = buf[m++];
- arho2[i][3] = buf[m++];
- arho2[i][4] = buf[m++];
- arho2[i][5] = buf[m++];
- for (k = 0; k < 10; k++) arho3[i][k] = buf[m++];
- arho3b[i][0] = buf[m++];
- arho3b[i][1] = buf[m++];
- arho3b[i][2] = buf[m++];
- t_ave[i][0] = buf[m++];
- t_ave[i][1] = buf[m++];
- t_ave[i][2] = buf[m++];
- tsq_ave[i][0] = buf[m++];
- tsq_ave[i][1] = buf[m++];
- tsq_ave[i][2] = buf[m++];
- }
-}
-
-/* ---------------------------------------------------------------------- */
-
-int PairMEAM::pack_reverse_comm(int n, int first, double *buf)
-{
- int i,k,m,last;
-
- m = 0;
- last = first + n;
- for (i = first; i < last; i++) {
- buf[m++] = rho0[i];
- buf[m++] = arho2b[i];
- buf[m++] = arho1[i][0];
- buf[m++] = arho1[i][1];
- buf[m++] = arho1[i][2];
- buf[m++] = arho2[i][0];
- buf[m++] = arho2[i][1];
- buf[m++] = arho2[i][2];
- buf[m++] = arho2[i][3];
- buf[m++] = arho2[i][4];
- buf[m++] = arho2[i][5];
- for (k = 0; k < 10; k++) buf[m++] = arho3[i][k];
- buf[m++] = arho3b[i][0];
- buf[m++] = arho3b[i][1];
- buf[m++] = arho3b[i][2];
- buf[m++] = t_ave[i][0];
- buf[m++] = t_ave[i][1];
- buf[m++] = t_ave[i][2];
- buf[m++] = tsq_ave[i][0];
- buf[m++] = tsq_ave[i][1];
- buf[m++] = tsq_ave[i][2];
- }
-
- return m;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void PairMEAM::unpack_reverse_comm(int n, int *list, double *buf)
-{
- int i,j,k,m;
-
- m = 0;
- for (i = 0; i < n; i++) {
- j = list[i];
- rho0[j] += buf[m++];
- arho2b[j] += buf[m++];
- arho1[j][0] += buf[m++];
- arho1[j][1] += buf[m++];
- arho1[j][2] += buf[m++];
- arho2[j][0] += buf[m++];
- arho2[j][1] += buf[m++];
- arho2[j][2] += buf[m++];
- arho2[j][3] += buf[m++];
- arho2[j][4] += buf[m++];
- arho2[j][5] += buf[m++];
- for (k = 0; k < 10; k++) arho3[j][k] += buf[m++];
- arho3b[j][0] += buf[m++];
- arho3b[j][1] += buf[m++];
- arho3b[j][2] += buf[m++];
- t_ave[j][0] += buf[m++];
- t_ave[j][1] += buf[m++];
- t_ave[j][2] += buf[m++];
- tsq_ave[j][0] += buf[m++];
- tsq_ave[j][1] += buf[m++];
- tsq_ave[j][2] += buf[m++];
- }
-}
-
-/* ----------------------------------------------------------------------
- memory usage of local atom-based arrays
-------------------------------------------------------------------------- */
-
-double PairMEAM::memory_usage()
-{
- double bytes = 11 * nmax * sizeof(double);
- bytes += (3 + 6 + 10 + 3 + 3 + 3) * nmax * sizeof(double);
- bytes += 3 * maxneigh * sizeof(double);
- return bytes;
-}
-
-/* ----------------------------------------------------------------------
- strip special bond flags from neighbor list entries
- are not used with MEAM
- need to do here so Fortran lib doesn't see them
- done once per reneighbor so that neigh_f2c and neigh_c2f don't see them
-------------------------------------------------------------------------- */
-
-void PairMEAM::neigh_strip(int inum, int *ilist,
- int *numneigh, int **firstneigh)
-{
- int i,j,ii,jnum;
- int *jlist;
-
- for (ii = 0; ii < inum; ii++) {
- i = ilist[ii];
- jlist = firstneigh[i];
- jnum = numneigh[i];
- for (j = 0; j < jnum; j++) jlist[j] &= NEIGHMASK;
- }
-}
-
-/* ----------------------------------------------------------------------
- toggle neighbor list indices between zero- and one-based values
- needed for access by MEAM Fortran library
-------------------------------------------------------------------------- */
-
-void PairMEAM::neigh_f2c(int inum, int *ilist, int *numneigh, int **firstneigh)
-{
- int i,j,ii,jnum;
- int *jlist;
-
- for (ii = 0; ii < inum; ii++) {
- i = ilist[ii];
- jlist = firstneigh[i];
- jnum = numneigh[i];
- for (j = 0; j < jnum; j++) jlist[j]--;
- }
-}
-
-void PairMEAM::neigh_c2f(int inum, int *ilist, int *numneigh, int **firstneigh)
-{
- int i,j,ii,jnum;
- int *jlist;
-
- for (ii = 0; ii < inum; ii++) {
- i = ilist[ii];
- jlist = firstneigh[i];
- jnum = numneigh[i];
- for (j = 0; j < jnum; j++) jlist[j]++;
- }
-}
diff --git a/src/MEAM/pair_meam.h b/src/MEAM/pair_meam.h
deleted file mode 100644
index 24aec1c3ed419713c3ea0cf7deb2106d779bc191..0000000000000000000000000000000000000000
--- a/src/MEAM/pair_meam.h
+++ /dev/null
@@ -1,159 +0,0 @@
-/* -*- c++ -*- ----------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
- http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
-
- Copyright (2003) Sandia Corporation. Under the terms of Contract
- DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
- the GNU General Public License.
-
- See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-#ifdef PAIR_CLASS
-
-PairStyle(meam,PairMEAM)
-
-#else
-
-#ifndef LMP_PAIR_MEAM_H
-#define LMP_PAIR_MEAM_H
-
-extern "C" {
- void meam_setup_global_(int *, int *, double *, int *, double *, double *,
- double *, double *, double *, double *, double *,
- double *, double *, double *, double *, double *,
- double *, double *, int *);
- void meam_setup_param_(int *, double *, int *, int *, int *);
- void meam_setup_done_(double *);
-
- void meam_dens_init_(int *, int *, int *, int *, int *,
- double *, int *, int *, int *, int *,
- double *, double *, double *, double *,
- double *, double *,
- double *, double *, double *, double *, double *,
- int *);
-
- void meam_dens_final_(int *, int *, int *, int *, int *, double *, double *,
- int *, int *, int *,
- double *, double *, double *, double *,
- double *, double *, double *,
- double *, double *, double *, double *,
- double *, double *,
- double *, double *, double *, double *, int *);
-
- void meam_force_(int *, int *, int *, int *, int *, int *,
- double *, double *, int *, int *, int *,
- double *, int *, int *, int *, int *, double *, double *,
- double *, double *, double *, double *, double *, double *,
- double *, double *, double *, double *, double *, double *,
- double *, double *, double *, double *, double *, double *, int *);
-
- void meam_cleanup_();
-}
-
-
-#include "pair.h"
-
-namespace LAMMPS_NS {
-
-class PairMEAM : public Pair {
- public:
- PairMEAM(class LAMMPS *);
- ~PairMEAM();
- void compute(int, int);
- void settings(int, char **);
- void coeff(int, char **);
- void init_style();
- void init_list(int, class NeighList *);
- double init_one(int, int);
-
- int pack_forward_comm(int, int *, double *, int, int *);
- void unpack_forward_comm(int, int, double *);
- int pack_reverse_comm(int, int, double *);
- void unpack_reverse_comm(int, int *, double *);
- double memory_usage();
-
- private:
- double cutmax; // max cutoff for all elements
- int nelements; // # of unique elements
- char **elements; // names of unique elements
- double *mass; // mass of each element
-
- int *map; // mapping from atom types to elements
- int *fmap; // Fortran version of map array for MEAM lib
-
- int maxneigh;
- double *scrfcn,*dscrfcn,*fcpair;
-
- int nmax;
- double *rho,*rho0,*rho1,*rho2,*rho3,*frhop;
- double *gamma,*dgamma1,*dgamma2,*dgamma3,*arho2b;
- double **arho1,**arho2,**arho3,**arho3b,**t_ave,**tsq_ave;
-
- void allocate();
- void read_files(char *, char *);
- void neigh_strip(int, int *, int *, int **);
- void neigh_f2c(int, int *, int *, int **);
- void neigh_c2f(int, int *, int *, int **);
-};
-
-}
-
-#endif
-#endif
-
-/* ERROR/WARNING messages:
-
-W: The pair_style meam command is unsupported. Please use pair_style meam/c instead
-
-UNDOCUMENTED
-
-E: MEAM library error %d
-
-A call to the MEAM Fortran library returned an error.
-
-E: Illegal ... command
-
-Self-explanatory. Check the input script syntax and compare to the
-documentation for the command. You can use -echo screen as a
-command-line option when running LAMMPS to see the offending line.
-
-E: Incorrect args for pair coefficients
-
-Self-explanatory. Check the input script or data file.
-
-E: Pair style MEAM requires newton pair on
-
-See the newton command. This is a restriction to use the MEAM
-potential.
-
-E: Cannot open MEAM potential file %s
-
-The specified MEAM potential file cannot be opened. Check that the
-path and name are correct.
-
-E: Incorrect format in MEAM potential file
-
-Incorrect number of words per line in the potential file.
-
-E: Unrecognized lattice type in MEAM file 1
-
-The lattice type in an entry of the MEAM library file is not
-valid.
-
-E: Did not find all elements in MEAM library file
-
-The requested elements were not found in the MEAM file.
-
-E: Keyword %s in MEAM parameter file not recognized
-
-Self-explanatory.
-
-E: Unrecognized lattice type in MEAM file 2
-
-The lattice type in an entry of the MEAM parameter file is not
-valid.
-
-*/
diff --git a/src/Makefile b/src/Makefile
index 1fda92b2c4f974bd7b0a7adb7dfb23cc9d3ffcd8..c58d5bd9eb0be6ccae0339d65bb602cf4b6468fe 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -53,9 +53,9 @@ endif
# PACKEXT = subset that require an external (downloaded) library
PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \
- granular kim kokkos kspace latte manybody mc meam message misc \
+ granular kim kokkos kspace latte manybody mc message misc \
molecule mpiio mscg opt peri poems \
- python qeq reax replica rigid shock snap spin srd voronoi
+ python qeq replica rigid shock snap spin srd voronoi
PACKUSER = user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-colvars \
user-diffraction user-dpd user-drude user-eff user-fep user-h5md \
@@ -65,15 +65,15 @@ PACKUSER = user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-colvars \
user-qtb user-quip user-reaxc user-scafacos user-smd user-smtbq \
user-sdpd user-sph user-tally user-uef user-vtk
-PACKLIB = compress gpu kim kokkos latte meam message mpiio mscg poems \
- python reax voronoi \
+PACKLIB = compress gpu kim kokkos latte message mpiio mscg poems \
+ python voronoi \
user-atc user-awpmd user-colvars user-h5md user-lb user-molfile \
user-netcdf user-plumed user-qmmm user-quip user-scafacos \
user-smd user-vtk
PACKSYS = compress mpiio python user-lb
-PACKINT = gpu kokkos meam message poems reax user-atc user-awpmd user-colvars
+PACKINT = gpu kokkos message poems user-atc user-awpmd user-colvars
PACKEXT = kim latte mscg voronoi \
user-h5md user-molfile user-netcdf user-plumed user-qmmm user-quip \
diff --git a/src/Purge.list b/src/Purge.list
index 6cfc580c25634d658809847a01560018759e22fa..6cd8276419627bc608fc3dcd41603e61ab526db8 100644
--- a/src/Purge.list
+++ b/src/Purge.list
@@ -24,6 +24,14 @@ style_nstencil.h
style_ntopo.h
# other auto-generated files
lmpinstalledpkgs.h
+# removed on 12 December 2018
+pair_reax.cpp
+pair_reax.h
+pair_reax_fortran.h
+fix_bond_reax.cpp
+fix_bond_reax.h
+pair_meam.cpp
+pair_meam.h
# renamed on 25 September 2018
compute_smd_triangle_mesh_vertices.h
compute_smd_triangle_mesh_vertices.cpp
diff --git a/src/REAX/Install.sh b/src/REAX/Install.sh
deleted file mode 100755
index bf8c8dbca2cbdfe488ef3cce5320cf8c4b1dee34..0000000000000000000000000000000000000000
--- a/src/REAX/Install.sh
+++ /dev/null
@@ -1,67 +0,0 @@
-# Install/unInstall package files in LAMMPS
-# mode = 0/1/2 for uninstall/install/update
-
-mode=$1
-
-# arg1 = file, arg2 = file it depends on
-
-# enforce using portable C locale
-LC_ALL=C
-export LC_ALL
-
-action () {
- if (test $mode = 0) then
- rm -f ../$1
- elif (! cmp -s $1 ../$1) then
- if (test -z "$2" || test -e ../$2) then
- cp $1 ..
- if (test $mode = 2) then
- echo " updating src/$1"
- fi
- fi
- elif (test -n "$2") then
- if (test ! -e ../$2) then
- rm -f ../$1
- fi
- fi
-}
-
-# all package files with no dependencies
-
-for file in *.cpp *.h; do
- test -f ${file} && action $file
-done
-
-# edit 2 Makefile.package files to include/exclude package info
-
-if (test $1 = 1) then
-
- if (test -e ../Makefile.package) then
- sed -i -e 's/[^ \t]*reax[^ \t]* //' ../Makefile.package
- sed -i -e 's|^PKG_INC =[ \t]*|&-I../../lib/reax |' ../Makefile.package
- sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/reax |' ../Makefile.package
- sed -i -e 's|^PKG_LIB =[ \t]*|&-lreax |' ../Makefile.package
- sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(reax_SYSINC) |' ../Makefile.package
- sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(reax_SYSLIB) |' ../Makefile.package
- sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(reax_SYSPATH) |' ../Makefile.package
- fi
-
- if (test -e ../Makefile.package.settings) then
- sed -i -e '/^include.*reax.*$/d' ../Makefile.package.settings
- # multiline form needed for BSD sed on Macs
- sed -i -e '4 i \
-include ..\/..\/lib\/reax\/Makefile.lammps
-' ../Makefile.package.settings
- fi
-
-elif (test $1 = 0) then
-
- if (test -e ../Makefile.package) then
- sed -i -e 's/[^ \t]*reax[^ \t]* //' ../Makefile.package
- fi
-
- if (test -e ../Makefile.package.settings) then
- sed -i -e '/^include.*reax.*$/d' ../Makefile.package.settings
- fi
-
-fi
diff --git a/src/REAX/fix_reax_bonds.cpp b/src/REAX/fix_reax_bonds.cpp
deleted file mode 100644
index c6c1d309ee1e3a9e8099f51ccd35a735e72dbf73..0000000000000000000000000000000000000000
--- a/src/REAX/fix_reax_bonds.cpp
+++ /dev/null
@@ -1,267 +0,0 @@
-/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
- http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
-
- Copyright (2003) Sandia Corporation. Under the terms of Contract
- DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
- the GNU General Public License.
-
- See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-/* ----------------------------------------------------------------------
- Contributing author: Aidan Thompson (Sandia)
-------------------------------------------------------------------------- */
-
-#ifdef LAMMPS_BIGBIG
-#error LAMMPS_BIGBIG is not supported by the REAX package
-#endif
-
-#include <cstdlib>
-#include <cstring>
-#include "fix_reax_bonds.h"
-#include "pair_reax_fortran.h"
-#include "atom.h"
-#include "update.h"
-#include "force.h"
-#include "modify.h"
-#include "compute.h"
-#include "input.h"
-#include "variable.h"
-#include "memory.h"
-#include "error.h"
-
-using namespace LAMMPS_NS;
-using namespace FixConst;
-
-/* ---------------------------------------------------------------------- */
-
-FixReaxBonds::FixReaxBonds(LAMMPS *lmp, int narg, char **arg) :
- Fix(lmp, narg, arg)
-{
- if (narg < 5) error->all(FLERR,"Illegal fix reax/bonds command");
-
- MPI_Comm_rank(world,&me);
-
- nevery = force->inumeric(FLERR,arg[3]);
- if (nevery < 1) error->all(FLERR,"Illegal fix reax/bonds command");
-
- if (me == 0) {
- char *suffix = strrchr(arg[4],'.');
- if (suffix && strcmp(suffix,".gz") == 0) {
-#ifdef LAMMPS_GZIP
- char gzip[128];
- snprintf(gzip,128,"gzip -6 > %s",arg[4]);
-#ifdef _WIN32
- fp = _popen(gzip,"wb");
-#else
- fp = popen(gzip,"w");
-#endif
-#else
- error->one(FLERR,"Cannot open gzipped file");
-#endif
- } else fp = fopen(arg[4],"w");
-
- if (fp == NULL) {
- char str[128];
- snprintf(str,128,"Cannot open fix reax/bonds file %s",arg[4]);
- error->one(FLERR,str);
- }
- }
-}
-
-/* ---------------------------------------------------------------------- */
-
-FixReaxBonds::~FixReaxBonds()
-{
- if (me == 0) fclose(fp);
-}
-
-/* ---------------------------------------------------------------------- */
-
-int FixReaxBonds::setmask()
-{
- int mask = 0;
- mask |= END_OF_STEP;
- return mask;
-}
-
-/* ----------------------------------------------------------------------
- perform initial write
-------------------------------------------------------------------------- */
-
-void FixReaxBonds::setup(int vflag)
-{
- end_of_step();
-}
-
-/* ---------------------------------------------------------------------- */
-
-void FixReaxBonds::init()
-{
- // insure ReaxFF is defined
-
- if (force->pair_match("reax",1) == NULL)
- error->all(FLERR,"Cannot use fix reax/bonds without pair_style reax");
-}
-
-/* ---------------------------------------------------------------------- */
-
-void FixReaxBonds::end_of_step()
-{
- OutputReaxBonds(update->ntimestep,fp);
- if (me == 0) fflush(fp);
-}
-
-/* ---------------------------------------------------------------------- */
-
-void FixReaxBonds::OutputReaxBonds(bigint ntimestep, FILE *fp)
-{
- int nparticles,nparticles_tot,nbuf,nbuf_local,most,j;
- int ii,jn,mbond,numbonds,nsbmax,nsbmax_most;
- int nprocs,nlocal_tmp,itmp;
- int k,kk,jj,jbufknum;
- double cutof3;
- double *buf;
- MPI_Request irequest;
-
- MPI_Comm_size(world,&nprocs);
-
- nparticles = atom->nlocal;
- nparticles_tot = static_cast<int> (atom->natoms);
-
- jn = ReaxParams::nat;
- mbond = ReaxParams::mbond;
- FORTRAN(getnsbmax,GETNSBMAX)(&nsbmax);
- FORTRAN(getcutof3,GETCUTOF3)(&cutof3);
- MPI_Allreduce(&nparticles,&most,1,MPI_INT,MPI_MAX,world);
- MPI_Allreduce(&nsbmax,&nsbmax_most,1,MPI_INT,MPI_MAX,world);
-
- if (me == 0) {
- fprintf(fp,"# Timestep " BIGINT_FORMAT " \n",ntimestep);
- fprintf(fp,"# \n");
- fprintf(fp,"# Number of particles %d \n",nparticles_tot);
- fprintf(fp,"# \n");
- fprintf(fp,"# Max number of bonds per atom %d with "
- "coarse bond order cutoff %5.3f \n",
- nsbmax_most,cutof3);
- fprintf(fp,"# Particle connection table and bond orders \n");
- fprintf(fp,"# id type nb id_1...id_nb mol bo_1...bo_nb abo nlp q \n");
- }
-
- // allocate a temporary buffer for the snapshot info
- // big enough for largest number of atoms on any one proc
- // nbuf_local = size of local buffer for table of atom bonds
-
- nbuf = 1+(2*nsbmax_most+7)*most;
- memory->create(buf,nbuf,"reax/bonds:buf");
-
- j = 0;
- buf[j++] = nparticles;
- for (int iparticle=0;iparticle<nparticles;iparticle++) {
- buf[j++] = atom->tag[iparticle]; //atom tag
- buf[j++] = FORTRAN(cbkia,CBKIA).iag[iparticle]; //atom type
- jbufknum = j++;
- numbonds = FORTRAN(cbkia,CBKIA).iag[iparticle+jn];
-
- // connection table based on coarse bond order cutoff (> cutof3)
-
- kk = 0;
- for (k=0;k<numbonds;k++) {
- ii = FORTRAN(cbknubon2,CBKNUBON2).nubon1[iparticle+jn*k];
- if (FORTRAN(cbkbo,CBKBO).bo[ii-1] > cutof3) {
- kk++;
- jj = FORTRAN(cbkia,CBKIA).iag[iparticle+jn*(k+2)];
- buf[j++] = FORTRAN(cbkc,CBKC).itag[jj-1];
- }
- }
- buf[jbufknum] = kk; //no.bonds
- buf[j++]=FORTRAN(cbkia,CBKIA).iag[iparticle+jn*(mbond+2)]; //molec.id
-
- // bond orders (> cutof3)
-
- kk = 0;
- for (k=0;k<numbonds;k++) {
- ii = FORTRAN(cbknubon2,CBKNUBON2).nubon1[iparticle+jn*k];
- if (FORTRAN(cbkbo,CBKBO).bo[ii-1] > cutof3) {
- kk++;
- buf[j++] = FORTRAN(cbkbo,CBKBO).bo[ii-1];
- }
- }
-
- // atom bond order (abo), no. of lone pairs (vlp), charge (ch)
-
- buf[j++] = FORTRAN(cbkabo,CBKABO).abo[iparticle];
- buf[j++] = FORTRAN(cbklonpar,CBKLONPAR).vlp[iparticle];
- buf[j++] = atom->q[iparticle];
- }
- nbuf_local = j-1;
-
- // node 0 pings each node, receives their buffer, writes to file
- // all other nodes wait for ping, send buffer to node 0
-
- if (me == 0) {
- for (int inode = 0; inode<nprocs; inode++) {
- j = 0;
- if (inode == 0) {
- nlocal_tmp = nparticles;
- j++;
- } else {
- MPI_Irecv(&buf[0],nbuf,MPI_DOUBLE,inode,0,world,&irequest);
- MPI_Send(&itmp,0,MPI_INT,inode,0,world);
- MPI_Wait(&irequest,MPI_STATUS_IGNORE);
- nlocal_tmp = nint(buf[j++]);
- }
-
- for (int iparticle=0;iparticle<nlocal_tmp;iparticle++) {
-
- // print atom tag, atom type, no.bonds
-
- numbonds = nint(buf[j+2]);
- fprintf(fp," %d %d %d",nint(buf[j]),nint(buf[j+1]),numbonds);
- j += 3;
- if (numbonds > nsbmax_most)
- error->one(FLERR,"Fix reax/bonds numbonds > nsbmax_most");
-
- // print connection table
-
- for (k=0;k<numbonds;k++)
- fprintf(fp," %d",nint(buf[j++]));
-
- // print molecule id
-
- fprintf(fp," %d",nint(buf[j++]));
-
- // print bond orders
-
- for (k=0;k<numbonds;k++)
- fprintf(fp,"%14.3f",buf[j++]);
-
- // print sum of bond orders, no. of lone pairs, charge
-
- fprintf(fp,"%14.3f%14.3f%14.3f\n",buf[j],buf[j+1],buf[j+2]);
- j+=3;
- }
- }
-
- } else {
- MPI_Recv(&itmp,0,MPI_INT,0,0,world,MPI_STATUS_IGNORE);
- MPI_Rsend(&buf[0],nbuf_local,MPI_DOUBLE,0,0,world);
- }
-
- if (me == 0) fprintf(fp,"# \n");
-
- memory->destroy(buf);
-}
-
-/* ---------------------------------------------------------------------- */
-
-int FixReaxBonds::nint(const double &r)
-{
- int i = 0;
- if (r>0.0) i = static_cast<int>(r+0.5);
- else if (r<0.0) i = static_cast<int>(r-0.5);
- return i;
-}
diff --git a/src/REAX/fix_reax_bonds.h b/src/REAX/fix_reax_bonds.h
deleted file mode 100644
index 03bad1ef16b3b0f45842ee709adef4e9be12868f..0000000000000000000000000000000000000000
--- a/src/REAX/fix_reax_bonds.h
+++ /dev/null
@@ -1,77 +0,0 @@
-/* -*- c++ -*- ----------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
- http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
-
- Copyright (2003) Sandia Corporation. Under the terms of Contract
- DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
- the GNU General Public License.
