diff --git a/doc/src/fix_msst.txt b/doc/src/fix_msst.txt
index 43f35d6880cda93c0984e17560233406e5dfc1bb..025c733897a6ec7a14ff21edbeafbeeb7536c073 100644
--- a/doc/src/fix_msst.txt
+++ b/doc/src/fix_msst.txt
@@ -25,7 +25,7 @@ keyword = {q} or {mu} or {p0} or {v0} or {e0} or {tscale} or {beta} or {dftb} :l
{e0} value = initial total energy (energy units)
{tscale} value = reduction in initial temperature (unitless fraction between 0.0 and 1.0)
{dftb} value = {yes} or {no} for whether using MSST in conjunction with DFTB+
- {beta} value = scale factor on energy contribution of DFTB+ :pre
+ {beta} value = scale factor for improved energy conservation :pre
:ule
[Examples:]
@@ -72,6 +72,14 @@ be calculated on the first step, after the energy specified by
{tscale} is removed. The value of {e0} is not used in the dynamical
equations, but is used in calculating the deviation from the Hugoniot.
+The keyword {beta} is a scaling term that can be added to the MSST
+ionic equations of motion to account for drift in the conserved
+quantity during long timescale simulations, similar to a Berendson
+thermostat. See "(Reed)"_#Reed and "(Goldman)"_#Goldman for more
+details. The value of {beta} must be between 0.0 and 1.0 inclusive.
+A value of 0.0 means no contribution, a value of 1.0 means a full
+contribution.
+
Values of shockvel less than a critical value determined by the
material response will not have compressive solutions. This will be
reflected in lack of significant change of the volume in the MSST.
@@ -95,23 +103,15 @@ or "_MSST_pe". The group for the new computes is "all".
:line
-The {dftb} and {beta} keywords are to allow this fix to be used when
-LAMMPS is being driven by DFTB+, a density-functional tight-binding
-code.
-
-If the keyword {dftb} is used with a value of {yes}, then the MSST
-equations are altered to account for an energy contribution compute by
-DFTB+. In this case, you must define a "fix
-external"_fix_external.html command in your input script, which is
-used to callback to DFTB+ during the LAMMPS timestepping. DFTB+ will
-communicate its info to LAMMPS via that fix.
-
-The keyword {beta} is a scale factor on the DFTB+ energy contribution.
-The value of {beta} must be between 0.0 and 1.0 inclusive. A value of
-0.0 means no contribution, a value of 1.0 means a full contribution.
-
-(July 2017) More information about these keywords and the use of
-LAMMPS with DFTB+ will be added to the LAMMMPS documention soon.
+The {dftb} keyword is to allow this fix to be used when LAMMPS is
+being driven by DFTB+, a density-functional tight-binding code. If the
+keyword {dftb} is used with a value of {yes}, then the MSST equations
+are altered to account for the electron entropy contribution to the
+Hugonio relations and total energy. See "(Reed2)"_#Reed2 and
+"(Goldman)"_#Goldman for details on this contribution. In this case,
+you must define a "fix external"_fix_external.html command in your
+input script, which is used to callback to DFTB+ during the LAMMPS
+timestepping. DFTB+ will communicate its info to LAMMPS via that fix.
:line
@@ -182,4 +182,12 @@ timestep.
:line
:link(Reed)
-[(Reed)] Reed, Fried, and Joannopoulos, Phys. Rev. Lett., 90, 235503 (2003).
+[(Reed)] Reed, Fried, and Joannopoulos, Phys. Rev. Lett., 90, 235503
+(2003).
+
+:link(Reed2)
+[(Reed2)] Reed, J. Phys. Chem. C, 116, 2205 (2012).
+
+:link(Goldman)
+[(Goldman)] Goldman, Srinivasan, Hamel, Fried, Gaus, and Elstner,
+J. Phys. Chem. C, 117, 7885 (2013).
diff --git a/doc/src/pair_kim.txt b/doc/src/pair_kim.txt
index 5a623e5ece39d4b482b9fa11a40921639df4b938..5ee607c2b090decb758af797419290a4a68444c3 100644
--- a/doc/src/pair_kim.txt
+++ b/doc/src/pair_kim.txt
@@ -27,13 +27,34 @@ pair_coeff * * Ar Ar :pre
[Description:]
This pair style is a wrapper on the "Knowledge Base for Interatomic
-Models (KIM)"_https://openkim.org repository of interatomic potentials,
-so that they can be used by LAMMPS scripts.
+Models (OpenKIM)"_https://openkim.org repository of interatomic
+potentials, so that they can be used by LAMMPS scripts.
-In KIM lingo, a potential is a "model" and a model contains both the
-analytic formulas that define the potential as well as the parameters
-needed to run it for one or more materials, including coefficients and
-cutoffs.
+Note that in LAMMPS lingo, a KIM model driver is a pair style
+(e.g. EAM or Tersoff). A KIM model is a pair style for a particular
+element or alloy and set of parameters, e.g. EAM for Cu with a
+specific EAM potential file.
+
+See the current list of "KIM model
+drivers"_https://openkim.org/kim-items/model-drivers/alphabetical.
+
+See the current list of all "KIM