-
- See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-#ifdef FIX_CLASS
-
-FixStyle(reax/bonds,FixReaxBonds)
-
-#else
-
-#ifndef LMP_FIX_REAX_BONDS_H
-#define LMP_FIX_REAX_BONDS_H
-
-#include <cstdio>
-#include "fix.h"
-
-namespace LAMMPS_NS {
-
-class FixReaxBonds : public Fix {
- public:
- FixReaxBonds(class LAMMPS *, int, char **);
- ~FixReaxBonds();
- int setmask();
- void init();
- void setup(int);
- void end_of_step();
-
- private:
- int me;
- int nfreq;
- FILE *fp;
-
- void OutputReaxBonds(bigint, FILE*);
- int nint(const double&);
-};
-
-}
-
-#endif
-#endif
-
-/* ERROR/WARNING messages:
-
-E: Illegal ... command
-
-Self-explanatory. Check the input script syntax and compare to the
-documentation for the command. You can use -echo screen as a
-command-line option when running LAMMPS to see the offending line.
-
-E: Cannot open gzipped file
-
-UNDOCUMENTED
-
-E: Cannot open fix reax/bonds file %s
-
-The output file for the fix reax/bonds command cannot be opened.
-Check that the path and name are correct.
-
-E: Cannot use fix reax/bonds without pair_style reax
-
-Self-explanatory.
-
-E: Fix reax/bonds numbonds > nsbmax_most
-
-The limit of the number of bonds expected by the ReaxFF force field
-was exceeded.
-
-*/
diff --git a/src/REAX/pair_reax.cpp b/src/REAX/pair_reax.cpp
deleted file mode 100644
index a430380711605f9d8fd068c66986d56bf232d720..0000000000000000000000000000000000000000
--- a/src/REAX/pair_reax.cpp
+++ /dev/null
@@ -1,1067 +0,0 @@
-/* ----------------------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
- http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
-
- Copyright (2003) Sandia Corporation. Under the terms of Contract
- DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
- the GNU General Public License.
-
- See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-/* ----------------------------------------------------------------------
- Contributing authors: Aidan Thompson (Sandia, athomps@sandia.gov)
- Hansohl Cho (MIT, hansohl@mit.edu)
- LAMMPS implementation of the Reactive Force Field (ReaxFF) is based on
- Aidan Thompson's GRASP code
- (General Reactive Atomistic Simulation Program)
- and Ardi Van Duin's original ReaxFF code
-------------------------------------------------------------------------- */
-
-#include <mpi.h>
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
-#include "pair_reax.h"
-#include "pair_reax_fortran.h"
-#include "atom.h"
-#include "update.h"
-#include "force.h"
-#include "comm.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "neigh_request.h"
-#include "memory.h"
-#include "error.h"
-
-using namespace LAMMPS_NS;
-
-#define SMALL 0.0001
-
-/* ---------------------------------------------------------------------- */
-
-PairREAX::PairREAX(LAMMPS *lmp) : Pair(lmp)
-{
- if (comm->me == 0)
- error->warning(FLERR,"THE pair_style reax COMMAND IS OBSOLETE AND "
- "WILL BE REMOVED VERY SOON. PLEASE USE reax/c");
-
- single_enable = 0;
- restartinfo = 0;
- one_coeff = 1;
- manybody_flag = 1;
- no_virial_fdotr_compute = 1;
-
- nextra = 14;
- pvector = new double[nextra];
-
- cutmax = 0.0;
- hbcut = 6.0;
- ihbnew = 1;
- itripstaball = 1;
- iprune = 4;
- ihb = 1;
- chpot = 0;
-
- nmax = 0;
- arow_ptr = NULL;
- ch = NULL;
- elcvec = NULL;
- rcg = NULL;
- wcg = NULL;
- pcg = NULL;
- poldcg = NULL;
- qcg = NULL;
-
- matmax = 0;
- aval = NULL;
- acol_ind = NULL;
-
- comm_forward = 1;
- comm_reverse = 1;
-
- precision = 1.0e-6;
-}
-
-/* ----------------------------------------------------------------------
- free all arrays
- check if allocated, since class can be destructed when incomplete
-------------------------------------------------------------------------- */
-
-PairREAX::~PairREAX()
-{
- delete [] pvector;
-
- if (allocated) {
- memory->destroy(setflag);
- memory->destroy(cutsq);
-
- for (int i = 1; i <= atom->ntypes; i++)
- delete [] param_list[i].params;
- delete [] param_list;
-
- delete [] map;
- }
-
- memory->destroy(arow_ptr);
- memory->destroy(ch);
- memory->destroy(elcvec);
- memory->destroy(rcg);
- memory->destroy(wcg);
- memory->destroy(pcg);
- memory->destroy(poldcg);
- memory->destroy(qcg);
-
- memory->destroy(aval);
- memory->destroy(acol_ind);
-}
-
-/* ---------------------------------------------------------------------- */
-
-void PairREAX::compute(int eflag, int vflag)
-{
- int i,j;
- double evdwl,ecoul;
- double energy_charge_equilibration;
-
- evdwl = ecoul = 0.0;
- if (eflag || vflag) ev_setup(eflag,vflag);
- else ev_unset();
-
- if (vflag_global) FORTRAN(cbkvirial, CBKVIRIAL).Lvirial = 1;
- else FORTRAN(cbkvirial, CBKVIRIAL).Lvirial = 0;
-
- if (vflag_atom) FORTRAN(cbkvirial, CBKVIRIAL).Latomvirial = 1;
- else FORTRAN(cbkvirial, CBKVIRIAL).Latomvirial = 0;
-
- // reallocate charge equilibration and CG arrays if necessary
-
- if (atom->nmax > nmax) {
- memory->destroy(rcg);
- memory->destroy(wcg);
- memory->destroy(pcg);
- memory->destroy(poldcg);
- memory->destroy(qcg);
-
- nmax = atom->nmax;
- int n = nmax+1;
-
- memory->create(arow_ptr,n,"reax:arow_ptr");
- memory->create(ch,n,"reax:ch");
- memory->create(elcvec,n,"reax:elcvec");
- memory->create(rcg,n,"reax:rcg");
- memory->create(wcg,n,"reax:wcg");
- memory->create(pcg,n,"reax:pcg");
- memory->create(poldcg,n,"reax:poldcg");
- memory->create(qcg,n,"reax:qcg");
- }
-
- // calculate the atomic charge distribution
-
- compute_charge(energy_charge_equilibration);
-
- // transfer LAMMPS positions and neighbor lists to REAX
-
- write_reax_positions();
- write_reax_vlist();
-
- // determine whether this bond is owned by the processor or not
-
- FORTRAN(srtbon1, SRTBON1)(&iprune, &ihb, &hbcut, &ihbnew, &itripstaball);
-
- // communicate local atomic bond order to ghost atomic bond order
-
- packflag = 0;
- comm->forward_comm_pair(this);
-
- FORTRAN(molec, MOLEC)();
- FORTRAN(encalc, ENCALC)();
- FORTRAN(mdsav, MDSAV)(&comm->me);
-
- // read forces from ReaxFF Fortran
-
- read_reax_forces();
-
- // extract global and per-atom energy from ReaxFF Fortran
- // compute_charge already contributed to eatom
-
- if (eflag_global) {
- evdwl += FORTRAN(cbkenergies, CBKENERGIES).eb;
- evdwl += FORTRAN(cbkenergies, CBKENERGIES).ea;
- evdwl += FORTRAN(cbkenergies, CBKENERGIES).elp;
- evdwl += FORTRAN(cbkenergies, CBKENERGIES).emol;
- evdwl += FORTRAN(cbkenergies, CBKENERGIES).ev;
- evdwl += FORTRAN(cbkenergies, CBKENERGIES).epen;
- evdwl += FORTRAN(cbkenergies, CBKENERGIES).ecoa;
- evdwl += FORTRAN(cbkenergies, CBKENERGIES).ehb;
- evdwl += FORTRAN(cbkenergies, CBKENERGIES).et;
- evdwl += FORTRAN(cbkenergies, CBKENERGIES).eco;
- evdwl += FORTRAN(cbkenergies, CBKENERGIES).ew;
- evdwl += FORTRAN(cbkenergies, CBKENERGIES).efi;
-
- ecoul += FORTRAN(cbkenergies, CBKENERGIES).ep;
- ecoul += energy_charge_equilibration;
-
- eng_vdwl += evdwl;
- eng_coul += ecoul;
-
- // Store the different parts of the energy
- // in a list for output by compute pair command
-
- pvector[0] = FORTRAN(cbkenergies, CBKENERGIES).eb;
- pvector[1] = FORTRAN(cbkenergies, CBKENERGIES).ea;
- pvector[2] = FORTRAN(cbkenergies, CBKENERGIES).elp;
- pvector[3] = FORTRAN(cbkenergies, CBKENERGIES).emol;
- pvector[4] = FORTRAN(cbkenergies, CBKENERGIES).ev;
- pvector[5] = FORTRAN(cbkenergies, CBKENERGIES).epen;
- pvector[6] = FORTRAN(cbkenergies, CBKENERGIES).ecoa;
- pvector[7] = FORTRAN(cbkenergies, CBKENERGIES).ehb;
- pvector[8] = FORTRAN(cbkenergies, CBKENERGIES).et;
- pvector[9] = FORTRAN(cbkenergies, CBKENERGIES).eco;
- pvector[10] = FORTRAN(cbkenergies, CBKENERGIES).ew;
- pvector[11] = FORTRAN(cbkenergies, CBKENERGIES).ep;
- pvector[12] = FORTRAN(cbkenergies, CBKENERGIES).efi;
- pvector[13] = energy_charge_equilibration;
-
- }
-
- if (eflag_atom) {
- int ntotal = atom->nlocal + atom->nghost;
- for (i = 0; i < ntotal; i++)
- eatom[i] += FORTRAN(cbkd,CBKD).estrain[i];
- }
-
- // extract global and per-atom virial from ReaxFF Fortran
-
- if (vflag_global) {
- virial[0] = -FORTRAN(cbkvirial, CBKVIRIAL).virial[0];
- virial[1] = -FORTRAN(cbkvirial, CBKVIRIAL).virial[1];
- virial[2] = -FORTRAN(cbkvirial, CBKVIRIAL).virial[2];
- virial[3] = -FORTRAN(cbkvirial, CBKVIRIAL).virial[3];
- virial[4] = -FORTRAN(cbkvirial, CBKVIRIAL).virial[4];
- virial[5] = -FORTRAN(cbkvirial, CBKVIRIAL).virial[5];
- }
-
- if (vflag_atom) {
- int ntotal = atom->nlocal + atom->nghost;
- j = 0;
- for (i = 0; i < ntotal; i++) {
- vatom[i][0] = -FORTRAN(cbkvirial, CBKVIRIAL).atomvirial[j+0];
- vatom[i][1] = -FORTRAN(cbkvirial, CBKVIRIAL).atomvirial[j+1];
- vatom[i][2] = -FORTRAN(cbkvirial, CBKVIRIAL).atomvirial[j+2];
- vatom[i][3] = -FORTRAN(cbkvirial, CBKVIRIAL).atomvirial[j+3];
- vatom[i][4] = -FORTRAN(cbkvirial, CBKVIRIAL).atomvirial[j+4];
- vatom[i][5] = -FORTRAN(cbkvirial, CBKVIRIAL).atomvirial[j+5];
- j += 6;
- }
- }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void PairREAX::write_reax_positions()
-{
- int j, jx, jy, jz, jia;
-
- double **x = atom->x;
- double *q = atom->q;
- int *type = atom->type;
- int *tag = atom->tag;
- int nlocal = atom->nlocal;
- int nghost = atom->nghost;
-
- FORTRAN(rsmall, RSMALL).na = nlocal+nghost;
- FORTRAN(rsmall, RSMALL).na_local = nlocal;
-
- if (nlocal+nghost > ReaxParams::nat)
- error->one(FLERR,"Reax_defs.h setting for NATDEF is too small");
-
- jx = 0;
- jy = ReaxParams::nat;
- jz = 2*ReaxParams::nat;
- jia = 0;
-
- j = 0;
- for (int i = 0; i < nlocal+nghost; i++, j++) {
- FORTRAN(cbkc, CBKC).c[j+jx] = x[i][0];
- FORTRAN(cbkc, CBKC).c[j+jy] = x[i][1];
- FORTRAN(cbkc, CBKC).c[j+jz] = x[i][2];
- FORTRAN(cbkch, CBKCH).ch[j] = q[i];
- FORTRAN(cbkia, CBKIA).ia[j+jia] = map[type[i]];
- FORTRAN(cbkia, CBKIA).iag[j+jia] = map[type[i]];
- FORTRAN(cbkc, CBKC).itag[j] = tag[i];
- }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void PairREAX::write_reax_vlist()
-{
- int ii, jj, i, j, iii, jjj;
- double xitmp, yitmp, zitmp;
- double xjtmp, yjtmp, zjtmp;
- int itag,jtag;
- int nvpair, nvlself, nvpairmax;
- int nbond;
- int inum,jnum;
- int *ilist,*jlist,*numneigh,**firstneigh;
- double delr2;
- double delx, dely, delz;
-
- double **x = atom->x;
- int *tag = atom->tag;
- int nlocal = atom->nlocal;
- int nghost = atom->nghost;
-
- nvpairmax = ReaxParams::nneighmax * ReaxParams::nat;
-
- nvpair = 0;
- nvlself =0;
- nbond = 0;
-
- inum = list->inum;
- ilist = list->ilist;
- numneigh = list->numneigh;
- firstneigh = list->firstneigh;
-
- for (ii = 0; ii < inum; ii++) {
- i = ilist[ii];
- xitmp = x[i][0];
- yitmp = x[i][1];
- zitmp = x[i][2];
- itag = tag[i];
- jlist = firstneigh[i];
- jnum = numneigh[i];
-
- for (jj = 0; jj < jnum; jj++) {
- j = jlist[jj];
- j &= NEIGHMASK;
-
- xjtmp = x[j][0];
- yjtmp = x[j][1];
- zjtmp = x[j][2];
- jtag = tag[j];
-
- delx = xitmp - xjtmp;
- dely = yitmp - yjtmp;
- delz = zitmp - zjtmp;
-
- delr2 = delx*delx+dely*dely+delz*delz;
-
- if (delr2 <= rcutvsq) {
- if (i < j) {
- iii = i+1;
- jjj = j+1;
- } else {
- iii = j+1;
- jjj = i+1;
- }
- if (nvpair >= nvpairmax)
- error->one(FLERR,"Reax_defs.h setting for NNEIGHMAXDEF is too small");
-
- FORTRAN(cbkpairs, CBKPAIRS).nvl1[nvpair] = iii;
- FORTRAN(cbkpairs, CBKPAIRS).nvl2[nvpair] = jjj;
- FORTRAN(cbknvlbo, CBKNVLBO).nvlbo[nvpair] = 0;
-
- if (delr2 <= rcutbsq) {
- FORTRAN(cbknvlbo, CBKNVLBO).nvlbo[nvpair] = 1;
- nbond++;
- }
-
- FORTRAN(cbknvlown, CBKNVLOWN).nvlown[nvpair] = 0;
-
- if (j < nlocal)
- FORTRAN(cbknvlown, CBKNVLOWN).nvlown[nvpair] = 1;
- else if (itag < jtag)
- FORTRAN(cbknvlown, CBKNVLOWN).nvlown[nvpair] = 1;
- else if (itag == jtag) {
- if (delz > SMALL)
- FORTRAN(cbknvlown, CBKNVLOWN).nvlown[nvpair] = 1;
- else if (fabs(delz) < SMALL) {
- if (dely > SMALL)
- FORTRAN(cbknvlown, CBKNVLOWN).nvlown[nvpair] = 1;
- else if (fabs(dely) < SMALL && delx > SMALL)
- FORTRAN(cbknvlown, CBKNVLOWN).nvlown[nvpair] = 1;
- }
- }
- nvpair++;
- }
- }
- }
-
- int ntotal = nlocal + nghost;
-
- for (int i = nlocal; i < ntotal; i++) {
- xitmp = x[i][0];
- yitmp = x[i][1];
- zitmp = x[i][2];
- itag = tag[i];
-
- for (int j = i+1; j < ntotal; j++) {
- xjtmp = x[j][0];
- yjtmp = x[j][1];
- zjtmp = x[j][2];
- jtag = tag[j];
-
- delx = xitmp - xjtmp;
- dely = yitmp - yjtmp;
- delz = zitmp - zjtmp;
-
- delr2 = delx*delx+dely*dely+delz*delz;
-
- // don't need to check the double count since i < j in the ghost region
-
- if (delr2 <= rcutvsq) {
- iii = i+1;
- jjj = j+1;
-
- if (nvpair >= nvpairmax)
- error->one(FLERR,"Reax_defs.h setting for NNEIGHMAXDEF is too small");
-
- FORTRAN(cbkpairs, CBKPAIRS).nvl1[nvpair] = iii;
- FORTRAN(cbkpairs, CBKPAIRS).nvl2[nvpair] = jjj;
- FORTRAN(cbknvlbo, CBKNVLBO).nvlbo[nvpair] = 0;
-
- if (delr2 <= rcutbsq) {
- FORTRAN(cbknvlbo, CBKNVLBO).nvlbo[nvpair] = 1;
- nbond++;
- }
-
- FORTRAN(cbknvlown, CBKNVLOWN).nvlown[nvpair] = 0;
- nvpair++;
- }
- }
- }
-
- FORTRAN(cbkpairs, CBKPAIRS).nvpair = nvpair;
- FORTRAN(cbkpairs, CBKPAIRS).nvlself = nvlself;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void PairREAX::read_reax_forces()
-{
- double ftmp[3];
-
- double **f = atom->f;
- int ntotal = atom->nlocal + atom->nghost;
-
- int j = 0;
- for (int i = 0; i < ntotal; i++) {
- ftmp[0] = -FORTRAN(cbkd, CBKD).d[j];
- ftmp[1] = -FORTRAN(cbkd, CBKD).d[j+1];
- ftmp[2] = -FORTRAN(cbkd, CBKD).d[j+2];
- f[i][0] = ftmp[0];
- f[i][1] = ftmp[1];
- f[i][2] = ftmp[2];
- j += 3;
- }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void PairREAX::allocate()
-{
- allocated = 1;
- int n = atom->ntypes;
-
- memory->create(setflag,n+1,n+1,"pair:setflag");
- memory->create(cutsq,n+1,n+1,"pair:cutsq");
-
- param_list = new ff_params[n+1];
- for (int i = 1; i <= n; i++)
- param_list[i].params = new double[5];
-
- map = new int[n+1];
-}
-
-/* ----------------------------------------------------------------------
- global settings
-------------------------------------------------------------------------- */
-
-void PairREAX::settings(int narg, char **arg)
-{
- if (narg != 0 && narg !=4) error->all(FLERR,"Illegal pair_style command");
-
- if (narg == 4) {
- hbcut = force->numeric(FLERR,arg[0]);
- ihbnew = static_cast<int> (force->numeric(FLERR,arg[1]));
- itripstaball = static_cast<int> (force->numeric(FLERR,arg[2]));
- precision = force->numeric(FLERR,arg[3]);
-
- if (hbcut <= 0.0 ||
- (ihbnew != 0 && ihbnew != 1) ||
- (itripstaball != 0 && itripstaball != 1) ||
- precision <= 0.0)
- error->all(FLERR,"Illegal pair_style command");
- }
-}
-
-/* ----------------------------------------------------------------------
- set coeffs for one or more type pairs
-------------------------------------------------------------------------- */
-
-void PairREAX::coeff(int narg, char **arg)
-{
- if (!allocated) allocate();
-
- if (narg != 3 + atom->ntypes)
- error->all(FLERR,"Incorrect args for pair coefficients");
-
- // insure I,J args are * *
-
- if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
- error->all(FLERR,"Incorrect args for pair coefficients");
-
- // insure filename is ffield.reax
-
- if (strcmp(arg[2],"ffield.reax") != 0)
- error->all(FLERR,"Incorrect args for pair coefficients");
-
- // read args that map atom types to elements in potential file
- // map[i] = which element the Ith atom type is, -1 if NULL
- // NOTE: for now throw an error if NULL is used to disallow use with hybrid
- // qEq matrix solver needs to be modified to exclude atoms
-
- for (int i = 3; i < narg; i++) {
- if (strcmp(arg[i],"NULL") == 0) {
- map[i-2] = -1;
- error->all(FLERR,"Cannot currently use pair reax with pair hybrid");
- continue;
- }
- map[i-2] = force->inumeric(FLERR,arg[i]);
- }
-
- int n = atom->ntypes;
-
- int count = 0;
- for (int i = 1; i <= n; i++)
- for (int j = i; j <= n; j++) {
- setflag[i][j] = 1;
- count++;
- }
-
- if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
-}
-
-/* ----------------------------------------------------------------------
- init specific to this pair style
-------------------------------------------------------------------------- */
-
-void PairREAX::init_style()
-{
- if (atom->tag_enable == 0)
- error->all(FLERR,"Pair style reax requires atom IDs");
- if (force->newton_pair == 0)
- error->all(FLERR,"Pair style reax requires newton pair on");
- if (!atom->q_flag)
- error->all(FLERR,"Pair style reax requires atom attribute q");
- if (strcmp(update->unit_style,"real") != 0 && comm->me == 0)
- error->warning(FLERR,"Not using real units with pair reax");
-
- int irequest = neighbor->request(this,instance_me);
- neighbor->requests[irequest]->newton = 2;
-
- FORTRAN(readc, READC)();
- FORTRAN(reaxinit, REAXINIT)();
- FORTRAN(ffinpt, FFINPT)();
- FORTRAN(tap7th, TAP7TH)();
-
- // turn off read_in by fort.3 in REAX Fortran
-
- int ngeofor_tmp = -1;
- FORTRAN(setngeofor, SETNGEOFOR)(&ngeofor_tmp);
- if (comm->me == 0) FORTRAN(readgeo, READGEO)();
-
- // initial setup for cutoff radius of VLIST and BLIST in ReaxFF
-
- double vlbora;
-
- FORTRAN(getswb, GETSWB)(&swb);
- cutmax=MAX(swb, hbcut);
- rcutvsq=cutmax*cutmax;
- FORTRAN(getvlbora, GETVLBORA)(&vlbora);
- rcutbsq=vlbora*vlbora;
-
- // parameters for charge equilibration from ReaxFF input, fort.4
- // verify that no LAMMPS type to REAX type mapping was invalid
-
- int nelements;
- FORTRAN(getnso, GETNSO)(&nelements);
-
- FORTRAN(getswa, GETSWA)(&swa);
- double chi, eta, gamma;
- for (int itype = 1; itype <= atom->ntypes; itype++) {
- if (map[itype] < 1 || map[itype] > nelements)
- error->all(FLERR,"Invalid REAX atom type");
- chi = FORTRAN(cbkchb, CBKCHB).chi[map[itype]-1];
- eta = FORTRAN(cbkchb, CBKCHB).eta[map[itype]-1];
- gamma = FORTRAN(cbkchb, CBKCHB).gam[map[itype]-1];
- param_list[itype].np = 5;
- param_list[itype].rcutsq = cutmax;
- param_list[itype].params[0] = chi;
- param_list[itype].params[1] = eta;
- param_list[itype].params[2] = gamma;
- param_list[itype].params[3] = swa;
- param_list[itype].params[4] = swb;
- }
-
- taper_setup();
-}
-
-/* ----------------------------------------------------------------------
- init for one type pair i,j and corresponding j,i
-------------------------------------------------------------------------- */
-
-double PairREAX::init_one(int i, int j)
-{
- return cutmax;
-}
-
-/* ---------------------------------------------------------------------- */
-
-int PairREAX::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
-{
- int i,j,m;
-
- m = 0;
-
- if (packflag == 0) {
- for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = FORTRAN(cbkabo, CBKABO).abo[j];
- }
-
- } else {
- for (i = 0; i < n; i++) {
- j = list[i];
- buf[m++] = wcg[j];
- }
- }
-
- return m;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void PairREAX::unpack_forward_comm(int n, int first, double *buf)
-{
- int i,m,last;
-
- m = 0;
- last = first + n;
-
- if (packflag == 0) {
- for (i = first; i < last; i++)
- FORTRAN(cbkabo, CBKABO).abo[i] = buf[m++];
-
- } else {
- for (i = first; i < last; i++)
- wcg[i] = buf[m++];
- }
-}
-
-/* ---------------------------------------------------------------------- */
-
-int PairREAX::pack_reverse_comm(int n, int first, double *buf)
-{
- int i,m,last;
-
- m = 0;
- last = first + n;
- for (i = first; i < last; i++)
- buf[m++] = wcg[i];
-
- return m;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void PairREAX::unpack_reverse_comm(int n, int *list, double *buf)
-{
- int i,j,m;
-
- m = 0;
- for (i = 0; i < n; i++) {
- j = list[i];
- wcg[j] += buf[m++];
- }
-}
-
-/* ----------------------------------------------------------------------
- charge equilibration routines
-------------------------------------------------------------------------- */
-
-/* ---------------------------------------------------------------------- */
-
-void PairREAX::taper_setup()
-{
- double swb2,swa2,swb3,swa3,d1,d7;
-
- d1=swb-swa;
- d7=pow(d1,7.0);
- swa2=swa*swa;
- swa3=swa2*swa;
- swb2=swb*swb;
- swb3=swb2*swb;
-
- swc7= 20.0e0/d7;
- swc6= -70.0e0*(swa+swb)/d7;
- swc5= 84.0e0*(swa2+3.0e0*swa*swb+swb2)/d7;
- swc4= -35.0e0*(swa3+9.0e0*swa2*swb+9.0e0*swa*swb2+swb3)/d7;
- swc3= 140.0e0*(swa3*swb+3.0e0*swa2*swb2+swa*swb3)/d7;
- swc2=-210.0e0*(swa3*swb2+swa2*swb3)/d7;
- swc1= 140.0e0*swa3*swb3/d7;
- swc0=(-35.0e0*swa3*swb2*swb2+21.0e0*swa2*swb3*swb2-
- 7.0e0*swa*swb3*swb3+swb3*swb3*swb)/d7;
-}
-
-/* ---------------------------------------------------------------------- */
-
-double PairREAX::taper_E(const double &r, const double &r2)
-{
- double r3=r2*r;
- return swc7*r3*r3*r+swc6*r3*r3+swc5*r3*r2+swc4*r2*r2+swc3*r3+swc2*r2+
- swc1*r+swc0;
-}
-
-/* ---------------------------------------------------------------------- */
-
-double PairREAX::taper_F(const double &r, const double &r2)
-{
- double r3=r2*r;
- return 7.0e0*swc7*r3*r3+6.0e0*swc6*r3*r2+5.0e0*swc5*r2*r2+
- 4.0e0*swc4*r3+3.0e0*swc3*r2+2.0e0*swc2*r+swc1;
-}
-
-/* ----------------------------------------------------------------------
- compute current charge distributions based on the charge equilibration
-------------------------------------------------------------------------- */
-
-void PairREAX::compute_charge(double &energy_charge_equilibration)
-{
- double xitmp, yitmp, zitmp;
- double xjtmp, yjtmp, zjtmp;
- int itype, jtype, itag, jtag;
- int ii, jj, i, j;
- double delr2, delr_norm, gamt, hulp1, hulp2;
- double delx, dely, delz;
- double qsum,qi;
- int nmatentries;
- double sw;
- int inum,jnum;
- int *ilist,*jlist,*numneigh,**firstneigh;
-
- double **x = atom->x;
- double *q = atom->q;
- int *type = atom->type;
- int *tag = atom->tag;
-
- int nlocal = atom->nlocal;
- int nghost = atom->nghost;
-
- inum = list->inum;
- ilist = list->ilist;
- numneigh = list->numneigh;
- firstneigh = list->firstneigh;
-
- // realloc neighbor based arrays if necessary
-
- int numneigh_total = 0;
- for (ii = 0; ii < inum; ii++)
- numneigh_total += numneigh[ilist[ii]];
-
- if (numneigh_total + 2*nlocal > matmax) {
- memory->destroy(aval);
- memory->destroy(acol_ind);
- matmax = numneigh_total + 2*nlocal;
- memory->create(aval,matmax,"reax:aval");
- memory->create(acol_ind,matmax,"reax:acol_ind");
- }
-
- // build linear system
-
- nmatentries = 0;
-
- for (ii = 0; ii < inum; ii++) {
- i = ilist[ii];
- xitmp = x[i][0];
- yitmp = x[i][1];
- zitmp = x[i][2];
- itype = type[i];
- itag = tag[i];
- jlist = firstneigh[i];
- jnum = numneigh[i];
-
- arow_ptr[i] = nmatentries;
- aval[nmatentries] = 2.0*param_list[itype].params[1];
- acol_ind[nmatentries] = i;
- nmatentries++;
-
- aval[nmatentries] = 1.0;
- acol_ind[nmatentries] = nlocal + nghost;
- nmatentries++;
-
- for (jj = 0; jj < jnum; jj++) {
- j = jlist[jj];
- j &= NEIGHMASK;
-
- xjtmp = x[j][0];
- yjtmp = x[j][1];
- zjtmp = x[j][2];
- jtype = type[j];
- jtag = tag[j];
-
- delx = xitmp - xjtmp;
- dely = yitmp - yjtmp;
- delz = zitmp - zjtmp;
-
- delr2 = delx*delx+dely*dely+delz*delz;
-
- // avoid counting local-ghost pair twice since
- // ReaxFF uses half neigh list with newton off
-
- if (j >= nlocal) {
- if (itag > jtag) {
- if ((itag+jtag) % 2 == 0) continue;
- } else if (itag < jtag) {
- if ((itag+jtag) % 2 == 1) continue;
- } else {
- if (zjtmp < zitmp) continue;
- if (zjtmp == zitmp && yjtmp < yitmp) continue;
- if (zjtmp == zitmp && yjtmp == yitmp && xjtmp < xitmp) continue;
- }
- }
-
- // rcutvsq = cutmax*cutmax, in ReaxFF
-
- if (delr2 <= rcutvsq) {
- gamt = sqrt(param_list[itype].params[2]*param_list[jtype].params[2]);
- delr_norm = sqrt(delr2);
- sw = taper_E(delr_norm, delr2);
- hulp1=(delr_norm*delr2+(1.0/(gamt*gamt*gamt)));
- hulp2=sw*14.40/cbrt(hulp1);
- aval[nmatentries] = hulp2;
- acol_ind[nmatentries] = j;
- nmatentries++;
- }
- }
- }
-
- // in this case, we don't use Midpoint method
- // so, we don't need to consider ghost-ghost interactions
- // but, need to fill the arow_ptr[] arrays for the ghost atoms
-
- for (i = nlocal; i < nlocal+nghost; i++)
- arow_ptr[i] = nmatentries;
- arow_ptr[nlocal+nghost] = nmatentries;
-
- // add rhs matentries to linear system
-
- for (ii =0; ii<inum; ii++) {
- i = ilist[ii];
- itype = type[i];
- elcvec[i] = -param_list[itype].params[0];
- }
-
- for (i = nlocal; i < nlocal+nghost; i++) elcvec[i] = 0.0;
-
- // assign current charges to charge vector
-
- qsum = 0.0;
- for (ii = 0; ii < inum; ii++) {
- i = ilist[ii];
- qi = q[i];
- ch[i] = qi;
- if (i < nlocal) qsum += qi;
- }
-
- for (i = nlocal; i < nlocal+nghost; i++) {
- qi = q[i];
- ch[i] = qi;
- }
-
- double qtot;
- MPI_Allreduce(&qsum,&qtot,1,MPI_DOUBLE,MPI_SUM,world);
- elcvec[nlocal+nghost] = 0.0;
- ch[nlocal+nghost] = chpot;
-
- // solve the linear system using CG sover
-
- charge_reax(nlocal,nghost,ch,aval,acol_ind,arow_ptr,elcvec);
-
- // calculate the charge equilibration energy
-
- energy_charge_equilibration = 0;
-
- // have already updated charge distributions for the current structure
-
- for (ii = 0; ii < inum; ii++) {
- i = ilist[ii];
- itype = type[i];
-
- // 23.02 is the ReaxFF conversion from eV to kcal/mol
- // should really use constants.evfactor ~23.06
- // but that would break consistency with serial ReaxFF code
- // NOTE: this hard-wired real units
- // if want other units would have to change params[] in file
-
- qi = 23.02 * (param_list[itype].params[0]*ch[i]+
- param_list[itype].params[1]*ch[i]*ch[i]);
- energy_charge_equilibration += qi;
- if (eflag_atom) eatom[i] += qi;
- }
-
- // copy charge vector back to particles from the calculated values
-
- for (i = 0; i < nlocal+nghost; i++) q[i] = ch[i];
- chpot = ch[nlocal+nghost];
-}
-
-/* ---------------------------------------------------------------------- */
-
-void PairREAX::charge_reax(const int & nlocal, const int & nghost,
- double ch[], double aval[], int acol_ind[],
- int arow_ptr[], double elcvec[])
-{
- cg_solve(nlocal,nghost,aval,acol_ind,arow_ptr,ch,elcvec);
-}
-
-/* ----------------------------------------------------------------------
- CG solver for linear systems
-------------------------------------------------------------------------- */
-
-void PairREAX::cg_solve(const int & nlocal, const int & nghost,
- double aval[], int acol_ind[], int arow_ptr[],
- double x[], double b[])
-{
- double one, rho, rho_old, alpha, beta, gamma;
- int iter, maxiter;
- int n;
- double sumtmp;
-
- // parallel CG method by A. P. Thompson
- // distributed (partial) vectors: b, r, q, A
- // accumulated (full) vectors: x, w, p
- // r = b-A.x
- // w = r (ReverseComm + Comm)
-
- double *r = rcg;
- double *w = wcg;
- double *p = pcg;
- double *p_old = poldcg;
- double *q = qcg;
-
- n = nlocal+nghost+1;
-
- one = 1.0;
- maxiter = 100;
-
- for (int i = 0; i < n; i++) w[i] = 0;
-
- // construct r = b-Ax
-
- sparse_product(n, nlocal, nghost, aval, acol_ind, arow_ptr, x, r);
-
- // not using BLAS library
-
- for (int i=0; i<n; i++) {
- r[i] = b[i] - r[i];
- w[i] = r[i];
- }
-
- packflag = 1;
- comm->reverse_comm_pair(this);
- comm->forward_comm_pair(this);
-
- MPI_Allreduce(&w[n-1], &sumtmp, 1, MPI_DOUBLE, MPI_SUM, world);
- w[n-1] = sumtmp;
- rho_old = one;
-
- for (iter = 1; iter < maxiter; iter++) {
- rho = 0.0;
- for (int i=0; i<nlocal; i++) rho += w[i]*w[i];
-
- MPI_Allreduce(&rho, &sumtmp, 1, MPI_DOUBLE, MPI_SUM, world);
- rho = sumtmp + w[n-1]*w[n-1];
- if (rho < precision) break;
-
- for (int i = 0; i<n; i++) p[i] = w[i];
-
- if (iter > 1) {
- beta = rho/rho_old;
- for (int i = 0; i<n; i++) p[i] += beta*p_old[i];
- }
-
- sparse_product(n, nlocal, nghost, aval, acol_ind, arow_ptr, p, q);
-
- gamma = 0.0;
- for (int i=0; i<n; i++) gamma += p[i]*q[i];
- MPI_Allreduce(&gamma, &sumtmp, 1, MPI_DOUBLE, MPI_SUM, world);
-
- gamma = sumtmp;
- alpha = rho/gamma;
-
- for (int i=0; i<n; i++) {
- x[i] += alpha*p[i];
- r[i] -= alpha*q[i];
- w[i] = r[i];
- }
-
- comm->reverse_comm_pair(this);
- comm->forward_comm_pair(this);
-
- MPI_Allreduce(&w[n-1], &sumtmp, 1, MPI_DOUBLE, MPI_SUM, world);
- w[n-1] = sumtmp;
-
- for (int i=0; i<n; i++) p_old[i] = p[i];
- rho_old = rho;
- }
-}
-
-/* ----------------------------------------------------------------------
- sparse maxtrix operations
-------------------------------------------------------------------------- */
-
-void PairREAX::sparse_product(const int &n, const int &nlocal,
- const int &nghost,
- double aval[], int acol_ind[], int arow_ptr[],
- double *x, double *r)
-{
- int i,j,jj;
-
- for (i=0; i<n; i++) r[i] = 0.0;
-
- for (i=0; i<nlocal; i++) {
- r[i] += aval[arow_ptr[i]]*x[i];
- for (j=arow_ptr[i]+1; j<arow_ptr[i+1]; j++) {
- jj = acol_ind[j];
- r[i] += aval[j]*x[jj];
- r[jj] += aval[j]*x[i];
- }
- }
-
- for (i=nlocal; i<nlocal+nghost; i++)
- for (j=arow_ptr[i]; j<arow_ptr[i+1]; j++) {
- jj = acol_ind[j];
- r[i] += aval[j]*x[jj];
- r[jj] += aval[j]*x[i];
- }
-}
-
-/* ----------------------------------------------------------------------
- memory usage of local atom-based arrays
-------------------------------------------------------------------------- */
-
-double PairREAX::memory_usage()
-{
- double bytes = nmax * sizeof(int);
- bytes += 7 * nmax * sizeof(double);
- bytes += matmax * sizeof(int);
- bytes += matmax * sizeof(double);
- return bytes;
-}
diff --git a/src/REAX/pair_reax.h b/src/REAX/pair_reax.h
deleted file mode 100644
index 89a176274366305ffaa96b03a27d5aea4d18aa79..0000000000000000000000000000000000000000
--- a/src/REAX/pair_reax.h
+++ /dev/null
@@ -1,154 +0,0 @@
-/* -*- c++ -*- ----------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
- http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
-
- Copyright (2003) Sandia Corporation. Under the terms of Contract
- DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
- the GNU General Public License.
-
- See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-#ifdef PAIR_CLASS
-
-PairStyle(reax,PairREAX)
-
-#else
-
-#ifndef LMP_PAIR_REAX_H
-#define LMP_PAIR_REAX_H
-
-#include "pair.h"
-
-namespace LAMMPS_NS {
-
-class PairREAX : public Pair {
- public:
- PairREAX(class LAMMPS *);
- ~PairREAX();
-
- void compute(int, int);
- void settings(int, char **);
- void coeff(int, char **);
- void init_style();
- double init_one(int, int);
- double memory_usage();
-
- int pack_forward_comm(int, int *, double *, int, int *);
- void unpack_forward_comm(int, int, double *);
- int pack_reverse_comm(int, int, double *);
- void unpack_reverse_comm(int, int *, double *);
-
- private:
- double cutmax;
- double rcutvsq,rcutbsq;
- int iprune,ihb,ihbnew,itripstaball;
- double hbcut,swb;
- double swa;
- double swc0, swc1, swc2, swc3, swc4, swc5, swc6, swc7;
- double precision;
- int packflag;
-
- struct ff_params {
- double rcutsq;
- int np;
- double *params;
- };
- ff_params *param_list;
- int *map;
-
- int nentries;
- double chpot;
- int *arow_ptr,*acol_ind;
- double *ch,*elcvec;
- double *rcg,*wcg,*pcg,*poldcg,*qcg;
- double *aval;
- int nmax,matmax;
-
- void allocate();
- void read_files(char *, char *);
- void neigh_f2c(int, int *, int *, int **);
- void neigh_c2f(int, int *, int *, int **);
-
- void write_reax_positions();
- void write_reax_vlist();
- void read_reax_forces();
- void read_reax_atom_virial();
-
- void taper_setup();
- double taper_E(const double &, const double &);
- double taper_F(const double &, const double &);
-
- void compute_charge(double &);
- void sparse_product(const int &, const int &, const int &, double[],
- int[], int[], double[], double[]);
- void cg_solve(const int &, const int &, double[], int[],
- int[], double[], double[]);
- void charge_reax(const int &, const int &, double[],
- double[], int[], int[], double[]);
-};
-
-}
-
-#endif
-#endif
-
-/* ERROR/WARNING messages:
-
-W: The pair_style reax command is unsupported. Please switch to pair_style reax/c instead
-
-UNDOCUMENTED
-
-E: Reax_defs.h setting for NATDEF is too small
-
-Edit the setting in the ReaxFF library and re-compile the
-library and re-build LAMMPS.
-
-E: Reax_defs.h setting for NNEIGHMAXDEF is too small
-
-Edit the setting in the ReaxFF library and re-compile the
-library and re-build LAMMPS.
-
-E: Illegal ... command
-
-Self-explanatory. Check the input script syntax and compare to the
-documentation for the command. You can use -echo screen as a
-command-line option when running LAMMPS to see the offending line.
-
-E: Incorrect args for pair coefficients
-
-Self-explanatory. Check the input script or data file.
-
-E: Cannot currently use pair reax with pair hybrid
-
-This is not yet supported.
-
-E: Pair style reax requires atom IDs
-
-This is a requirement to use the ReaxFF potential.
-
-E: Pair style reax requires newton pair on
-
-This is a requirement to use the ReaxFF potential.
-
-E: Pair style reax requires atom attribute q
-
-The atom style defined does not have this attribute.
-
-W: Not using real units with pair reax
-
-This is most likely an error, unless you have created your own ReaxFF
-parameter file in a different set of units.
-
-E: Invalid REAX atom type
-
-There is a mis-match between LAMMPS atom types and the elements
-listed in the ReaxFF force field file.
-
-U: pair style reax is now deprecated and will soon be retired. Users should switch to pair_style reax/c
-
-Self-explanatory.
-
-*/
diff --git a/src/REAX/pair_reax_fortran.h b/src/REAX/pair_reax_fortran.h
deleted file mode 100644
index 5268fdcdf021e03f7f63e9216647705c1a13f794..0000000000000000000000000000000000000000
--- a/src/REAX/pair_reax_fortran.h
+++ /dev/null
@@ -1,210 +0,0 @@
-/* -*- c++ -*- ----------------------------------------------------------
- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
- http://lammps.sandia.gov, Sandia National Laboratories
- Steve Plimpton, sjplimp@sandia.gov
-
- Copyright (2003) Sandia Corporation. Under the terms of Contract
- DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
- certain rights in this software. This software is distributed under
- the GNU General Public License.
-
- See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-// machine-specific C++ -> Fortran calling syntax
-// It defines the FORTRAN macro for converting variable and function
-// names from FORTRAN to C. Different compilers do this in different
-// ways. The default is add an underscore to the lower case string.
-// Other definitions of the macro can be invoked by defining the
-// corresponding macro at compile time using -D e.g. -D_IBM
-
-// CONS(a,b) should return ab, the concatenation of its arguments.
-// If compiler is using strict ISO C standards, the ## works.
-// Otherwise try the old /**/ trick and test.
-// If that fails, you will need to figure out
-// a definition for the FORTRAN macro that works on your machine.
-
-#if __STDC__
-#define CONS(a,b) a##b
-#elif defined(_IBM)
-#define CONS(a,b) a##b
-#else
-#define CONS(a,b) a/**/b
-#warning "The following declaration is a test of the CONS macro"
-#warning "If it fails, pair_reax_fortran.h must be modified by hand"
-static int my_apples_my_oranges = 1;
-static int my_applesoroanges = CONS(my_apples,_my_oranges);
-#endif
-
-
-#ifdef _IBM
-#define FORTRAN(lcname,ucname) lcname
-#endif
-
-#ifdef _F2C_LINUX
-#define FORTRAN(lcname,ucname) CONS(lcname,__)
-#endif
-
-#ifndef FORTRAN
-#define FORTRAN(lcname,ucname) CONS(lcname,_)
-#endif
-
-// hard-wired array sizes set in Fortran library
-// accesses include file from Fortran library
-
-#include "reax_defs.h"
-
-class ReaxParams {
- public:
- enum {nneighmax=NNEIGHMAXDEF,
- nat=NATDEF,
- nattot=NATTOTDEF,
- nsort=NSORTDEF,
- mbond=MBONDDEF,
- nbomax=NBOMAXDEF,
- };
-};
-
-// data structures corresponding to values in Fortran library
-
-extern "C" struct {
- double abo[ReaxParams::nat];
-} FORTRAN(cbkabo,CBKABO);
-
-extern "C" struct {
- double bo[ReaxParams::nbomax];
-} FORTRAN(cbkbo,CBKBO);
-
-extern "C" struct {
- double c[3*ReaxParams::nat]; double cglobal[3*ReaxParams::nattot];
- int itag[ReaxParams::nat];
-} FORTRAN(cbkc,CBKC);
-
-extern "C" struct {
-double ch[ReaxParams::nat];
-} FORTRAN(cbkch,CBKCH);
-
-extern "C" struct {
- double chi[ReaxParams::nsort];
- double eta[ReaxParams::nsort];
- double gam[ReaxParams::nsort];
-} FORTRAN(cbkchb,CBKCHB);
-
-extern "C" struct {
- double d[3*ReaxParams::nat]; double estrain[ReaxParams::nat];
-} FORTRAN(cbkd,CBKD);
-
-extern "C" struct {
- double atomvirial[6*ReaxParams::nat];
- double virial[6];
- int Lvirial;
- int Latomvirial;
-} FORTRAN(cbkvirial,CBKVIRIAL);
-
-extern "C" struct {
- int ia[ReaxParams::nat*(ReaxParams::mbond+3)];
- int iag[ReaxParams::nat*(ReaxParams::mbond+3)];
-} FORTRAN(cbkia,CBKIA);
-
-extern "C" struct {
- double vlp[ReaxParams::nat];
- double dvlpdsbo[ReaxParams::nat];
-} FORTRAN(cbklonpar,CBKLONPAR);
-
-extern "C" struct {
- int nubon1[ReaxParams::nat*(ReaxParams::mbond)];
- int nubon2[ReaxParams::nat*(ReaxParams::mbond)];
-} FORTRAN(cbknubon2,CBKNUBON2);
-
-extern "C" struct {
- int nvl1[ReaxParams::nneighmax * ReaxParams::nat];
- int nvl2[ReaxParams::nneighmax * ReaxParams::nat];
- int nvpair;
- int nvlself;
-} FORTRAN(cbkpairs,CBKPAIRS);
-
-extern "C" struct {
- int nvlbo[ReaxParams::nneighmax * ReaxParams::nat];
-} FORTRAN(cbknvlbo,CBKNVLBO);
-
-extern "C" struct {
- int nvlown[ReaxParams::nneighmax * ReaxParams::nat];
-} FORTRAN(cbknvlown,CBKNVLOWN);
-
-extern "C" struct {
- char qa[20*ReaxParams::nattot+10];
-} FORTRAN(cbkqa,CBKQA);
-
-extern "C" struct {
- double eb;
- double eoop;
- double epen;
- double estrc;
- double deda[3];
- double pressu;
- double efi;
- double elp;
- double emol;
- double ea;
- double eres;
- double et;
- double eradbo;
- double ev;
- double eco;
- double ecoa;
- double ehb;
- double sw;
- double ew;
- double ep;
- double ekin;
-} FORTRAN(cbkenergies,CBKENERGIES);
-
-extern "C" struct {
- double tset;
- double dseed;
- double tempmd;
- double ts2;
- double ts22;
- int nmolo;
- int nmolo5;
- int nbon;
- int na;
- int namov;
- int na_local;
-} FORTRAN(rsmall,RSMALL);
-
-// external routines provided by Fortran library
-
-extern "C" void FORTRAN(readc,READC)();
-extern "C" void FORTRAN(reaxinit,REAXINIT)();
-extern "C" void FORTRAN(ffinpt,FFINPT)();
-extern "C" void FORTRAN(tap7th,TAP7TH)();
-extern "C" void FORTRAN(taper,TAPER)(double*,double*);
-extern "C" void FORTRAN(readgeo,READGEO)();
-extern "C" void FORTRAN(srtatom,SRTATOM)();
-extern "C" void FORTRAN(vlist,VLIST) ();
-extern "C" void FORTRAN(srtbon1,SRTBON1)(int*,int*,double*,int*,int*);
-extern "C" void FORTRAN(molec,MOLEC)();
-extern "C" void FORTRAN(encalc,ENCALC)();
-extern "C" void FORTRAN(getswb,GETSWB)(double*);
-extern "C" void FORTRAN(getswa,GETSWA)(double*);
-extern "C" void FORTRAN(getvrange,GET_VRANGE)(double*);
-extern "C" void FORTRAN(getnvlist,GET_NVLIST)(int*);
-extern "C" void FORTRAN(getvlbora,GETVLBORA)(double*);
-extern "C" void FORTRAN(cgsolve,CGSOLVE)
- (int*,double*,int*,double*,double*,int*);
-extern "C" void FORTRAN(getnval,GETNVAL)(int*);
-extern "C" void FORTRAN(getntor,GETNTOR)(int*);
-extern "C" void FORTRAN(getnhb,GETNHB)(int*);
-extern "C" void FORTRAN(getnbonall,GETNBONALL)(int*);
-extern "C" void FORTRAN(getnneighmax,GETNNEIGHMAX)(int*);
-extern "C" void FORTRAN(getnat,GETNAT)(int*);
-extern "C" void FORTRAN(getnattot,GETNATTOT)(int*);
-extern "C" void FORTRAN(getnsort,GETNSORT)(int*);
-extern "C" void FORTRAN(getmbond,GETMBOND)(int*);
-extern "C" void FORTRAN(getnso,GETNSO)(int*);
-extern "C" void FORTRAN(setngeofor,SETNGEOFOR)(int*);
-extern "C" void FORTRAN(mdsav,MDSAV)(int*);
-extern "C" void FORTRAN(getnsbmax,GETNSBMAX)(int*);
-extern "C" void FORTRAN(getnsbma2,GETNSBMA2)(int*);
-extern "C" void FORTRAN(getcutof3,GETCUTOF3)(double*);
diff --git a/src/USER-MEAMC/pair_meamc.h b/src/USER-MEAMC/pair_meamc.h
index 476a70dd04d420365d5d52454cad695357a87896..a006e70bdbc9ba94034eac294f537de547894ad8 100644
--- a/src/USER-MEAMC/pair_meamc.h
+++ b/src/USER-MEAMC/pair_meamc.h
@@ -14,6 +14,7 @@
#ifdef PAIR_CLASS
PairStyle(meam/c,PairMEAMC)
+PairStyle(meam,PairMEAMC)
#else
diff --git a/src/pair_deprecated.cpp b/src/pair_deprecated.cpp
index d8b371634185836a5fbb09a29a48003d22deb79b..0b1342fb2d4137b192d7cad031cfe7da1e3ed05a 100644
--- a/src/pair_deprecated.cpp
+++ b/src/pair_deprecated.cpp
@@ -48,10 +48,13 @@ void PairDeprecated::settings(int, char **)
my_style = hybrid->keywords[hybrid->nstyles];
}
+ if (strcmp(my_style,"reax") == 0) {
+ writemsg(lmp,"\nPair style 'reax' has been removed from LAMMPS "
+ "after the 12 December 2018 version\n\n",1);
+ }
+
if (strcmp(my_style,"DEPRECATED") == 0) {
writemsg(lmp,"\nPair style 'DEPRECATED' is a dummy style\n\n",0);
}
}
-
-
diff --git a/src/pair_deprecated.h b/src/pair_deprecated.h
index 29d6efffaff6fb7497826d21c3e6d8d18e2bfdef..029ec5e6d4d7c00bafb39b8ed20647d662ee826a 100644
--- a/src/pair_deprecated.h
+++ b/src/pair_deprecated.h
@@ -14,6 +14,7 @@
#ifdef PAIR_CLASS
PairStyle(DEPRECATED,PairDeprecated)
+PairStyle(reax,PairDeprecated)
#else
diff --git a/tools/reax/README.txt b/tools/reax/README.txt
index 2a7ff29f26264c674df1fa25df16e393c1f23c21..3c9fe4506be3415a1b56dd9f16065d2404802d6d 100644
--- a/tools/reax/README.txt
+++ b/tools/reax/README.txt
@@ -4,19 +4,7 @@
The programs in this folder can be used to analyze the
output of simulations using the ReaxFF potentials;
-mol_fra.c: reads the output of fix reax/bonds
- and identifies fragments
- Compile it using a C compiler
- To test, run it with Cutoff.dic and bonds.reax
- Contact: Aidan Thompson
-
-bondConnectCheck.f90: reads the output of fix reax/bonds.
- Does not do fragment analysis.
- Compile it using FORTRAN compiler
- To test, run it with bonds.reax
- Contact: Paul Liangliang Huang <lhuang4@ncsu.edu>
-
reaxc_bond.pl: reads the bonding information in the
.trj file produced by pair_style reax/c and
- outputs molecule counts for each frame.
+ outputs molecule counts for each frame.
diff --git a/tools/reax/bondConnectCheck.f90 b/tools/reax/bondConnectCheck.f90
deleted file mode 100644
index feff1ed3ed97fdb015c41e8ecce4653a4c6befec..0000000000000000000000000000000000000000
--- a/tools/reax/bondConnectCheck.f90
+++ /dev/null
@@ -1,232 +0,0 @@
-!# DEC.9, 2010
-!# HLL
-!# NCSU
-!#
-!# This is a program to read the output from 'fix reax/bond', TPRD, Lammps
-!# The output is saved into file "bonds.reax", where each image is divided
-!# into three parts:
-!#
-!# (1) Head, 7 Lines;
-!# (2) Body, No._of_atom Lines;
-!# (3) Tail, 1 Line
-!#
-!# The total number of images is related with the output frequence and number of iterations.
-!# In this case, it is "number of iteration+1".
-!#
-!# Each line in Body part is made up of the following parameters:
-!# id, type, nb, id_1, id_2, ... id_nb, mol, bo_1, bo_2, ... bo_nb, abo, nlp, q
-!# abo = atomic bond order
-!# nlp = number of lone pairs
-!# q = atomic charge
-!#
-!# PLEASE DOUBLE CHECK YOUR OWN LAMMPS INPUT SCRIPT & OUTPUT AND MAKE CORRESPONDING CHSNGES
-
-program main
-implicit none
-
-integer I, J, K, L
-integer image, natom
-integer headline, tailline
-integer id, atype, nb, bd1, bd2, bd3, bd4, mol
-double precision bo1, bo2, bo3, bo4, abo, nlp, q
-
-open (unit=10, file='bonds.reax')
-
-open (unit=20, file='N129.txt', status='unknown')
-open (unit=21, file='N133.txt', status='unknown')
-open (unit=22, file='N137.txt', status='unknown')
-open (unit=23, file='N141.txt', status='unknown')
-open (unit=24, file='N145.txt', status='unknown')
-open (unit=25, file='N149.txt', status='unknown')
-open (unit=26, file='N153.txt', status='unknown')
-open (unit=27, file='N157.txt', status='unknown')
-
-open (unit=30, file='reactionRecord.txt', status='unknown')
-
-!# Make changes accordingly.
-image = 1
-headline = 7
-tailline = 1
-natom = 384
-
-do I = 1, image+1
-
-! Skip the head part
- do J = 1, headline
- read(10,*)
- end do
-
-! Each image has 'natom' lines
- do K = 1, natom
-
-! read in the first three number each line to determine:
-! (1) what type of atom it is, atype
-! the correspondence in Lammps: 1-C, 2-H, 3-O, 4-N, 5-S
-! (2) how many bonds it has, nb
-! this 'nb' determines the following bond_link information & bond_order paramaters of the same line
-
- read(10,*) id, atype, nb
-
-! TEST
-! write(*,*) id, atype, nb
-
- if (atype .eq. 4) then
-
- backspace 10
-
-! Should have some easier way to replace this "IF", I am just toooo lazy.
-! Thanks to the fact that the maximum number of bonds is 4. ^-^
-!??? is it possible that nb = 0 ??? KEEP THAT IN MIND.
-
- if (nb.eq.0) then
-
- read(10,*) id, atype, nb, mol, abo, nlp, q
-
- if (id .eq. 129) then
- write(20, 200) id, atype, nb, mol, abo, nlp, q
- elseif (id .eq. 133) then
- write(21, 200) id, atype, nb, mol, abo, nlp, q
- elseif (id .eq. 137) then
- write(22, 200) id, atype, nb, mol, abo, nlp, q
- elseif (id .eq. 141) then
- write(23, 200) id, atype, nb, mol, abo, nlp, q
- elseif (id .eq. 145) then
- write(24, 200) id, atype, nb, mol, abo, nlp, q
- elseif (id .eq. 149) then
- write(25, 200) id, atype, nb, mol, abo, nlp, q
- elseif (id .eq. 153) then
- write(26, 200) id, atype, nb, mol, abo, nlp, q
- elseif (id .eq. 157) then
- write(27, 200) id, atype, nb, mol, abo, nlp, q
- 200 format(4I4, 3f14.3)
- endif
-
-! If bd .ne. 3, it measn reaction is happening to Nitrogen atom.
- write (30, 300) I, id, atype, nb, mol, abo, nlp, q
- 300 format(5I4, 3f14.3)
-
-
- elseif (nb.eq.1) then
-
- read(10,*) id, atype, nb, bd1, mol, bo1, abo, nlp, q
-
- if (id .eq. 129) then
- write(20, 201) id, atype, nb, bd1, mol, bo1, abo, nlp, q
- elseif (id .eq. 133) then
- write(21, 201) id, atype, nb, bd1, mol, bo1, abo, nlp, q
- elseif (id .eq. 137) then
- write(22, 201) id, atype, nb, bd1, mol, bo1, abo, nlp, q
- elseif (id .eq. 141) then
- write(23, 201) id, atype, nb, bd1, mol, bo1, abo, nlp, q
- elseif (id .eq. 145) then
- write(24, 201) id, atype, nb, bd1, mol, bo1, abo, nlp, q
- elseif (id .eq. 149) then
- write(25, 201) id, atype, nb, bd1, mol, bo1, abo, nlp, q
- elseif (id .eq. 153) then
- write(26, 201) id, atype, nb, bd1, mol, bo1, abo, nlp, q
- elseif (id .eq. 157) then
- write(27, 201) id, atype, nb, bd1, mol, bo1, abo, nlp, q
- 201 format(5I4, 4f14.3)
- endif
-
- ! If bd .ne. 3, it measn reaction is happening to Nitrogen atom.
- write (30, 301) I, id, atype, nb, bd1, mol, bo1, abo, nlp, q
- 301 format(6I4, 4f14.3)
-
- elseif (nb.eq.2) then
-
- read(10,*) id, atype, nb, bd1, bd2, mol, bo1, bo2, abo, nlp, q
-
- if (id .eq. 129) then
- write(20, 202) id, atype, nb, bd1, bd2, mol, bo1, bo2, abo, nlp, q
- elseif (id .eq. 133) then
- write(21, 202) id, atype, nb, bd1, bd2, mol, bo1, bo2, abo, nlp, q
- elseif (id .eq. 137) then
- write(22, 202) id, atype, nb, bd1, bd2, mol, bo1, bo2, abo, nlp, q
- elseif (id .eq. 141) then
- write(23, 202) id, atype, nb, bd1, bd2, mol, bo1, bo2, abo, nlp, q
- elseif (id .eq. 145) then
- write(24, 202) id, atype, nb, bd1, bd2, mol, bo1, bo2, abo, nlp, q
- elseif (id .eq. 149) then
- write(25, 202) id, atype, nb, bd1, bd2, mol, bo1, bo2, abo, nlp, q
- elseif (id .eq. 153) then
- write(26, 202) id, atype, nb, bd1, bd2, mol, bo1, bo2, abo, nlp, q
- elseif (id .eq. 157) then
- write(27, 202) id, atype, nb, bd1, bd2, mol, bo1, bo2, abo, nlp, q
- 202 format(6I4, 5f14.3)
- endif
-
-! If bd .ne. 3, it measn reaction is happening to Nitrogen atom.
- write (30, 302) I, id, atype, nb, bd1, bd2, mol, bo1, bo2, abo, nlp, q
- 302 format(7I4, 5f14.3)
-
- elseif (nb.eq.3) then
-
- read(10,*) id, atype, nb, bd1, bd2, bd3, mol, bo1, bo2, bo3, abo, nlp, q
-
-
- if (id .eq. 129) then
- write(20, 203) id, atype, nb, bd1, bd2, bd3, mol, bo1, bo2, bo3, abo, nlp, q
- elseif (id .eq. 133) then
- write(21, 203) id, atype, nb, bd1, bd2, bd3, mol, bo1, bo2, bo3, abo, nlp, q
- elseif (id .eq. 137) then
- write(22, 203) id, atype, nb, bd1, bd2, bd3, mol, bo1, bo2, bo3, abo, nlp, q
- elseif (id .eq. 141) then
- write(23, 203) id, atype, nb, bd1, bd2, bd3, mol, bo1, bo2, bo3, abo, nlp, q
- elseif (id .eq. 145) then
- write(24, 203) id, atype, nb, bd1, bd2, bd3, mol, bo1, bo2, bo3, abo, nlp, q
- elseif (id .eq. 149) then
- write(25, 203) id, atype, nb, bd1, bd2, bd3, mol, bo1, bo2, bo3, abo, nlp, q
- elseif (id .eq. 153) then
- write(26, 203) id, atype, nb, bd1, bd2, bd3, mol, bo1, bo2, bd3, abo, nlp, q
- elseif (id .eq. 157) then
- write(27, 203) id, atype, nb, bd1, bd2, bd3, mol, bo1, bo2, bo3, abo, nlp, q
- 203 format(7I4, 6f14.3)
- endif
-
- elseif (nb.eq.4) then
-
- read(10,*) id, atype, nb, bd1, bd2, bd3, bd4, mol, bo1, bo2, bo3, bo4, abo, nlp, q
-
- if (id .eq. 129) then
- write(20, 204) id, atype, nb, bd1, bd2, bd3, bd4, mol, bo1, bo2, bo3, bo4, abo, nlp, q
- elseif (id .eq. 133) then
- write(21, 204) id, atype, nb, bd1, bd2, bd3, bd4, mol, bo1, bo2, bo3, bo4, abo, nlp, q
- elseif (id .eq. 137) then
- write(22, 204) id, atype, nb, bd1, bd2, bd3, bd4, mol, bo1, bo2, bo3, bo4, abo, nlp, q
- elseif (id .eq. 141) then
- write(23, 204) id, atype, nb, bd1, bd2, bd3, bd4, mol, bo1, bo2, bo3, bo4, abo, nlp, q
- elseif (id .eq. 145) then
- write(24, 204) id, atype, nb, bd1, bd2, bd3, bd4, mol, bo1, bo2, bo3, bo4, abo, nlp, q
- elseif (id .eq. 149) then
- write(25, 204) id, atype, nb, bd1, bd2, bd3, bd4, mol, bo1, bo2, bo3, bo4, abo, nlp, q
- elseif (id .eq. 153) then
- write(26, 204) id, atype, nb, bd1, bd2, bd3, bd4, mol, bo1, bo2, bd3, bo4, abo, nlp, q
- elseif (id .eq. 157) then
- write(27, 204) id, atype, nb, bd1, bd2, bd3, bd4, mol, bo1, bo2, bo3, bo4, abo, nlp, q
- 204 format(8I4, 7f14.3)
- endif
-
-! If bd .ne. 3, it measn reaction is happening to Nitrogen atom.
- write (30, 304) I, id, atype, nb, bd1, bd2, bd3, bd4, mol, bo1, bo2, bo3, bo4, abo, nlp, q
- 304 format(9I4, 7f14.3)
-
-! Corresponding to "if (nb.eq.0) then "
-
- endif
-
-! Corresponding to "if (atype .eq. 4) then"
- endif
-
-
- enddo
-
- do L =1,tailline
- read(10,*)
- enddo
-
- enddo
-
- end program main
-
-
diff --git a/tools/reax/bonds.reax b/tools/reax/bonds.reax
deleted file mode 100644
index 4c7af471ba4fc73db325d8fbdb1d9cd14f7fad58..0000000000000000000000000000000000000000
--- a/tools/reax/bonds.reax
+++ /dev/null
@@ -1,784 +0,0 @@
-# Timestep 0
-#
-# Number of particles 384
-#
-# Max.number of bonds per atom 3 with coarse bond order cutoff 0.300
-# Particle connection table and bond orders
-# id type nb id_1...id_nb mol bo_1...bo_nb abo nlp q
- 1 1 3 2 6 13 0 1.324 1.332 1.109 3.767 0.000 -0.073
- 2 1 3 1 3 14 0 1.324 1.345 1.300 3.969 0.000 0.193
- 3 1 3 2 4 15 0 1.345 1.336 1.083 3.767 0.000 -0.060
- 4 1 3 3 5 16 0 1.336 1.306 1.324 3.967 0.000 0.196
- 5 1 3 4 6 17 0 1.306 1.317 1.143 3.769 0.000 -0.063
- 6 1 3 1 5 18 0 1.332 1.317 1.318 3.967 0.000 0.191
- 7 2 1 14 0 0.873 1.075 0.000 0.366
- 8 2 1 14 0 0.897 1.056 0.000 0.386
- 9 2 1 16 0 0.905 1.051 0.000 0.379
- 10 2 2 16 23 0 0.838 0.267 1.105 0.000 0.385
- 11 2 2 18 24 0 0.868 0.216 1.083 0.000 0.377
- 12 2 1 18 0 0.881 1.069 0.000 0.386
- 13 4 3 1 20 19 0 1.109 1.198 1.197 3.504 0.165 0.344
- 14 4 3 2 7 8 0 1.300 0.873 0.897 3.070 0.966 -0.469
- 15 4 3 3 21 22 0 1.083 1.211 1.214 3.508 0.160 0.371
- 16 4 3 4 9 10 0 1.324 0.905 0.838 3.068 0.968 -0.443
- 17 4 3 5 23 24 0 1.143 1.171 1.190 3.504 0.165 0.341
- 18 4 3 6 11 12 0 1.318 0.868 0.881 3.067 0.969 -0.438
- 19 3 1 13 0 1.197 1.393 2.000 -0.381
- 20 3 1 13 0 1.198 1.407 2.000 -0.413
- 21 3 1 15 0 1.211 1.378 2.000 -0.375
- 22 3 1 15 0 1.214 1.368 2.000 -0.399
- 23 3 2 10 17 0 0.267 1.171 1.446 2.000 -0.388
- 24 3 2 11 17 0 0.216 1.190 1.413 2.000 -0.411
- 25 1 3 30 26 37 0 1.332 1.324 1.109 3.767 0.000 -0.073
- 26 1 3 25 27 38 0 1.324 1.345 1.300 3.969 0.000 0.193
- 27 1 3 26 28 39 0 1.345 1.336 1.083 3.767 0.000 -0.060
- 28 1 3 27 29 40 0 1.336 1.306 1.324 3.967 0.000 0.196
- 29 1 3 28 30 41 0 1.306 1.317 1.143 3.769 0.000 -0.063
- 30 1 3 25 29 42 0 1.332 1.317 1.318 3.967 0.000 0.191
- 31 2 1 38 0 0.873 1.075 0.000 0.366
- 32 2 1 38 0 0.897 1.056 0.000 0.386
- 33 2 1 40 0 0.905 1.051 0.000 0.379
- 34 2 2 47 40 0 0.267 0.838 1.105 0.000 0.385
- 35 2 2 42 48 0 0.868 0.216 1.083 0.000 0.377
- 36 2 1 42 0 0.881 1.069 0.000 0.386
- 37 4 3 25 43 44 0 1.109 1.197 1.198 3.504 0.165 0.344
- 38 4 3 26 32 31 0 1.300 0.897 0.873 3.070 0.966 -0.469
- 39 4 3 27 45 46 0 1.083 1.211 1.214 3.508 0.160 0.371
- 40 4 3 28 33 34 0 1.324 0.905 0.838 3.068 0.968 -0.443
- 41 4 3 29 47 48 0 1.143 1.171 1.190 3.504 0.165 0.341
- 42 4 3 30 35 36 0 1.318 0.868 0.881 3.067 0.969 -0.438
- 43 3 1 37 0 1.197 1.393 2.000 -0.381
- 44 3 1 37 0 1.198 1.407 2.000 -0.413
- 45 3 1 39 0 1.211 1.378 2.000 -0.375
- 46 3 1 39 0 1.214 1.368 2.000 -0.399
- 47 3 2 34 41 0 0.267 1.171 1.446 2.000 -0.388
- 48 3 2 35 41 0 0.216 1.190 1.413 2.000 -0.411
- 49 1 3 50 54 61 0 1.324 1.332 1.109 3.767 0.000 -0.073
- 50 1 3 49 51 62 0 1.324 1.345 1.300 3.969 0.000 0.193
- 51 1 3 50 52 63 0 1.345 1.336 1.083 3.767 0.000 -0.060
- 52 1 3 51 53 64 0 1.336 1.306 1.324 3.967 0.000 0.196
- 53 1 3 52 54 65 0 1.306 1.317 1.143 3.769 0.000 -0.063
- 54 1 3 49 53 66 0 1.332 1.317 1.318 3.967 0.000 0.191
- 55 2 1 62 0 0.873 1.075 0.000 0.366
- 56 2 1 62 0 0.897 1.056 0.000 0.386
- 57 2 1 64 0 0.905 1.051 0.000 0.379
- 58 2 2 64 71 0 0.838 0.267 1.105 0.000 0.385
- 59 2 2 66 72 0 0.868 0.216 1.083 0.000 0.377
- 60 2 1 66 0 0.881 1.069 0.000 0.386
- 62 4 3 50 55 56 0 1.300 0.873 0.897 3.070 0.966 -0.469
- 63 4 3 51 69 70 0 1.083 1.211 1.214 3.508 0.160 0.371
- 64 4 3 52 57 58 0 1.324 0.905 0.838 3.068 0.968 -0.443
- 65 4 3 53 71 72 0 1.143 1.171 1.190 3.504 0.165 0.341
- 66 4 3 54 59 60 0 1.318 0.868 0.881 3.067 0.969 -0.438
- 69 3 1 63 0 1.211 1.378 2.000 -0.375
- 70 3 1 63 0 1.214 1.368 2.000 -0.399
- 71 3 2 58 65 0 0.267 1.171 1.446 2.000 -0.388
- 72 3 2 59 65 0 0.216 1.190 1.413 2.000 -0.411
- 73 1 3 78 74 85 0 1.332 1.324 1.109 3.767 0.000 -0.073
- 74 1 3 73 75 86 0 1.324 1.345 1.300 3.969 0.000 0.193
- 75 1 3 74 76 87 0 1.345 1.336 1.083 3.767 0.000 -0.060
- 76 1 3 75 77 88 0 1.336 1.306 1.324 3.967 0.000 0.196
- 77 1 3 76 78 89 0 1.306 1.317 1.143 3.769 0.000 -0.063
- 78 1 3 73 77 90 0 1.332 1.317 1.318 3.967 0.000 0.191
- 79 2 1 86 0 0.873 1.075 0.000 0.366
- 80 2 1 86 0 0.897 1.056 0.000 0.386
- 81 2 1 88 0 0.905 1.051 0.000 0.379
- 82 2 2 95 88 0 0.267 0.838 1.105 0.000 0.385
- 83 2 2 90 96 0 0.868 0.216 1.083 0.000 0.377
- 84 2 1 90 0 0.881 1.069 0.000 0.386
- 85 4 3 73 91 92 0 1.109 1.197 1.198 3.504 0.165 0.344
- 86 4 3 74 80 79 0 1.300 0.897 0.873 3.070 0.966 -0.469
- 87 4 3 75 93 94 0 1.083 1.211 1.214 3.508 0.160 0.371
- 88 4 3 76 81 82 0 1.324 0.905 0.838 3.068 0.968 -0.443
- 89 4 3 77 95 96 0 1.143 1.171 1.190 3.504 0.165 0.341
- 90 4 3 78 83 84 0 1.318 0.868 0.881 3.067 0.969 -0.438
- 91 3 1 85 0 1.197 1.393 2.000 -0.381
- 92 3 1 85 0 1.198 1.407 2.000 -0.413
- 93 3 1 87 0 1.211 1.378 2.000 -0.375
- 94 3 1 87 0 1.214 1.368 2.000 -0.399
- 95 3 2 82 89 0 0.267 1.171 1.446 2.000 -0.388
- 96 3 2 83 89 0 0.216 1.190 1.413 2.000 -0.411
- 97 1 3 98 102 109 0 1.324 1.332 1.109 3.767 0.000 -0.073
- 98 1 3 97 99 110 0 1.324 1.345 1.300 3.969 0.000 0.193
- 99 1 3 98 100 111 0 1.345 1.337 1.083 3.767 0.000 -0.060
- 100 1 3 99 101 112 0 1.337 1.306 1.324 3.967 0.000 0.196
- 101 1 3 100 113 102 0 1.306 1.143 1.317 3.769 0.000 -0.063
- 102 1 3 97 101 114 0 1.332 1.317 1.318 3.967 0.000 0.191
- 103 2 1 110 0 0.873 1.075 0.000 0.366
- 104 2 1 110 0 0.897 1.056 0.000 0.386
- 105 2 1 112 0 0.905 1.051 0.000 0.379
- 106 2 2 119 112 0 0.267 0.838 1.105 0.000 0.385
- 107 2 2 114 120 0 0.868 0.216 1.083 0.000 0.377
- 108 2 1 114 0 0.881 1.069 0.000 0.386
- 109 4 3 116 97 115 0 1.198 1.109 1.197 3.504 0.165 0.344
- 110 4 3 103 104 98 0 0.873 0.897 1.300 3.070 0.966 -0.469
- 111 4 3 99 117 118 0 1.083 1.211 1.214 3.508 0.160 0.371
- 112 4 3 100 105 106 0 1.324 0.905 0.838 3.068 0.968 -0.443
- 113 4 3 101 119 120 0 1.143 1.171 1.190 3.504 0.165 0.341
- 114 4 3 102 107 108 0 1.318 0.868 0.881 3.067 0.969 -0.438
- 115 3 1 109 0 1.197 1.393 2.000 -0.381
- 116 3 1 109 0 1.198 1.407 2.000 -0.413
- 117 3 1 111 0 1.211 1.378 2.000 -0.375
- 118 3 1 111 0 1.214 1.368 2.000 -0.399
- 119 3 2 106 113 0 0.267 1.171 1.446 2.000 -0.388
- 120 3 2 107 113 0 0.216 1.190 1.413 2.000 -0.411
- 121 1 3 126 122 133 0 1.332 1.324 1.109 3.767 0.000 -0.073
- 122 1 3 121 123 134 0 1.324 1.345 1.300 3.969 0.000 0.193
- 123 1 3 122 124 135 0 1.345 1.336 1.083 3.767 0.000 -0.060
- 124 1 3 123 125 136 0 1.336 1.306 1.324 3.967 0.000 0.196
- 125 1 3 124 126 137 0 1.306 1.317 1.143 3.769 0.000 -0.063
- 126 1 3 121 125 138 0 1.332 1.317 1.318 3.967 0.000 0.191
- 127 2 1 134 0 0.873 1.075 0.000 0.366
- 128 2 1 134 0 0.897 1.056 0.000 0.386
- 129 2 1 136 0 0.905 1.051 0.000 0.379
- 130 2 2 143 136 0 0.267 0.838 1.105 0.000 0.385
- 131 2 2 138 144 0 0.868 0.216 1.083 0.000 0.377
- 132 2 1 138 0 0.881 1.069 0.000 0.386
- 133 4 3 121 139 140 0 1.109 1.197 1.198 3.504 0.165 0.344
- 134 4 3 122 127 128 0 1.300 0.873 0.897 3.070 0.966 -0.469
- 135 4 3 123 141 142 0 1.083 1.211 1.214 3.508 0.160 0.371
- 136 4 3 124 129 130 0 1.324 0.905 0.838 3.068 0.968 -0.443
- 137 4 3 125 143 144 0 1.143 1.171 1.190 3.504 0.165 0.341
- 138 4 3 126 131 132 0 1.318 0.868 0.881 3.067 0.969 -0.438
- 139 3 1 133 0 1.197 1.393 2.000 -0.381
- 140 3 1 133 0 1.198 1.407 2.000 -0.413
- 141 3 1 135 0 1.211 1.378 2.000 -0.375
- 142 3 1 135 0 1.214 1.368 2.000 -0.399
- 143 3 2 130 137 0 0.267 1.171 1.446 2.000 -0.388
- 144 3 2 131 137 0 0.216 1.190 1.413 2.000 -0.411
- 145 1 3 146 150 157 0 1.324 1.332 1.109 3.767 0.000 -0.073
- 146 1 3 145 147 158 0 1.324 1.345 1.300 3.969 0.000 0.193
- 147 1 3 146 148 159 0 1.345 1.337 1.083 3.767 0.000 -0.060
- 148 1 3 147 149 160 0 1.337 1.306 1.324 3.967 0.000 0.196
- 149 1 3 148 161 150 0 1.306 1.143 1.317 3.769 0.000 -0.063
- 150 1 3 145 149 162 0 1.332 1.317 1.318 3.967 0.000 0.191
- 151 2 1 158 0 0.873 1.075 0.000 0.366
- 152 2 1 158 0 0.897 1.056 0.000 0.386
- 153 2 1 160 0 0.905 1.051 0.000 0.379
- 154 2 2 167 160 0 0.267 0.838 1.105 0.000 0.385
- 155 2 2 168 162 0 0.216 0.868 1.083 0.000 0.377
- 156 2 1 162 0 0.881 1.069 0.000 0.386
- 158 4 3 151 152 146 0 0.873 0.897 1.300 3.070 0.966 -0.469
- 159 4 3 147 165 166 0 1.083 1.211 1.214 3.508 0.160 0.371
- 160 4 3 148 153 154 0 1.324 0.905 0.838 3.068 0.968 -0.443
- 161 4 3 149 167 168 0 1.143 1.171 1.190 3.504 0.165 0.341
- 162 4 3 150 155 156 0 1.318 0.868 0.881 3.067 0.969 -0.438
- 165 3 1 159 0 1.211 1.378 2.000 -0.375
- 166 3 1 159 0 1.214 1.368 2.000 -0.399
- 167 3 2 154 161 0 0.267 1.171 1.446 2.000 -0.388
- 168 3 2 155 161 0 0.216 1.190 1.413 2.000 -0.411
- 169 1 3 174 170 181 0 1.332 1.324 1.109 3.767 0.000 -0.073
- 170 1 3 169 171 182 0 1.324 1.345 1.300 3.969 0.000 0.193
- 171 1 3 170 172 183 0 1.345 1.336 1.083 3.767 0.000 -0.060
- 172 1 3 171 173 184 0 1.336 1.306 1.324 3.967 0.000 0.196
- 173 1 3 172 174 185 0 1.306 1.317 1.143 3.769 0.000 -0.063
- 174 1 3 169 173 186 0 1.332 1.317 1.318 3.967 0.000 0.191
- 175 2 1 182 0 0.873 1.075 0.000 0.366
- 176 2 1 182 0 0.897 1.056 0.000 0.386
- 177 2 1 184 0 0.905 1.051 0.000 0.379
- 178 2 2 191 184 0 0.267 0.838 1.105 0.000 0.385
- 179 2 2 186 192 0 0.868 0.216 1.083 0.000 0.377
- 180 2 1 186 0 0.881 1.069 0.000 0.386
- 181 4 3 169 187 188 0 1.109 1.197 1.198 3.504 0.165 0.344
- 182 4 3 170 175 176 0 1.300 0.873 0.897 3.070 0.966 -0.469
- 183 4 3 171 189 190 0 1.083 1.211 1.214 3.508 0.160 0.371
- 184 4 3 172 177 178 0 1.324 0.905 0.838 3.068 0.968 -0.443
- 185 4 3 173 191 192 0 1.143 1.171 1.190 3.504 0.165 0.341
- 186 4 3 174 179 180 0 1.318 0.868 0.881 3.067 0.969 -0.438
- 187 3 1 181 0 1.197 1.393 2.000 -0.381
- 188 3 1 181 0 1.198 1.407 2.000 -0.413
- 189 3 1 183 0 1.211 1.378 2.000 -0.375
- 190 3 1 183 0 1.214 1.368 2.000 -0.399
- 191 3 2 178 185 0 0.267 1.171 1.446 2.000 -0.388
- 192 3 2 179 185 0 0.216 1.190 1.413 2.000 -0.411
- 193 1 3 194 198 205 0 1.324 1.332 1.109 3.767 0.000 -0.073
- 194 1 3 193 195 206 0 1.324 1.345 1.300 3.969 0.000 0.193
- 195 1 3 194 196 207 0 1.345 1.336 1.083 3.767 0.000 -0.060
- 196 1 3 195 197 208 0 1.336 1.306 1.324 3.967 0.000 0.196
- 197 1 3 196 198 209 0 1.306 1.317 1.143 3.769 0.000 -0.063
- 198 1 3 193 197 210 0 1.332 1.317 1.318 3.967 0.000 0.191
- 199 2 1 206 0 0.873 1.075 0.000 0.366
- 200 2 1 206 0 0.897 1.056 0.000 0.386
- 201 2 1 208 0 0.905 1.051 0.000 0.379
- 202 2 2 208 215 0 0.838 0.267 1.105 0.000 0.385
- 203 2 2 210 216 0 0.868 0.216 1.083 0.000 0.377
- 204 2 1 210 0 0.881 1.069 0.000 0.386
- 205 4 3 212 193 211 0 1.198 1.109 1.197 3.504 0.165 0.344
- 206 4 3 199 200 194 0 0.873 0.897 1.300 3.070 0.966 -0.469
- 207 4 3 195 213 214 0 1.083 1.211 1.214 3.508 0.160 0.371
- 208 4 3 196 201 202 0 1.324 0.905 0.838 3.068 0.968 -0.443
- 209 4 3 197 215 216 0 1.143 1.171 1.190 3.504 0.165 0.341
- 210 4 3 198 203 204 0 1.318 0.868 0.881 3.067 0.969 -0.438
- 211 3 1 205 0 1.197 1.393 2.000 -0.381
- 212 3 1 205 0 1.198 1.407 2.000 -0.413
- 213 3 1 207 0 1.211 1.378 2.000 -0.375
- 214 3 1 207 0 1.214 1.368 2.000 -0.399
- 215 3 2 202 209 0 0.267 1.171 1.446 2.000 -0.388
- 216 3 2 203 209 0 0.216 1.190 1.413 2.000 -0.411
- 217 1 3 218 222 229 0 1.324 1.332 1.109 3.767 0.000 -0.073
- 218 1 3 217 219 230 0 1.324 1.345 1.300 3.969 0.000 0.193
- 219 1 3 218 220 231 0 1.345 1.336 1.083 3.767 0.000 -0.060
- 220 1 3 219 221 232 0 1.336 1.306 1.324 3.967 0.000 0.196
- 221 1 3 220 222 233 0 1.306 1.317 1.143 3.769 0.000 -0.063
- 222 1 3 217 221 234 0 1.332 1.317 1.318 3.967 0.000 0.191
- 223 2 1 230 0 0.873 1.075 0.000 0.366
- 224 2 1 230 0 0.897 1.056 0.000 0.386
- 225 2 1 232 0 0.905 1.051 0.000 0.379
- 226 2 2 239 232 0 0.267 0.838 1.105 0.000 0.385
- 227 2 2 234 240 0 0.868 0.216 1.083 0.000 0.377
- 228 2 1 234 0 0.881 1.069 0.000 0.386
- 229 4 3 217 235 236 0 1.109 1.197 1.198 3.504 0.165 0.344
- 230 4 3 218 223 224 0 1.300 0.873 0.897 3.070 0.966 -0.469
- 231 4 3 219 237 238 0 1.083 1.211 1.214 3.508 0.160 0.371
- 232 4 3 225 226 220 0 0.905 0.838 1.324 3.068 0.968 -0.443
- 233 4 3 221 239 240 0 1.143 1.171 1.190 3.504 0.165 0.341
- 234 4 3 222 227 228 0 1.318 0.868 0.881 3.067 0.969 -0.438
- 235 3 1 229 0 1.197 1.393 2.000 -0.381
- 236 3 1 229 0 1.198 1.407 2.000 -0.413
- 237 3 1 231 0 1.211 1.378 2.000 -0.375
- 238 3 1 231 0 1.214 1.368 2.000 -0.399
- 239 3 2 233 226 0 1.171 0.267 1.446 2.000 -0.388
- 240 3 2 227 233 0 0.216 1.190 1.413 2.000 -0.411
- 241 1 3 242 246 253 0 1.324 1.332 1.109 3.767 0.000 -0.073
- 242 1 3 241 243 254 0 1.324 1.345 1.300 3.969 0.000 0.193
- 243 1 3 242 244 255 0 1.345 1.336 1.083 3.767 0.000 -0.060
- 244 1 3 243 245 256 0 1.336 1.306 1.324 3.967 0.000 0.196
- 245 1 3 244 246 257 0 1.306 1.317 1.143 3.769 0.000 -0.063
- 246 1 3 241 245 258 0 1.332 1.317 1.318 3.967 0.000 0.191
- 247 2 1 254 0 0.873 1.075 0.000 0.366
- 248 2 1 254 0 0.897 1.056 0.000 0.386
- 249 2 1 256 0 0.905 1.051 0.000 0.379
- 250 2 2 256 263 0 0.838 0.267 1.105 0.000 0.385
- 251 2 2 258 264 0 0.868 0.216 1.083 0.000 0.377
- 252 2 1 258 0 0.881 1.069 0.000 0.386
- 254 4 3 247 248 242 0 0.873 0.897 1.300 3.070 0.966 -0.469
- 255 4 3 243 261 262 0 1.083 1.211 1.214 3.508 0.160 0.371
- 256 4 3 244 249 250 0 1.324 0.905 0.838 3.068 0.968 -0.443
- 257 4 3 245 263 264 0 1.143 1.171 1.190 3.504 0.165 0.341
- 258 4 3 246 251 252 0 1.318 0.868 0.881 3.067 0.969 -0.438
- 261 3 1 255 0 1.211 1.378 2.000 -0.375
- 262 3 1 255 0 1.214 1.368 2.000 -0.399
- 263 3 2 250 257 0 0.267 1.171 1.446 2.000 -0.388
- 264 3 2 251 257 0 0.216 1.190 1.413 2.000 -0.411
- 265 1 3 266 270 277 0 1.324 1.332 1.109 3.767 0.000 -0.073
- 266 1 3 265 267 278 0 1.324 1.345 1.300 3.969 0.000 0.193
- 267 1 3 266 268 279 0 1.345 1.336 1.083 3.767 0.000 -0.060
- 268 1 3 267 269 280 0 1.336 1.306 1.324 3.967 0.000 0.196
- 269 1 3 268 270 281 0 1.306 1.317 1.143 3.769 0.000 -0.063
- 270 1 3 265 269 282 0 1.332 1.317 1.318 3.967 0.000 0.191
- 271 2 1 278 0 0.873 1.075 0.000 0.366
- 272 2 1 278 0 0.897 1.056 0.000 0.386
- 273 2 1 280 0 0.905 1.051 0.000 0.379
- 274 2 2 287 280 0 0.267 0.838 1.105 0.000 0.385
- 275 2 2 282 288 0 0.868 0.216 1.083 0.000 0.377
- 276 2 1 282 0 0.881 1.069 0.000 0.386
- 277 4 3 265 283 284 0 1.109 1.197 1.198 3.504 0.165 0.344
- 278 4 3 266 271 272 0 1.300 0.873 0.897 3.070 0.966 -0.469
- 279 4 3 267 285 286 0 1.083 1.211 1.214 3.508 0.160 0.371
- 280 4 3 273 274 268 0 0.905 0.838 1.324 3.068 0.968 -0.443
- 281 4 3 269 287 288 0 1.143 1.171 1.190 3.504 0.165 0.341
- 282 4 3 270 275 276 0 1.318 0.868 0.881 3.067 0.969 -0.438
- 283 3 1 277 0 1.197 1.393 2.000 -0.381
- 284 3 1 277 0 1.198 1.407 2.000 -0.413
- 285 3 1 279 0 1.211 1.378 2.000 -0.375
- 286 3 1 279 0 1.214 1.368 2.000 -0.399
- 287 3 2 281 274 0 1.171 0.267 1.446 2.000 -0.388
- 288 3 2 275 281 0 0.216 1.190 1.413 2.000 -0.411
- 289 1 3 290 294 301 0 1.324 1.332 1.109 3.767 0.000 -0.073
- 290 1 3 289 291 302 0 1.324 1.345 1.300 3.969 0.000 0.193
- 291 1 3 290 303 292 0 1.345 1.083 1.337 3.767 0.000 -0.060
- 292 1 3 291 293 304 0 1.337 1.306 1.324 3.967 0.000 0.196
- 293 1 3 292 294 305 0 1.306 1.317 1.143 3.769 0.000 -0.063
- 294 1 3 289 293 306 0 1.332 1.317 1.318 3.967 0.000 0.191
- 295 2 1 302 0 0.873 1.075 0.000 0.366
- 296 2 1 302 0 0.897 1.056 0.000 0.386
- 297 2 1 304 0 0.905 1.051 0.000 0.379
- 298 2 2 311 304 0 0.267 0.838 1.105 0.000 0.385
- 299 2 2 312 306 0 0.216 0.868 1.083 0.000 0.377
- 300 2 1 306 0 0.881 1.069 0.000 0.386
- 301 4 3 289 308 307 0 1.109 1.198 1.197 3.504 0.165 0.344
- 302 4 3 290 295 296 0 1.300 0.873 0.897 3.070 0.966 -0.469
- 303 4 3 291 309 310 0 1.083 1.211 1.214 3.508 0.160 0.371
- 304 4 3 292 297 298 0 1.324 0.905 0.838 3.068 0.968 -0.443
- 305 4 3 293 311 312 0 1.143 1.171 1.190 3.504 0.165 0.341
- 306 4 3 294 299 300 0 1.318 0.868 0.881 3.067 0.969 -0.438
- 307 3 1 301 0 1.197 1.393 2.000 -0.381
- 308 3 1 301 0 1.198 1.407 2.000 -0.413
- 309 3 1 303 0 1.211 1.378 2.000 -0.375
- 310 3 1 303 0 1.214 1.368 2.000 -0.399
- 311 3 2 298 305 0 0.267 1.171 1.446 2.000 -0.388
- 312 3 2 299 305 0 0.216 1.190 1.413 2.000 -0.411
- 313 1 3 314 318 325 0 1.324 1.332 1.109 3.767 0.000 -0.073
- 314 1 3 313 315 326 0 1.324 1.345 1.300 3.969 0.000 0.193
- 315 1 3 314 316 327 0 1.345 1.336 1.083 3.767 0.000 -0.060
- 316 1 3 315 317 328 0 1.336 1.306 1.324 3.967 0.000 0.196
- 317 1 3 316 318 329 0 1.306 1.317 1.143 3.769 0.000 -0.063
- 318 1 3 313 317 330 0 1.332 1.317 1.318 3.967 0.000 0.191
- 319 2 1 326 0 0.873 1.075 0.000 0.366
- 320 2 1 326 0 0.897 1.056 0.000 0.386
- 321 2 1 328 0 0.905 1.051 0.000 0.379
- 322 2 2 335 328 0 0.267 0.838 1.105 0.000 0.385
- 323 2 2 330 336 0 0.868 0.216 1.083 0.000 0.377
- 324 2 1 330 0 0.881 1.069 0.000 0.386
- 325 4 3 313 331 332 0 1.109 1.197 1.198 3.504 0.165 0.344
- 326 4 3 314 320 319 0 1.300 0.897 0.873 3.070 0.966 -0.469
- 327 4 3 315 333 334 0 1.083 1.211 1.214 3.508 0.160 0.371
- 328 4 3 321 322 316 0 0.905 0.838 1.324 3.068 0.968 -0.443
- 329 4 3 317 335 336 0 1.143 1.171 1.190 3.504 0.165 0.341
- 330 4 3 318 323 324 0 1.318 0.868 0.881 3.067 0.969 -0.438
- 331 3 1 325 0 1.197 1.393 2.000 -0.381
- 332 3 1 325 0 1.198 1.407 2.000 -0.413
- 333 3 1 327 0 1.211 1.378 2.000 -0.375
- 334 3 1 327 0 1.214 1.368 2.000 -0.399
- 335 3 2 329 322 0 1.171 0.267 1.446 2.000 -0.388
- 336 3 2 323 329 0 0.216 1.190 1.413 2.000 -0.411
- 337 1 3 338 342 349 0 1.324 1.332 1.109 3.767 0.000 -0.073
- 338 1 3 337 339 350 0 1.324 1.345 1.300 3.969 0.000 0.193
- 339 1 3 338 351 340 0 1.345 1.083 1.337 3.767 0.000 -0.060
- 340 1 3 339 341 352 0 1.337 1.306 1.324 3.967 0.000 0.196
- 341 1 3 340 342 353 0 1.306 1.317 1.143 3.769 0.000 -0.063
- 342 1 3 337 341 354 0 1.332 1.317 1.318 3.967 0.000 0.191
- 343 2 1 350 0 0.873 1.075 0.000 0.366
- 344 2 1 350 0 0.897 1.056 0.000 0.386
- 345 2 1 352 0 0.905 1.051 0.000 0.379
- 346 2 2 352 359 0 0.838 0.267 1.105 0.000 0.385
- 347 2 2 360 354 0 0.216 0.868 1.083 0.000 0.377
- 348 2 1 354 0 0.881 1.069 0.000 0.386
- 350 4 3 338 343 344 0 1.300 0.873 0.897 3.070 0.966 -0.469
- 351 4 3 339 357 358 0 1.083 1.211 1.214 3.508 0.160 0.371
- 352 4 3 340 345 346 0 1.324 0.905 0.838 3.068 0.968 -0.443
- 353 4 3 341 360 359 0 1.143 1.190 1.171 3.504 0.165 0.341
- 354 4 3 342 347 348 0 1.318 0.868 0.881 3.067 0.969 -0.438
- 357 3 1 351 0 1.211 1.378 2.000 -0.375
- 358 3 1 351 0 1.214 1.368 2.000 -0.399
- 359 3 2 346 353 0 0.267 1.171 1.446 2.000 -0.388
- 360 3 2 347 353 0 0.216 1.190 1.413 2.000 -0.411
- 361 1 3 362 366 373 0 1.324 1.332 1.109 3.767 0.000 -0.073
- 362 1 3 361 363 374 0 1.324 1.345 1.300 3.969 0.000 0.193
- 363 1 3 362 364 375 0 1.345 1.336 1.083 3.767 0.000 -0.060
- 364 1 3 363 365 376 0 1.336 1.306 1.324 3.967 0.000 0.196
- 365 1 3 364 366 377 0 1.306 1.317 1.143 3.769 0.000 -0.063
- 366 1 3 361 365 378 0 1.332 1.317 1.318 3.967 0.000 0.191
- 367 2 1 374 0 0.873 1.075 0.000 0.366
- 368 2 1 374 0 0.897 1.056 0.000 0.386
- 369 2 1 376 0 0.905 1.051 0.000 0.379
- 370 2 2 383 376 0 0.267 0.838 1.105 0.000 0.385
- 371 2 2 378 384 0 0.868 0.216 1.083 0.000 0.377
- 372 2 1 378 0 0.881 1.069 0.000 0.386
- 373 4 3 361 379 380 0 1.109 1.197 1.198 3.504 0.165 0.344
- 374 4 3 362 368 367 0 1.300 0.897 0.873 3.070 0.966 -0.469
- 375 4 3 363 381 382 0 1.083 1.211 1.214 3.508 0.160 0.371
- 376 4 3 369 370 364 0 0.905 0.838 1.324 3.068 0.968 -0.443
- 377 4 3 365 383 384 0 1.143 1.171 1.190 3.504 0.165 0.341
- 378 4 3 366 371 372 0 1.318 0.868 0.881 3.067 0.969 -0.438
- 379 3 1 373 0 1.197 1.393 2.000 -0.381
- 380 3 1 373 0 1.198 1.407 2.000 -0.413
- 381 3 1 375 0 1.211 1.378 2.000 -0.375
- 382 3 1 375 0 1.214 1.368 2.000 -0.399
- 383 3 2 377 370 0 1.171 0.267 1.446 2.000 -0.388
- 384 3 2 371 377 0 0.216 1.190 1.413 2.000 -0.411
- 61 4 3 49 68 67 0 1.109 1.198 1.197 3.504 0.165 0.344
- 67 3 1 61 0 1.197 1.393 2.000 -0.381
- 68 3 1 61 0 1.198 1.407 2.000 -0.413
- 157 4 3 164 145 163 0 1.198 1.109 1.197 3.504 0.165 0.344
- 163 3 1 157 0 1.197 1.393 2.000 -0.381
- 164 3 1 157 0 1.198 1.407 2.000 -0.413
- 253 4 3 260 241 259 0 1.198 1.109 1.197 3.504 0.165 0.344
- 259 3 1 253 0 1.197 1.393 2.000 -0.381
- 260 3 1 253 0 1.198 1.407 2.000 -0.413
- 349 4 3 337 356 355 0 1.109 1.198 1.197 3.504 0.165 0.344
- 355 3 1 349 0 1.197 1.393 2.000 -0.381
- 356 3 1 349 0 1.198 1.407 2.000 -0.413
-#
-# Timestep 25
-#
-# Number of particles 384
-#
-# Max.number of bonds per atom 3 with coarse bond order cutoff 0.300
-# Particle connection table and bond orders
-# id type nb id_1...id_nb mol bo_1...bo_nb abo nlp q
- 1 1 3 2 6 13 0 1.321 1.328 1.129 3.783 0.000 -0.075
- 2 1 3 1 3 14 0 1.321 1.341 1.325 3.987 0.000 0.190
- 3 1 3 2 4 15 0 1.341 1.333 1.103 3.783 0.000 -0.063
- 4 1 3 3 5 16 0 1.333 1.303 1.350 3.985 0.000 0.194
- 5 1 3 4 6 17 0 1.303 1.313 1.161 3.784 0.000 -0.066
- 6 1 3 1 5 18 0 1.328 1.313 1.344 3.985 0.000 0.188
- 7 2 2 14 20 0 0.855 0.269 1.123 0.000 0.366
- 8 2 2 14 21 0 0.878 0.236 1.114 0.000 0.387
- 9 2 2 16 22 0 0.885 0.232 1.116 0.000 0.380
- 10 2 2 16 23 0 0.827 0.291 1.118 0.000 0.385
- 11 2 2 18 24 0 0.852 0.273 1.124 0.000 0.377
- 12 2 2 18 19 0 0.862 0.262 1.125 0.000 0.387
- 13 4 3 1 20 19 0 1.129 1.232 1.231 3.591 0.083 0.362
- 14 4 3 2 7 8 0 1.325 0.855 0.878 3.058 0.977 -0.457
- 15 4 3 3 21 22 0 1.103 1.245 1.247 3.595 0.081 0.390
- 16 4 3 4 9 10 0 1.350 0.885 0.827 3.061 0.974 -0.433
- 17 4 3 5 23 24 0 1.161 1.206 1.224 3.591 0.084 0.359
- 18 4 3 6 11 12 0 1.344 0.852 0.862 3.058 0.977 -0.427
- 19 3 2 12 13 0 0.262 1.231 1.504 2.000 -0.395
- 20 3 2 7 13 0 0.269 1.232 1.511 2.000 -0.426
- 21 3 2 8 15 0 0.236 1.245 1.491 2.000 -0.389
- 22 3 2 9 15 0 0.232 1.247 1.489 2.000 -0.415
- 23 3 2 10 17 0 0.291 1.206 1.508 2.000 -0.397
- 24 3 2 11 17 0 0.273 1.224 1.507 2.000 -0.422
- 25 1 3 30 26 37 0 1.328 1.321 1.129 3.783 0.000 -0.075
- 26 1 3 25 27 38 0 1.321 1.341 1.325 3.987 0.000 0.190
- 27 1 3 26 28 39 0 1.341 1.333 1.103 3.783 0.000 -0.063
- 28 1 3 27 29 40 0 1.333 1.303 1.350 3.985 0.000 0.194
- 29 1 3 28 30 41 0 1.303 1.313 1.161 3.784 0.000 -0.066
- 30 1 3 25 29 42 0 1.328 1.313 1.344 3.985 0.000 0.188
- 31 2 2 44 38 0 0.269 0.855 1.123 0.000 0.366
- 32 2 2 38 45 0 0.878 0.236 1.114 0.000 0.387
- 33 2 2 40 46 0 0.885 0.232 1.116 0.000 0.380
- 34 2 2 47 40 0 0.291 0.827 1.118 0.000 0.385
- 35 2 2 42 48 0 0.852 0.273 1.124 0.000 0.377
- 36 2 2 42 43 0 0.862 0.262 1.125 0.000 0.387
- 37 4 3 25 43 44 0 1.129 1.231 1.232 3.591 0.083 0.362
- 38 4 3 26 32 31 0 1.325 0.878 0.855 3.058 0.977 -0.457
- 39 4 3 27 45 46 0 1.103 1.245 1.247 3.595 0.081 0.390
- 40 4 3 28 33 34 0 1.350 0.885 0.827 3.061 0.974 -0.433
- 41 4 3 29 47 48 0 1.161 1.206 1.224 3.591 0.084 0.359
- 42 4 3 30 35 36 0 1.344 0.852 0.862 3.058 0.977 -0.427
- 43 3 2 36 37 0 0.262 1.231 1.504 2.000 -0.395
- 44 3 2 31 37 0 0.269 1.232 1.511 2.000 -0.426
- 45 3 2 32 39 0 0.236 1.245 1.491 2.000 -0.389
- 46 3 2 33 39 0 0.232 1.247 1.489 2.000 -0.415
- 47 3 2 34 41 0 0.291 1.206 1.508 2.000 -0.397
- 48 3 2 35 41 0 0.273 1.224 1.507 2.000 -0.422
- 49 1 3 50 54 61 0 1.321 1.328 1.129 3.783 0.000 -0.075
- 50 1 3 49 51 62 0 1.321 1.341 1.325 3.987 0.000 0.190
- 51 1 3 50 52 63 0 1.341 1.333 1.103 3.783 0.000 -0.063
- 52 1 3 51 53 64 0 1.333 1.303 1.350 3.985 0.000 0.194
- 53 1 3 52 54 65 0 1.303 1.313 1.161 3.784 0.000 -0.066
- 54 1 3 49 53 66 0 1.328 1.313 1.344 3.985 0.000 0.188
- 55 2 2 62 68 0 0.855 0.269 1.123 0.000 0.366
- 56 2 2 62 69 0 0.878 0.236 1.114 0.000 0.387
- 57 2 2 64 70 0 0.885 0.232 1.116 0.000 0.380
- 58 2 2 64 71 0 0.827 0.291 1.118 0.000 0.385
- 59 2 2 66 72 0 0.852 0.273 1.124 0.000 0.377
- 60 2 2 66 67 0 0.862 0.262 1.125 0.000 0.387
- 62 4 3 50 55 56 0 1.325 0.855 0.878 3.058 0.977 -0.457
- 63 4 3 51 69 70 0 1.103 1.245 1.247 3.595 0.081 0.390
- 64 4 3 52 57 58 0 1.350 0.885 0.827 3.061 0.974 -0.433
- 65 4 3 53 71 72 0 1.161 1.206 1.224 3.591 0.084 0.359
- 66 4 3 54 59 60 0 1.344 0.852 0.862 3.058 0.977 -0.427
- 69 3 2 56 63 0 0.236 1.245 1.491 2.000 -0.389
- 70 3 2 57 63 0 0.232 1.247 1.489 2.000 -0.415
- 71 3 2 58 65 0 0.291 1.206 1.508 2.000 -0.397
- 72 3 2 59 65 0 0.273 1.224 1.507 2.000 -0.422
- 73 1 3 78 74 85 0 1.328 1.321 1.129 3.783 0.000 -0.075
- 74 1 3 73 75 86 0 1.321 1.341 1.325 3.987 0.000 0.190
- 75 1 3 74 76 87 0 1.341 1.333 1.103 3.783 0.000 -0.063
- 76 1 3 75 77 88 0 1.333 1.303 1.350 3.985 0.000 0.194
- 77 1 3 76 78 89 0 1.303 1.313 1.161 3.784 0.000 -0.066
- 78 1 3 73 77 90 0 1.328 1.313 1.344 3.985 0.000 0.188
- 79 2 2 92 86 0 0.269 0.855 1.123 0.000 0.366
- 80 2 2 86 93 0 0.878 0.236 1.114 0.000 0.387
- 81 2 2 88 94 0 0.885 0.232 1.116 0.000 0.380
- 82 2 2 95 88 0 0.291 0.827 1.118 0.000 0.385
- 83 2 2 90 96 0 0.852 0.273 1.124 0.000 0.377
- 84 2 2 90 91 0 0.862 0.262 1.125 0.000 0.387
- 85 4 3 73 91 92 0 1.129 1.231 1.232 3.591 0.083 0.362
- 86 4 3 74 80 79 0 1.325 0.878 0.855 3.058 0.977 -0.457
- 87 4 3 75 93 94 0 1.103 1.245 1.247 3.595 0.081 0.390
- 88 4 3 76 81 82 0 1.350 0.885 0.827 3.061 0.974 -0.433
- 89 4 3 77 95 96 0 1.161 1.206 1.224 3.591 0.084 0.359
- 90 4 3 78 83 84 0 1.344 0.852 0.862 3.058 0.977 -0.427
- 91 3 2 84 85 0 0.262 1.231 1.504 2.000 -0.395
- 92 3 2 79 85 0 0.269 1.232 1.511 2.000 -0.426
- 93 3 2 80 87 0 0.236 1.245 1.491 2.000 -0.389
- 94 3 2 81 87 0 0.232 1.247 1.489 2.000 -0.415
- 95 3 2 82 89 0 0.291 1.206 1.508 2.000 -0.397
- 96 3 2 83 89 0 0.273 1.224 1.507 2.000 -0.422
- 97 1 3 109 98 102 0 1.129 1.321 1.328 3.783 0.000 -0.075
- 98 1 3 99 97 110 0 1.341 1.321 1.325 3.987 0.000 0.190
- 99 1 3 98 100 111 0 1.341 1.333 1.103 3.783 0.000 -0.063
- 100 1 3 99 101 112 0 1.333 1.303 1.350 3.985 0.000 0.194
- 101 1 3 100 113 102 0 1.303 1.161 1.313 3.784 0.000 -0.066
- 102 1 3 101 114 97 0 1.313 1.344 1.328 3.985 0.000 0.188
- 103 2 2 110 116 0 0.855 0.269 1.123 0.000 0.366
- 104 2 2 110 117 0 0.878 0.236 1.114 0.000 0.387
- 105 2 2 112 118 0 0.885 0.232 1.116 0.000 0.380
- 106 2 2 119 112 0 0.291 0.827 1.118 0.000 0.385
- 107 2 2 114 120 0 0.852 0.273 1.124 0.000 0.377
- 108 2 2 114 115 0 0.862 0.262 1.125 0.000 0.387
- 109 4 3 97 116 115 0 1.129 1.232 1.231 3.591 0.083 0.362
- 110 4 3 103 104 98 0 0.855 0.878 1.325 3.058 0.977 -0.457
- 111 4 3 99 117 118 0 1.103 1.245 1.247 3.595 0.081 0.390
- 112 4 3 100 105 106 0 1.350 0.885 0.827 3.061 0.974 -0.433
- 113 4 3 101 119 120 0 1.161 1.206 1.224 3.591 0.084 0.359
- 114 4 3 102 107 108 0 1.344 0.852 0.862 3.058 0.977 -0.427
- 115 3 2 109 108 0 1.231 0.262 1.504 2.000 -0.395
- 116 3 2 103 109 0 0.269 1.232 1.511 2.000 -0.426
- 117 3 2 111 104 0 1.245 0.236 1.491 2.000 -0.389
- 118 3 2 105 111 0 0.232 1.247 1.489 2.000 -0.415
- 119 3 2 106 113 0 0.291 1.206 1.508 2.000 -0.397
- 120 3 2 107 113 0 0.273 1.224 1.507 2.000 -0.422
- 121 1 3 126 122 133 0 1.328 1.321 1.129 3.783 0.000 -0.075
- 122 1 3 121 123 134 0 1.321 1.341 1.325 3.987 0.000 0.190
- 123 1 3 122 124 135 0 1.341 1.333 1.103 3.783 0.000 -0.063
- 124 1 3 123 125 136 0 1.333 1.303 1.350 3.985 0.000 0.194
- 125 1 3 124 126 137 0 1.303 1.313 1.161 3.784 0.000 -0.066
- 126 1 3 121 125 138 0 1.328 1.313 1.344 3.985 0.000 0.188
- 127 2 2 134 140 0 0.855 0.269 1.123 0.000 0.366
- 128 2 2 134 141 0 0.878 0.236 1.114 0.000 0.387
- 129 2 2 136 142 0 0.885 0.232 1.116 0.000 0.380
- 130 2 2 143 136 0 0.291 0.827 1.118 0.000 0.385
- 131 2 2 138 144 0 0.852 0.273 1.124 0.000 0.377
- 132 2 2 138 139 0 0.862 0.262 1.125 0.000 0.387
- 133 4 3 121 139 140 0 1.129 1.231 1.232 3.591 0.083 0.362
- 134 4 3 122 127 128 0 1.325 0.855 0.878 3.058 0.977 -0.457
- 135 4 3 123 141 142 0 1.103 1.245 1.247 3.595 0.081 0.390
- 136 4 3 124 129 130 0 1.350 0.885 0.827 3.061 0.974 -0.433
- 137 4 3 125 143 144 0 1.161 1.206 1.224 3.591 0.084 0.359
- 138 4 3 126 131 132 0 1.344 0.852 0.862 3.058 0.977 -0.427
- 139 3 2 132 133 0 0.262 1.231 1.504 2.000 -0.395
- 140 3 2 127 133 0 0.269 1.232 1.511 2.000 -0.426
- 141 3 2 128 135 0 0.236 1.245 1.491 2.000 -0.389
- 142 3 2 129 135 0 0.232 1.247 1.489 2.000 -0.415
- 143 3 2 130 137 0 0.291 1.206 1.508 2.000 -0.397
- 144 3 2 131 137 0 0.273 1.224 1.507 2.000 -0.422
- 145 1 3 157 146 150 0 1.129 1.321 1.328 3.783 0.000 -0.075
- 146 1 3 147 145 158 0 1.341 1.321 1.325 3.987 0.000 0.190
- 147 1 3 146 148 159 0 1.341 1.333 1.103 3.783 0.000 -0.063
- 148 1 3 147 149 160 0 1.333 1.303 1.350 3.985 0.000 0.194
- 149 1 3 148 161 150 0 1.303 1.161 1.313 3.784 0.000 -0.066
- 150 1 3 149 162 145 0 1.313 1.344 1.328 3.985 0.000 0.188
- 151 2 2 158 164 0 0.855 0.269 1.123 0.000 0.366
- 152 2 2 158 165 0 0.878 0.236 1.114 0.000 0.387
- 153 2 2 160 166 0 0.885 0.232 1.116 0.000 0.380
- 154 2 2 167 160 0 0.291 0.827 1.118 0.000 0.385
- 155 2 2 168 162 0 0.273 0.852 1.124 0.000 0.377
- 156 2 2 162 163 0 0.862 0.262 1.125 0.000 0.387
- 158 4 3 151 152 146 0 0.855 0.878 1.325 3.058 0.977 -0.457
- 159 4 3 147 165 166 0 1.103 1.245 1.247 3.595 0.081 0.390
- 160 4 3 148 153 154 0 1.350 0.885 0.827 3.061 0.974 -0.433
- 161 4 3 149 167 168 0 1.161 1.206 1.224 3.591 0.084 0.359
- 162 4 3 150 155 156 0 1.344 0.852 0.862 3.058 0.977 -0.427
- 165 3 2 159 152 0 1.245 0.236 1.491 2.000 -0.389
- 166 3 2 153 159 0 0.232 1.247 1.489 2.000 -0.415
- 167 3 2 154 161 0 0.291 1.206 1.508 2.000 -0.397
- 168 3 2 155 161 0 0.273 1.224 1.507 2.000 -0.422
- 169 1 3 174 170 181 0 1.328 1.321 1.129 3.783 0.000 -0.075
- 170 1 3 169 171 182 0 1.321 1.341 1.325 3.987 0.000 0.190
- 171 1 3 170 172 183 0 1.341 1.333 1.103 3.783 0.000 -0.063
- 172 1 3 171 173 184 0 1.333 1.303 1.350 3.985 0.000 0.194
- 173 1 3 172 174 185 0 1.303 1.313 1.161 3.784 0.000 -0.066
- 174 1 3 169 173 186 0 1.328 1.313 1.344 3.985 0.000 0.188
- 175 2 2 182 188 0 0.855 0.269 1.123 0.000 0.366
- 176 2 2 182 189 0 0.878 0.236 1.114 0.000 0.387
- 177 2 2 184 190 0 0.885 0.232 1.116 0.000 0.380
- 178 2 2 191 184 0 0.291 0.827 1.118 0.000 0.385
- 179 2 2 186 192 0 0.852 0.273 1.124 0.000 0.377
- 180 2 2 186 187 0 0.862 0.262 1.125 0.000 0.387
- 181 4 3 169 187 188 0 1.129 1.231 1.232 3.591 0.083 0.362
- 182 4 3 170 175 176 0 1.325 0.855 0.878 3.058 0.977 -0.457
- 183 4 3 171 189 190 0 1.103 1.245 1.247 3.595 0.081 0.390
- 184 4 3 172 177 178 0 1.350 0.885 0.827 3.061 0.974 -0.433
- 185 4 3 173 191 192 0 1.161 1.206 1.224 3.591 0.084 0.359
- 186 4 3 174 179 180 0 1.344 0.852 0.862 3.058 0.977 -0.427
- 187 3 2 180 181 0 0.262 1.231 1.504 2.000 -0.395
- 188 3 2 175 181 0 0.269 1.232 1.511 2.000 -0.426
- 189 3 2 176 183 0 0.236 1.245 1.491 2.000 -0.389
- 190 3 2 177 183 0 0.232 1.247 1.489 2.000 -0.415
- 191 3 2 178 185 0 0.291 1.206 1.508 2.000 -0.397
- 192 3 2 179 185 0 0.273 1.224 1.507 2.000 -0.422
- 193 1 3 205 194 198 0 1.129 1.321 1.328 3.783 0.000 -0.075
- 194 1 3 195 193 206 0 1.341 1.321 1.325 3.987 0.000 0.190
- 195 1 3 194 196 207 0 1.341 1.333 1.103 3.783 0.000 -0.063
- 196 1 3 195 197 208 0 1.333 1.303 1.350 3.985 0.000 0.194
- 197 1 3 196 198 209 0 1.303 1.313 1.161 3.784 0.000 -0.066
- 198 1 3 197 193 210 0 1.313 1.328 1.344 3.985 0.000 0.188
- 199 2 2 206 212 0 0.855 0.269 1.123 0.000 0.366
- 200 2 2 206 213 0 0.878 0.236 1.114 0.000 0.387
- 201 2 2 214 208 0 0.232 0.885 1.116 0.000 0.380
- 202 2 2 208 215 0 0.827 0.291 1.118 0.000 0.385
- 203 2 2 210 216 0 0.852 0.273 1.124 0.000 0.377
- 204 2 2 210 211 0 0.862 0.262 1.125 0.000 0.387
- 205 4 3 193 212 211 0 1.129 1.232 1.231 3.591 0.083 0.362
- 206 4 3 199 200 194 0 0.855 0.878 1.325 3.058 0.977 -0.457
- 207 4 3 195 213 214 0 1.103 1.245 1.247 3.595 0.081 0.390
- 208 4 3 196 201 202 0 1.350 0.885 0.827 3.061 0.974 -0.433
- 209 4 3 197 215 216 0 1.161 1.206 1.224 3.591 0.084 0.359
- 210 4 3 198 203 204 0 1.344 0.852 0.862 3.058 0.977 -0.427
- 211 3 2 205 204 0 1.231 0.262 1.504 2.000 -0.395
- 212 3 2 199 205 0 0.269 1.232 1.511 2.000 -0.426
- 213 3 2 207 200 0 1.245 0.236 1.491 2.000 -0.389
- 214 3 2 201 207 0 0.232 1.247 1.489 2.000 -0.415
- 215 3 2 202 209 0 0.291 1.206 1.508 2.000 -0.397
- 216 3 2 203 209 0 0.273 1.224 1.507 2.000 -0.422
- 217 1 3 218 222 229 0 1.321 1.328 1.129 3.783 0.000 -0.075
- 218 1 3 217 219 230 0 1.321 1.341 1.325 3.987 0.000 0.190
- 219 1 3 218 220 231 0 1.341 1.333 1.103 3.783 0.000 -0.063
- 220 1 3 219 221 232 0 1.333 1.303 1.350 3.985 0.000 0.194
- 221 1 3 220 222 233 0 1.303 1.313 1.161 3.784 0.000 -0.066
- 222 1 3 217 221 234 0 1.328 1.313 1.344 3.985 0.000 0.188
- 223 2 2 230 236 0 0.855 0.269 1.123 0.000 0.366
- 224 2 2 230 237 0 0.878 0.236 1.114 0.000 0.387
- 225 2 2 232 238 0 0.885 0.232 1.116 0.000 0.380
- 226 2 2 239 232 0 0.291 0.827 1.118 0.000 0.385
- 227 2 2 234 240 0 0.852 0.273 1.124 0.000 0.377
- 228 2 2 234 235 0 0.862 0.262 1.125 0.000 0.387
- 229 4 3 217 235 236 0 1.129 1.231 1.232 3.591 0.083 0.362
- 230 4 3 218 223 224 0 1.325 0.855 0.878 3.058 0.977 -0.457
- 231 4 3 219 237 238 0 1.103 1.245 1.247 3.595 0.081 0.390
- 232 4 3 225 226 220 0 0.885 0.827 1.350 3.061 0.974 -0.433
- 233 4 3 221 239 240 0 1.161 1.206 1.224 3.591 0.084 0.359
- 234 4 3 222 227 228 0 1.344 0.852 0.862 3.058 0.977 -0.427
- 235 3 2 228 229 0 0.262 1.231 1.504 2.000 -0.395
- 236 3 2 223 229 0 0.269 1.232 1.511 2.000 -0.426
- 237 3 2 231 224 0 1.245 0.236 1.491 2.000 -0.389
- 238 3 2 225 231 0 0.232 1.247 1.489 2.000 -0.415
- 239 3 2 233 226 0 1.206 0.291 1.508 2.000 -0.397
- 240 3 2 227 233 0 0.273 1.224 1.507 2.000 -0.422
- 241 1 3 253 242 246 0 1.129 1.321 1.328 3.783 0.000 -0.075
- 242 1 3 243 241 254 0 1.341 1.321 1.325 3.987 0.000 0.190
- 243 1 3 242 244 255 0 1.341 1.333 1.103 3.783 0.000 -0.063
- 244 1 3 243 245 256 0 1.333 1.303 1.350 3.985 0.000 0.194
- 245 1 3 244 246 257 0 1.303 1.313 1.161 3.784 0.000 -0.066
- 246 1 3 245 241 258 0 1.313 1.328 1.344 3.985 0.000 0.188
- 247 2 2 254 260 0 0.855 0.269 1.123 0.000 0.366
- 248 2 2 254 261 0 0.878 0.236 1.114 0.000 0.387
- 249 2 2 262 256 0 0.232 0.885 1.116 0.000 0.380
- 250 2 2 256 263 0 0.827 0.291 1.118 0.000 0.385
- 251 2 2 258 264 0 0.852 0.273 1.124 0.000 0.377
- 252 2 2 258 259 0 0.862 0.262 1.125 0.000 0.387
- 254 4 3 247 248 242 0 0.855 0.878 1.325 3.058 0.977 -0.457
- 255 4 3 243 261 262 0 1.103 1.245 1.247 3.595 0.081 0.390
- 256 4 3 244 249 250 0 1.350 0.885 0.827 3.061 0.974 -0.433
- 257 4 3 245 263 264 0 1.161 1.206 1.224 3.591 0.084 0.359
- 258 4 3 246 251 252 0 1.344 0.852 0.862 3.058 0.977 -0.427
- 261 3 2 255 248 0 1.245 0.236 1.491 2.000 -0.389
- 262 3 2 249 255 0 0.232 1.247 1.489 2.000 -0.415
- 263 3 2 250 257 0 0.291 1.206 1.508 2.000 -0.397
- 264 3 2 251 257 0 0.273 1.224 1.507 2.000 -0.422
- 265 1 3 266 270 277 0 1.321 1.328 1.129 3.783 0.000 -0.075
- 266 1 3 265 267 278 0 1.321 1.341 1.325 3.987 0.000 0.190
- 267 1 3 266 268 279 0 1.341 1.333 1.103 3.783 0.000 -0.063
- 268 1 3 267 269 280 0 1.333 1.303 1.350 3.985 0.000 0.194
- 269 1 3 268 270 281 0 1.303 1.313 1.161 3.784 0.000 -0.066
- 270 1 3 265 269 282 0 1.328 1.313 1.344 3.985 0.000 0.188
- 271 2 2 278 284 0 0.855 0.269 1.123 0.000 0.366
- 272 2 2 278 285 0 0.878 0.236 1.114 0.000 0.387
- 273 2 2 280 286 0 0.885 0.232 1.116 0.000 0.380
- 274 2 2 287 280 0 0.291 0.827 1.118 0.000 0.385
- 275 2 2 282 288 0 0.852 0.273 1.124 0.000 0.377
- 276 2 2 282 283 0 0.862 0.262 1.125 0.000 0.387
- 277 4 3 265 283 284 0 1.129 1.231 1.232 3.591 0.083 0.362
- 278 4 3 266 271 272 0 1.325 0.855 0.878 3.058 0.977 -0.457
- 279 4 3 267 285 286 0 1.103 1.245 1.247 3.595 0.081 0.390
- 280 4 3 273 274 268 0 0.885 0.827 1.350 3.061 0.974 -0.433
- 281 4 3 269 287 288 0 1.161 1.206 1.224 3.591 0.084 0.359
- 282 4 3 270 275 276 0 1.344 0.852 0.862 3.058 0.977 -0.427
- 283 3 2 276 277 0 0.262 1.231 1.504 2.000 -0.395
- 284 3 2 271 277 0 0.269 1.232 1.511 2.000 -0.426
- 285 3 2 279 272 0 1.245 0.236 1.491 2.000 -0.389
- 286 3 2 273 279 0 0.232 1.247 1.489 2.000 -0.415
- 287 3 2 281 274 0 1.206 0.291 1.508 2.000 -0.397
- 288 3 2 275 281 0 0.273 1.224 1.507 2.000 -0.422
- 289 1 3 290 294 301 0 1.321 1.328 1.129 3.783 0.000 -0.075
- 290 1 3 289 291 302 0 1.321 1.341 1.325 3.987 0.000 0.190
- 291 1 3 290 303 292 0 1.341 1.103 1.333 3.783 0.000 -0.063
- 292 1 3 291 293 304 0 1.333 1.303 1.350 3.985 0.000 0.194
- 293 1 3 292 294 305 0 1.303 1.313 1.161 3.784 0.000 -0.066
- 294 1 3 289 293 306 0 1.328 1.313 1.344 3.985 0.000 0.188
- 295 2 2 302 308 0 0.855 0.269 1.123 0.000 0.366
- 296 2 2 302 309 0 0.878 0.236 1.114 0.000 0.387
- 297 2 2 310 304 0 0.232 0.885 1.116 0.000 0.380
- 298 2 2 311 304 0 0.291 0.827 1.118 0.000 0.385
- 299 2 2 312 306 0 0.273 0.852 1.124 0.000 0.377
- 300 2 2 306 307 0 0.862 0.262 1.125 0.000 0.387
- 301 4 3 289 308 307 0 1.129 1.232 1.231 3.591 0.083 0.362
- 302 4 3 290 295 296 0 1.325 0.855 0.878 3.058 0.977 -0.457
- 303 4 3 291 309 310 0 1.103 1.245 1.247 3.595 0.081 0.390
- 304 4 3 292 297 298 0 1.350 0.885 0.827 3.061 0.974 -0.433
- 305 4 3 293 311 312 0 1.161 1.206 1.224 3.591 0.084 0.359
- 306 4 3 294 299 300 0 1.344 0.852 0.862 3.058 0.977 -0.427
- 307 3 2 300 301 0 0.262 1.231 1.504 2.000 -0.395
- 308 3 2 295 301 0 0.269 1.232 1.511 2.000 -0.426
- 309 3 2 296 303 0 0.236 1.245 1.491 2.000 -0.389
- 310 3 2 297 303 0 0.232 1.247 1.489 2.000 -0.415
- 311 3 2 298 305 0 0.291 1.206 1.508 2.000 -0.397
- 312 3 2 299 305 0 0.273 1.224 1.507 2.000 -0.422
- 313 1 3 314 318 325 0 1.321 1.328 1.129 3.783 0.000 -0.075
- 314 1 3 313 315 326 0 1.321 1.341 1.325 3.987 0.000 0.190
- 315 1 3 314 316 327 0 1.341 1.333 1.103 3.783 0.000 -0.063
- 316 1 3 315 317 328 0 1.333 1.303 1.350 3.985 0.000 0.194
- 317 1 3 316 318 329 0 1.303 1.313 1.161 3.784 0.000 -0.066
- 318 1 3 313 317 330 0 1.328 1.313 1.344 3.985 0.000 0.188
- 319 2 2 332 326 0 0.269 0.855 1.123 0.000 0.366
- 320 2 2 326 333 0 0.878 0.236 1.114 0.000 0.387
- 321 2 2 328 334 0 0.885 0.232 1.116 0.000 0.380
- 322 2 2 335 328 0 0.291 0.827 1.118 0.000 0.385
- 323 2 2 330 336 0 0.852 0.273 1.124 0.000 0.377
- 324 2 2 330 331 0 0.862 0.262 1.125 0.000 0.387
- 325 4 3 313 331 332 0 1.129 1.231 1.232 3.591 0.083 0.362
- 326 4 3 314 320 319 0 1.325 0.878 0.855 3.058 0.977 -0.457
- 327 4 3 315 333 334 0 1.103 1.245 1.247 3.595 0.081 0.390
- 328 4 3 321 322 316 0 0.885 0.827 1.350 3.061 0.974 -0.433
- 329 4 3 317 335 336 0 1.161 1.206 1.224 3.591 0.084 0.359
- 330 4 3 318 323 324 0 1.344 0.852 0.862 3.058 0.977 -0.427
- 331 3 2 324 325 0 0.262 1.231 1.504 2.000 -0.395
- 332 3 2 319 325 0 0.269 1.232 1.511 2.000 -0.426
- 333 3 2 327 320 0 1.245 0.236 1.491 2.000 -0.389
- 334 3 2 321 327 0 0.232 1.247 1.489 2.000 -0.415
- 335 3 2 329 322 0 1.206 0.291 1.508 2.000 -0.397
- 336 3 2 323 329 0 0.273 1.224 1.507 2.000 -0.422
- 337 1 3 338 342 349 0 1.321 1.328 1.129 3.783 0.000 -0.075
- 338 1 3 337 339 350 0 1.321 1.341 1.325 3.987 0.000 0.190
- 339 1 3 338 351 340 0 1.341 1.103 1.333 3.783 0.000 -0.063
- 340 1 3 339 341 352 0 1.333 1.303 1.350 3.985 0.000 0.194
- 341 1 3 340 342 353 0 1.303 1.313 1.161 3.784 0.000 -0.066
- 342 1 3 337 341 354 0 1.328 1.313 1.344 3.985 0.000 0.188
- 343 2 2 350 356 0 0.855 0.269 1.123 0.000 0.366
- 344 2 2 350 357 0 0.878 0.236 1.114 0.000 0.387
- 345 2 2 358 352 0 0.232 0.885 1.116 0.000 0.380
- 346 2 2 352 359 0 0.827 0.291 1.118 0.000 0.385
- 347 2 2 360 354 0 0.273 0.852 1.124 0.000 0.377
- 348 2 2 354 355 0 0.862 0.262 1.125 0.000 0.387
- 350 4 3 338 343 344 0 1.325 0.855 0.878 3.058 0.977 -0.457
- 351 4 3 339 357 358 0 1.103 1.245 1.247 3.595 0.081 0.390
- 352 4 3 340 345 346 0 1.350 0.885 0.827 3.061 0.974 -0.433
- 353 4 3 341 360 359 0 1.161 1.224 1.206 3.591 0.084 0.359
- 354 4 3 342 347 348 0 1.344 0.852 0.862 3.058 0.977 -0.427
- 357 3 2 344 351 0 0.236 1.245 1.491 2.000 -0.389
- 358 3 2 345 351 0 0.232 1.247 1.489 2.000 -0.415
- 359 3 2 346 353 0 0.291 1.206 1.508 2.000 -0.397
- 360 3 2 347 353 0 0.273 1.224 1.507 2.000 -0.422
- 361 1 3 362 366 373 0 1.321 1.328 1.129 3.783 0.000 -0.075
- 362 1 3 361 363 374 0 1.321 1.341 1.325 3.987 0.000 0.190
- 363 1 3 362 364 375 0 1.341 1.333 1.103 3.783 0.000 -0.063
- 364 1 3 363 365 376 0 1.333 1.303 1.350 3.985 0.000 0.194
- 365 1 3 364 366 377 0 1.303 1.313 1.161 3.784 0.000 -0.066
- 366 1 3 361 365 378 0 1.328 1.313 1.344 3.985 0.000 0.188
- 367 2 2 380 374 0 0.269 0.855 1.123 0.000 0.366
- 368 2 2 374 381 0 0.878 0.236 1.114 0.000 0.387
- 369 2 2 376 382 0 0.885 0.232 1.116 0.000 0.380
- 370 2 2 383 376 0 0.291 0.827 1.118 0.000 0.385
- 371 2 2 378 384 0 0.852 0.273 1.124 0.000 0.377
- 372 2 2 378 379 0 0.862 0.262 1.125 0.000 0.387
- 373 4 3 361 379 380 0 1.129 1.231 1.232 3.591 0.083 0.362
- 374 4 3 362 368 367 0 1.325 0.878 0.855 3.058 0.977 -0.457
- 375 4 3 363 381 382 0 1.103 1.245 1.247 3.595 0.081 0.390
- 376 4 3 369 370 364 0 0.885 0.827 1.350 3.061 0.974 -0.433
- 377 4 3 365 383 384 0 1.161 1.206 1.224 3.591 0.084 0.359
- 378 4 3 366 371 372 0 1.344 0.852 0.862 3.058 0.977 -0.427
- 379 3 2 372 373 0 0.262 1.231 1.504 2.000 -0.395
- 380 3 2 367 373 0 0.269 1.232 1.511 2.000 -0.426
- 381 3 2 375 368 0 1.245 0.236 1.491 2.000 -0.389
- 382 3 2 369 375 0 0.232 1.247 1.489 2.000 -0.415
- 383 3 2 377 370 0 1.206 0.291 1.508 2.000 -0.397
- 384 3 2 371 377 0 0.273 1.224 1.507 2.000 -0.422
- 61 4 3 49 68 67 0 1.129 1.232 1.231 3.591 0.083 0.362
- 67 3 2 60 61 0 0.262 1.231 1.504 2.000 -0.395
- 68 3 2 55 61 0 0.269 1.232 1.511 2.000 -0.426
- 157 4 3 145 164 163 0 1.129 1.232 1.231 3.591 0.083 0.362
- 163 3 2 157 156 0 1.231 0.262 1.504 2.000 -0.395
- 164 3 2 151 157 0 0.269 1.232 1.511 2.000 -0.426
- 253 4 3 241 260 259 0 1.129 1.232 1.231 3.591 0.083 0.362
- 259 3 2 253 252 0 1.231 0.262 1.504 2.000 -0.395
- 260 3 2 247 253 0 0.269 1.232 1.511 2.000 -0.426
- 349 4 3 337 356 355 0 1.129 1.232 1.231 3.591 0.083 0.362
- 355 3 2 348 349 0 0.262 1.231 1.504 2.000 -0.395
- 356 3 2 343 349 0 0.269 1.232 1.511 2.000 -0.426
-#
diff --git a/tools/reax/mol_fra.c b/tools/reax/mol_fra.c
deleted file mode 100644
index cd217db21cb465e7316238ebec2da62e1ed55d64..0000000000000000000000000000000000000000
--- a/tools/reax/mol_fra.c
+++ /dev/null
@@ -1,801 +0,0 @@
-/*** modified on 12/09/2010 by Aidan Thompson ***/
-/*** modified on 10/21/2010 by avv/cfdrc ***/
-/*** this code was given to LAMMPS by Sergey Zybin, CalTech ***/
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <math.h>
-
-#define Cutoff "Cutoff.dic"
-#define Snapshots "bonds.reax"
-#define Output1 "fra.out"
-#define Output2 "mol.out"
-#define Output3 "num.out"
-#define Output4 "dipol.out"
-#define Output5 "vibtemp.out"
-#define Output6 "conc.out"
-
-#define MaxNumBonds 10 //Max Number of bonds per atom
-#define MaxMolTypes 80000 //Max Number of molecule types
-#define Natomtypes 4 //C,H,O,N
-
-#define Carbon 0
-#define Hydrogen 1
-#define Nitrogen 3
-#define Oxygen 2
-
-// Prototypes for functions
-
-void FileOpenError(FILE *fp,char *name);
-void Allocation();
-int AtomIndicator(char *symbol);
-void SkipLine(FILE *fp);
-
-int Natom,Nmolecule;//total numbers of atoms and molecules
-int Nmoltype=0;//number of species
-int *Atomdic;//this array stores atom type accessible by atom id-1.
-int *MolName;//an array that stores number of atoms of each type for each molecule by using counters of Natomtypes*imoleculetypes+atomtype so if H2 is the second molecule entry the array will have 4=0, 5=2, 6=0, 7=0.
-int *MolType;//array with the same info as MolName but accessed by Nmoltype, not molecule id.
-int *Mol;//an array that stores the molecule id for each atom
-int *NMol;//an array that stores the number of molecules of this species for this frame
-double *Netc;//an array that stores charge
-double Mass[Natomtypes];
-double *rx,*ry,*rz,*Charge;
-double *vx,*vy,*vz;
-double COdic[Natomtypes][Natomtypes];
-double latc_x[3],latc_y[3],latc_z[3];//lattice parameters of the box read from config.out
-double Ilatc_x[3],Ilatc_y[3],Ilatc_z[3];//normalized box lengths
-double Origin[3];//origin coordinates of the box
-FILE *trj,*dpol,*vtemp,*conc;
-
-main() {
-
- void GetAtomlist();
- void GetAtomlist_mod();
- void GetCOdict();
- void AnalyzeTrajectory();
- void PostProcess();
-
- GetAtomlist_mod(Snapshots);
- GetCOdict(Cutoff);
- AnalyzeTrajectory(Snapshots,Output3);
- PostProcess(Output1,Output2,Output3);
-
-}
-
-void GetAtomlist_mod(char *name) {
-/*This subroutine reads the bonds.petn file to set the number of atoms. It also checks that a full frame exists because it loops over the first frame to populate the Atomdic with the proper type for each atom id.*/
- FILE *fp;
- char buffer[1000];
- int i,j, Nlink, iatom, itemp, id;
- double BO,dtemp;//BO is bond order
-
- fp=fopen(name,"r");
- FileOpenError(fp,name);
-
- while(fscanf(fp,"%s",buffer)!=EOF) {
-
- if(strcmp(buffer,"particles")==0) {
- fscanf(fp,"%d",&Natom);
- printf("# of atoms : %d\n",Natom);
- Allocation();
- }
- if(strcmp(buffer,"q")==0) {
-
- for(i=0;i<Natom;i++) {
- fscanf(fp,"%d",&iatom);
- iatom--;
- fscanf(fp,"%d",&itemp);
- itemp--;
- if (itemp == Carbon){
- sprintf(buffer, "C");
- }else if(itemp == Hydrogen) {
- sprintf(buffer, "H");
- }else if(itemp == Oxygen) {
- sprintf(buffer, "O");
- }else if(itemp == Nitrogen) {
- sprintf(buffer, "N");
- }
-
- fscanf(fp,"%d",&Nlink);
- for(j=0;j<Nlink;j++) {
- fscanf(fp,"%d",&itemp);
- itemp--;
- }
- fscanf(fp,"%d",&itemp);
-
- for(j=0;j<Nlink;j++) {
- fscanf(fp,"%lf",&BO);
- }
- fscanf(fp,"%lf",&dtemp);
- fscanf(fp,"%lf",&dtemp);
- fscanf(fp,"%lf",&dtemp);
-
- id=AtomIndicator(buffer);
- Atomdic[iatom]=id;
- }
- if (i == Natom) goto Ending;
- }
-}
-Ending:;
-}
-
-
-
-void GetAtomlist(char *name) {
-/*This subroutine reads the head of the configuration file to set the lattice parameters and the number of atoms. It also checks that a full frame exists because it loops over the first frame to populate the Atomdic with the proper type for each atom id.*/
-
- FILE *fp;
- int i,iatom,count=0,itemp,id,flag;
- double dtemp;
- double a,b,c,d,e,f,g,h,ii,det;
- char buffer[1000];
-
- FILE *temp;
- fp=fopen(name,"r");
- FileOpenError(fp,name);
-
- while(fscanf(fp,"%s",buffer)!=EOF) {
- if(strcmp(buffer,"vectors:")==0) {
- fscanf(fp,"%s",buffer);
- for(i=0;i<3;i++) fscanf(fp,"%lf",&latc_x[i]);
- fscanf(fp,"%s",buffer);
- for(i=0;i<3;i++) fscanf(fp,"%lf",&latc_y[i]);
- fscanf(fp,"%s",buffer);
- for(i=0;i<3;i++) fscanf(fp,"%lf",&latc_z[i]);
- }
- else if(strcmp(buffer,"origin:")==0) {
- fscanf(fp,"%s",buffer);
- for(i=0;i<3;i++) fscanf(fp,"%lf",&Origin[i]);
- }
- else if(strcmp(buffer,"particles")==0) {
- fscanf(fp,"%d",&Natom);
- printf("# of atoms : %d\n",Natom);
- Allocation();
- }
- else if(strcmp(buffer,"positions")==0) {
- for(i=0,flag=0;i<Natom;i++) {
- fscanf(fp,"%d",&id);
- id--;
- fscanf(fp,"%s",buffer);
- iatom=AtomIndicator(buffer);
- Atomdic[id]=iatom;
- count++;
-// fscanf(fp,"%d",&itemp);
-// fprintf(temp,"\t%d",itemp);
-// fscanf(fp,"%lf",&dtemp);
-// fprintf(temp,"\t%lf",dtemp);
-// fscanf(fp,"%lf",&dtemp);
-// fprintf(temp,"\t%lf",dtemp);
-// fscanf(fp,"%lf",&dtemp);
-// fprintf(temp,"\t%lf",dtemp);
-// fscanf(fp,"%lf",&dtemp);
-// fprintf(temp,"\t%lf\n",dtemp);
- fgets(buffer,1000,fp);
- flag=1;
-/* fscanf(fp,"%lf",&dtemp); */
-/* fscanf(fp,"%lf",&dtemp); */
-/* fscanf(fp,"%lf",&dtemp); */
-/* fscanf(fp,"%lf",&dtemp); */
- }
- if(flag==1) break;
- }
- }
- if(Natom!=count) {
- printf("Can't read whole # of atoms.\n");
- exit(0);
- }
-
-
- a=latc_x[0]; b=latc_y[0]; c=latc_z[0];
- d=latc_x[1]; e=latc_y[1]; f=latc_z[1];
- g=latc_x[2]; h=latc_y[2]; ii=latc_z[2];
- det=a*e*ii-a*f*h-d*b*ii+d*c*h+g*b*f-g*c*e;
- if (det != 0) {
- Ilatc_x[0]=(e*ii-f*h)/det;
- Ilatc_x[1]=-(b*ii-c*h)/det;
- Ilatc_x[2]=(b*f-c*e)/det;
-
- Ilatc_y[0]=-(d*ii-f*g)/det;
- Ilatc_y[1]=(a*ii-c*g)/det;
- Ilatc_y[2]=-(a*f-c*d)/det;
-
- Ilatc_z[0]=(e*g-d*h)/det;
- Ilatc_z[1]=-(b*g-a*h)/det;
- Ilatc_z[2]=(a*e-b*d)/det;
- }
-
- close(fp);
-}
-
-void GetCOdict(char *name) {
-/* This subroutine populates the cut-off dictionary for each bond and throws an error if any possible combination of atoms do not have a specified bond*/
- FILE *fp;
- int i,j,iatom,jatom;
- double cut;
-#define BUFLEN 1000
- char buffer[BUFLEN];
- fp=fopen(name,"r");
- FileOpenError(fp,name);
-
- for(i=0;i<Natomtypes;i++) {
- for(j=0;j<Natomtypes;j++) COdic[i][j]=-1;
- }
-
- while(fscanf(fp,"%s",buffer)!=EOF) {
- if (strcmp(buffer,"#") == 0) {
- SkipLine(fp);
- continue;
- }
- iatom=AtomIndicator(buffer);
- fscanf(fp,"%s",buffer);
- jatom=AtomIndicator(buffer);
- fscanf(fp,"%lf",&cut);
- COdic[iatom][jatom]=cut;
- COdic[jatom][iatom]=cut;
- }
- for(i=0;i<Natomtypes;i++) {
- for(j=0;j<Natomtypes;j++) {
- if(COdic[i][j]==-1) {
- printf("Can't fine a certain pair for cut off dictionary!\n");
- exit(0);
- }
- }
- }
-
-
- close(fp);
-}
-void AnalyzeTrajectory(char *name,char *name2) {
-/***************************************************************************/
-/* This subroutine loops through the data both with the bond lists and the position files.
- Step 1: It checks the timestep for the bond list and then reads in the position data ensuring that the timesteps match.
- Step 2: It loops over the bonds to identify molecules
- Step 3: It loops over the molecules to determine name and species.
- Step 4: It calculates and writes dipole.out and vibtemp.out.
- Step 5: It writes num.out */
-/**************************************************************************/
-
- FILE *fp,*out3;//fp is the file with the bond lists. out3 refers to a scratch file to keep track of how many of each type of molecules exist.
- int i,j,k,l,iatom,jatom,Nlink,count,iatomtype,jatomtype;
-/* jatom is the neighbor, iatom is the self, Nlink is the number of neighbors, count is a running index to identify order of atoms (e.g. atom 5 is on line 38)*/
- int frame;
- int itemp,Molid;
-/*itemp is a generic variable as needed, Molid is the line of the atom (e.g. atom 5 is on line 38 means Molid[4]=37 because of the zero).*/
-
- double BO,dtemp;//BO is bond order
- char buffer[1000];
- int Cnct[MaxNumBonds];//connectivity table for a given atom
-
- int Nspec,flag_mol,flag_spec,flag_identity,nd,timestep;
-/* Nspec is the number of species during this frame. flag_mol is a binary flag with 1 indicating that this atom belongs to this molecule. flag_spec is a binary flag with 1 indicating that a new species has been found. I have no idea what purpose flag_identity serves, but a 1 indicates that flag_spec is 1.
-nd is a return value from CheckExistence.*/
-
- int Name[Natomtypes],MolTemp[Natom];
-/*Name is a counter for how many atoms of a given type are in this particular molecule. MolTemp is an array that keeps track of molecule id by atom id. For example, if atom 5 belongs to molecule 3 MolTemp[4]=3*/
-
- int CheckExistence();
- void GetAtomdata();
- void GetCOMDipole();
-
- fp=fopen(name,"r");
- FileOpenError(fp,name);
- out3=fopen(name2,"w");
- FileOpenError(out3,name2);
-
- frame=0;
-
- while(fscanf(fp,"%s",buffer)!=EOF) {
-/* Step 1 */
- if(strcmp(buffer,"Timestep")==0) {
- fscanf(fp,"%d",×tep);
- // GetAtomdata(timestep);
- }
-
-/* Step 2 */
- if(strcmp(buffer,"q")==0) {
- frame++;
- count=0;
-/* zeroing out the counters */
- for(i=0;i<Natom;i++) {
- MolTemp[i]=-1;
- NMol[i]=1;
- }
-/* Step 2A reads the atomid as iatom, the first itemp is a discard of the atom type, Nlink is the number of neighbors, and then the loop over all the bonded neighbors is stored in Cnct, and the last itemp is the ignored 0 to mark the end.*/
- for(i=0;i<Natom;i++) {
- fscanf(fp,"%d",&iatom);
- iatom--;
- if(MolTemp[iatom]==-1) {
- MolTemp[iatom]=count;
- count++;
- }
- fscanf(fp,"%d",&itemp);
- fscanf(fp,"%d",&Nlink);
- for(j=0;j<Nlink;j++) {
- fscanf(fp,"%d",&itemp);
- itemp--;
- Cnct[j]=itemp;
- }
- fscanf(fp,"%d",&itemp);
-
-/* Step 2B reads the bond orders from the bond file and assigns atoms to molecules. The first check is if a bond exists. The second check is if i and j already belong to the same molecule. If they don't and j has no molecule, assign it to i's molecule. If they do, then j was assigned to a different number so loop through the molecule list and set all the atoms on that molecule to the new i molecule. Then read and discard the remainder of the line.*/
-
- for(j=0;j<Nlink;j++) {
- fscanf(fp,"%lf",&BO);
- jatom=Cnct[j];
- Molid=MolTemp[jatom];
- iatomtype=Atomdic[iatom];
- jatomtype=Atomdic[jatom];
- if(BO>COdic[iatomtype][jatomtype]) {
- if(Molid!=MolTemp[iatom]) {
- if(MolTemp[jatom]==-1) MolTemp[jatom]=MolTemp[iatom];
- else {
- for(k=0;k<Natom;k++) {
- if(MolTemp[k]==Molid) MolTemp[k]=MolTemp[iatom];
- }
- }
- }
- }
- }
- fscanf(fp,"%lf",&dtemp);
- fscanf(fp,"%lf",&dtemp);
- fscanf(fp,"%lf",&dtemp);
- }
-
-/* Step 3 builds the chemical formula for each molecule. For each molecule (the for loop over i with count as the maximum), loop over all the atoms.*/
-
- for(i=0;i<MaxMolTypes;i++) Netc[i]=0.0;
- for(i=0,Nspec=0,Nmolecule=0;i<count;i++) {
-
- /* Step 3A: if the atom belongs to this molecule, increment the appropriate type counter (e.g. we have another carbon), flip flag_mol to 1, set the Mol value to this molecule, and add the atomic charge to the running charge total. */
-
- for(j=0;j<Natomtypes;j++) Name[j]=0;
- for(j=0,flag_mol=0;j<Natom;j++) {
- if(MolTemp[j]==i) {
- jatom=Atomdic[j];
- Name[jatom]++;
- flag_mol=1;
- Mol[j]=Nmolecule;
- Netc[Nmolecule]+=Charge[j];
- }
- }
-
-/* Step 3B: If this molecule contains any atoms (flag_mol==1), then determine if it is a new species. MolName is populated as new species are found. In one of the least efficient matching mechanisms ever, we walk through all the known species names. If no match is found, the flag_spec is set to 1. A zero flag_spec means that we have a match, increment the appropriate species counter. Otherwise, if we have a zero number of species or a flipped flag_spec, we have a new species and need to populate its name. Then we increment the number of species as appropriate and always add a new molecule.*/
-
- if(flag_mol==1) {
- flag_identity=1;
- for(k=0;k<Nspec;k++) {
- flag_spec=0;
- for(l=0;l<Natomtypes;l++) {
- if(MolName[Natomtypes*k+l]!=Name[l]) flag_spec=1;
- }
- if(flag_spec==0) NMol[k]++;
- flag_identity*=flag_spec;
- }
- if(Nspec==0 || flag_identity==1) {
- for(l=0;l<Natomtypes;l++) {
- MolName[Natomtypes*Nspec+l]=Name[l];
- }
- Nspec++;
- }
- Nmolecule++;
- }//ends the if(flag_mol==1) loop
-
- }//ends the for i up to count loop
-
-/* Step 4 does the end of frame cleanup including the writes for COM */
- fprintf(out3,"%d\t",timestep);
- printf("Timestep = %d\n",timestep);
- fprintf(dpol,"%d\n",Nmolecule);
- fprintf(dpol,"TSTEP %d\n",timestep);
- fprintf(vtemp,"%d\n",Nmolecule);
- fprintf(vtemp,"TSTEP %d\n",timestep);
- fprintf(conc,"TSTEP %d\n",timestep);
- fprintf(conc,"%d\n",Nmolecule);
- GetCOMDipole(Nmolecule,timestep,frame);
-
-/* Step 5 prints the list of species and their quantities */
- fprintf(out3,"%d\t",Nspec);
- for(i=0;i<Nspec;i++) {
- nd=CheckExistence(i);
- fprintf(out3,"%d ",nd);
- fprintf(out3,"%d\t",NMol[i]);
- }
- fprintf(out3,"\n");
- }
- }
- fflush(out3);
- fclose(out3);
- fclose(fp);
-}
-
-int CheckExistence(int id) {
-/* The purpose of this function is to have a list of only the species that occur in this frame. */
-
- int i,j,num,molid,itemp;
- int flag,flag_identity=1;
-
- for(i=0;i<Nmoltype;i++) {
- flag=0;
- for(j=0;j<Natomtypes;j++) {
- molid=MolType[Natomtypes*i+j];
- if(molid!=MolName[Natomtypes*id+j]) flag=1;
- }
- if(flag==0) return i;
- flag_identity*=flag;
- }
-
- for(i=0;i<Natomtypes;i++) {
- MolType[Natomtypes*Nmoltype+i]=MolName[Natomtypes*id+i];
- }
- Nmoltype++;
-
- return Nmoltype-1;
-}
-
-void FileOpenError(FILE *fp,char *name) {
- if(fp==NULL) {
- printf("file open error(%s).\n",name);
- exit(0);
- }
-}
-
-void Allocation() {
-/* This subroutine sets up most of the important adjustable arrays based on the number of atoms. It also opens the dipole and vibtemp files for writing.*/
- int flag=0;
- char name[100];
- Atomdic=(int *)malloc(Natom*sizeof(int));
- Mol=(int *)malloc(Natom*sizeof(int));
- MolName=(int *)malloc(Natom*Natomtypes*sizeof(int));
-//20Jun07 JLB: I have made the absurdly huge array much smaller
-// MolType=(int *)malloc(Natom*MaxMolTypes*sizeof(int));
- MolType=(int *)malloc((Natomtypes+20)*MaxMolTypes*sizeof(int));
- NMol=(int *)malloc(Natom*sizeof(int));
- rx=(double *)malloc(Natom*sizeof(double));
- ry=(double *)malloc(Natom*sizeof(double));
- rz=(double *)malloc(Natom*sizeof(double));
- vx=(double *)malloc(Natom*sizeof(double));
- vy=(double *)malloc(Natom*sizeof(double));
- vz=(double *)malloc(Natom*sizeof(double));
- Charge=(double *)malloc(Natom*sizeof(double));
- Netc=(double *)malloc(MaxMolTypes*sizeof(double));
-
- if(Atomdic==NULL || NMol==NULL || Mol==NULL || MolType==NULL) flag=1;
- if(rx==NULL || ry==NULL || rz==NULL || Charge==NULL) flag=1;
- if(vx==NULL || vy==NULL || vz==NULL) flag=1;
- if(Netc==NULL) flag=1;
-
- if(flag==1) {
- printf("malloc error.\n");
- exit(0);
- }
- // trj=fopen(Atomlist,"r");
- // FileOpenError(trj,Atomlist);
- dpol=fopen(Output4,"w");
- FileOpenError(dpol,Output4);
- vtemp=fopen(Output5,"w");
- FileOpenError(vtemp,Output5);
- conc=fopen(Output6,"w");
- FileOpenError(conc,Output6);
-}
-
-int AtomIndicator(char *symbol) {
-/* This subroutine identifies the atom type from the config file and sets the masses. Why set the masses here, I don't know.*/
-
- int value;
- Mass[Hydrogen]=1.0079;
- Mass[Carbon]=12.0107;
- Mass[Oxygen]=15.9994;
- Mass[Nitrogen]=14.0067;
- if(strcmp(symbol,"H")==0) value=Hydrogen;
- else if(strcmp(symbol,"C")==0) value=Carbon;
- else if(strcmp(symbol,"O")==0) value=Oxygen;
- else if(strcmp(symbol,"N")==0) value=Nitrogen;
- else {
- printf("Can't recognize the atom type : %s.\n",symbol);
- exit(0);
- }
-
- return value;
-}
-void PostProcess(char *name,char *name2,char *name3) {
-
-/* This subroutine does the global lists after all the frames have been read. out is the fra.out with the list of species and number of each per frame. out2 is mol.out with the chemical identities of each species. out3 is num.out which is the scratch file with number of species per frame in a non-plottable format.*/
-
- int i,j;
- FILE *out,*out2,*out3;
- int step,molnum,id,num,itemp;
- int numcount[Nmoltype];
-
- out=fopen(name,"w");
- FileOpenError(out,name);
- out2=fopen(name2,"w");
- FileOpenError(out2,name2);
- out3=fopen(name3,"r");
- FileOpenError(out3,name3);
-
- fprintf(out,"Timestep\t");
- fprintf(out2,"%d\n\n",Nmoltype);
-
-/* To get the chemical identity of a species, this process loops over each atom type and writes the number of atoms of that type in the formula. */
- for(i=0;i<Nmoltype;i++) {
- fprintf(out2,"%d\t",i);
- for(j=0;j<Natomtypes;j++) {
- itemp=MolType[Natomtypes*i+j];
- if(itemp!=0) {
- if(j==Carbon) {
- fprintf(out,"C");
- fprintf(out2,"C");
- }
- else if(j==Hydrogen) {
- fprintf(out,"H");
- fprintf(out2,"H");
- }
- else if(j==Oxygen) {
- fprintf(out,"O");
- fprintf(out2,"O");
- }
- else if(j==Nitrogen) {
- fprintf(out,"N");
- fprintf(out2,"N");
- }
- if(itemp!=1) {
- fprintf(out,"%d",itemp);
- fprintf(out2,"%d",itemp);
- }
- }
- }
- fprintf(out,"\t");
- fprintf(out2,"\n");
- }
- fprintf(out,"\n");
-
-/* for each molecule type, read the num.out scratch file and find the number of those molecules. Then write it out in a nice column format suitable for plotting. */
- while(fscanf(out3,"%d",&step)!=EOF) {
- fscanf(out3,"%d",&num);
- for(i=0;i<Nmoltype;i++) numcount[i]=0;
- for(i=0;i<num;i++) {
- fscanf(out3,"%d",&id);
- fscanf(out3,"%d",&molnum);
- numcount[id]=molnum;
- }
- fprintf(out,"%d\t",step);
- for(i=0;i<Nmoltype;i++) {
- fprintf(out,"%d\t",numcount[i]);
- }
- fprintf(out,"\n");
- }
-}
-void GetAtomdata(int tstep) {
-/* This subroutine reads in the position data for a frame*/
-
- int i,iatom,count=0,itemp,id,flag;
- double dtemp;
- int step;
- char buffer[1000];
-
- while(fscanf(trj,"%s",buffer)!=EOF) {
- if(strcmp(buffer,"Timestep")==0) {
- fscanf(trj,"%d",&step);
- if(step!=tstep) {
- printf("The sequences are not matched between bond data file and coordinate file\n");
- printf("step in config file : %d\tStep in bond file : %d\n",tstep,step);
- exit(0);
- }
- }
- else if(strcmp(buffer,"positions")==0) {
- for(i=0,flag=0;i<Natom;i++) {
- fscanf(trj,"%d",&id);
- id--;
- fscanf(trj,"%s",buffer);
- iatom=AtomIndicator(buffer);
- Atomdic[id]=iatom;
- fscanf(trj,"%d",&itemp);
- fscanf(trj,"%lf",&dtemp);
- Charge[id]=dtemp;
- fscanf(trj,"%lf",&dtemp);
- rx[id]=dtemp;
- fscanf(trj,"%lf",&dtemp);
- ry[id]=dtemp;
- fscanf(trj,"%lf",&dtemp);
- rz[id]=dtemp;
- fscanf(trj,"%lf",&dtemp);
- vx[id]=dtemp;
- fscanf(trj,"%lf",&dtemp);
- vy[id]=dtemp;
- fscanf(trj,"%lf",&dtemp);
- vz[id]=dtemp;
- fscanf(trj,"%lf",&dtemp);
- flag=1;
- }
- if(flag==1) break;
- }
- }
-}
-void GetCOMDipole(int max,int tstep,int frame) {
-/* max is the number of molecules */
- int i;
- void AnalCOMDipole();
-
- for(i=0;i<max;i++) AnalCOMDipole(i);
-
-}
-void AnalCOMDipole(int molid) {
-
- int i,j,ix,iy,iz,count,itemp;
- int ntot;
- double mass,chg;
- int atomid;
- double totmass;
- double x0,y0,z0,xtemp,ytemp,ztemp,x,y,z,r2,minr2,dx,dy,dz;
- double COMx,COMy,COMz;
- double vCOMx,vCOMy,vCOMz;
- double Dpolx,Dpoly,Dpolz,Dpol;
- double VibTempx,VibTempy,VibTempz,VibTemp;
- int Name[Natomtypes];
-
- double tempx,tempy,tempz;
-
- totmass=0.0;
- vCOMx=vCOMy=vCOMz=0.0;
-
-/* Again in an inefficient way, we loop over all the atoms to find the ones that are members of this molecule (molid). Then calculate the desired quantities, including the fact that the first atom sets our standard for measurement. Then, we write the quantities to the COM files.
-
-JB 26Sep07: to facilitate my write out of the chemical formula, redo the molecule determination here. */
- for(j=0;j<Natomtypes;j++) Name[j]=0;
- for(i=0,count=0;i<Natom;i++) {
- if(Mol[i]==molid) {
- atomid=Atomdic[i];
- Name[atomid]++;
- mass=Mass[atomid];
- chg=Charge[i];
- totmass+=mass;
- vCOMx+=mass*vx[i];
- vCOMy+=mass*vy[i];
- vCOMz+=mass*vz[i];
- if(count==0) {
-// printf("i, rx[i], ry[i], rz[i] , mass %d %e %e %e %e\n", i, rx[i], ry[i], rz[i] , mass);
- x0=rx[i];
- y0=ry[i];
- z0=rz[i];
- COMx=mass*x0;
- COMy=mass*y0;
- COMz=mass*z0;
- }
- if(count!=0) {
- minr2=1.0e8;
- for(ix=-1;ix<2;ix++) {
- for(iy=-1;iy<2;iy++) {
- for(iz=-1;iz<2;iz++) {
- xtemp=rx[i]+ix*latc_x[0]+iy*latc_y[0]+iz*latc_z[0];
- ytemp=ry[i]+ix*latc_x[1]+iy*latc_y[1]+iz*latc_z[1];
- ztemp=rz[i]+ix*latc_x[2]+iy*latc_y[2]+iz*latc_z[2];
- dx=xtemp-x0;
- dy=ytemp-y0;
- dz=ztemp-z0;
- r2=dx*dx+dy*dy+dz*dz;
- if(r2<minr2) {
- minr2=r2;
- x=xtemp;
- y=ytemp;
- z=ztemp;
- }
- }
- }
- }
- rx[i]=x;
- ry[i]=y;
- rz[i]=z;
-// printf("AAA i, rx[i], ry[i], rz[i] , mass %d %e %e %e %e\n", i, rx[i], ry[i], rz[i] , mass);
- COMx+=mass*x;
- COMy+=mass*y;
- COMz+=mass*z;
- }
- count++;
- }
- }
-// printf ("AAA totmass %e\n",totmass);
- COMx/=totmass;
- COMy/=totmass;
- COMz/=totmass;
-
- vCOMx/=totmass;
- vCOMy/=totmass;
- vCOMz/=totmass;
-
- VibTempx=VibTempy=VibTempz=0.0;
- for(i=0,ntot=0,Dpolx=0.0,Dpoly=0.0,Dpolz=0.0;i<Natom;i++) {
- if(Mol[i]==molid) {
- atomid=Atomdic[i];
- mass=Mass[atomid];
- chg=Charge[i];
- totmass+=mass;
- x=rx[i]-COMx;
- y=ry[i]-COMy;
- z=rz[i]-COMz;
- Dpolx+=chg*x;
- Dpoly+=chg*y;
- Dpolz+=chg*z;
- VibTempx+=mass*(vx[i]-vCOMx)*(vx[i]-vCOMx);
- VibTempy+=mass*(vy[i]-vCOMy)*(vy[i]-vCOMy);
- VibTempz+=mass*(vz[i]-vCOMz)*(vz[i]-vCOMz);
- ntot++;
- }
- }
- VibTempx/=(double)ntot;
- VibTempy/=(double)ntot;
- VibTempz/=(double)ntot;
-
- VibTemp=(VibTempx+VibTempy+VibTempz)/3.0;
-
- VibTemp*=1.2027E+06;
-
-
- COMx-=Origin[0]; COMy-=Origin[1]; COMz-=Origin[2];
-// printf("VVVV %e %e %e\n",Ilatc_x[0],Ilatc_x[1],Ilatc_x[2]);
- tempx=Ilatc_x[0]*COMx;
- tempx+=Ilatc_x[1]*COMy;
- tempx+=Ilatc_x[2]*COMz;
-
- tempy=Ilatc_y[0]*COMx;
- tempy+=Ilatc_y[1]*COMy;
- tempy+=Ilatc_y[2]*COMz;
-
- tempz=Ilatc_z[0]*COMx;
- tempz+=Ilatc_z[1]*COMy;
- tempz+=Ilatc_z[2]*COMz;
-
- tempx-=floor(tempx);
- tempy-=floor(tempy);
- tempz-=floor(tempz);
-
- COMx=latc_x[0]*tempx+latc_y[0]*tempy+latc_z[0]*tempz;
- COMy=latc_x[1]*tempx+latc_y[1]*tempy+latc_z[1]*tempz;
- COMz=latc_x[2]*tempx+latc_y[2]*tempy+latc_z[2]*tempz;
-// printf ("LATICE %e %e %e %e %e %e \n",latc_x[0], tempx, latc_y[0], tempy,latc_z[0],tempz );
- COMx+=Origin[0]; COMy+=Origin[1]; COMz+=Origin[2];
-
- Dpolx/=0.2082267;
- Dpoly/=0.2082267;
- Dpolz/=0.2082267;
-
- Dpol=Dpolx*Dpolx+Dpoly*Dpoly+Dpolz*Dpolz;
- Dpol=sqrt(Dpol);
-// printf("BBB %e %e %e\n",COMx,COMy,COMz);
- fprintf(dpol,"He %e %e %e ",COMx,COMy,COMz);
- fprintf(dpol,"%e %e %e %e\n",Dpol,Dpolx,Dpoly,Dpolz);
- fprintf(vtemp,"He %e %e %e",COMx,COMy,COMz);
- fprintf(vtemp,"%e %e %e %e\n",VibTemp,vCOMx,vCOMy,vCOMz);
-
-/* JB 26Sep07: I am adding the routines that will write the chemical formula and the COM to a separate file for use with the composition profile. Step 1: determine the chemical formula for this molecule.*/
- for(j=0;j<Natomtypes;j++) {
- itemp=Name[j];
- if(itemp!=0) {
- if(j==Carbon) {
- fprintf(conc,"C");
- }
- else if(j==Hydrogen) {
- fprintf(conc,"H");
- }
- else if(j==Oxygen) {
- fprintf(conc,"O");
- }
- else if(j==Nitrogen) {
- fprintf(conc,"N");
- }
- if(itemp!=1) {
- fprintf(conc,"%d",itemp);
- }
- }
- }
- fprintf(conc,"\t");
- fprintf(conc,"%e %e %e\n",COMx,COMy,COMz);
-
-}
-
-void SkipLine(FILE *fp) {
- int c;
- while ((c = getc(fp)) != EOF)
- if (c == '\n') break;
-}
-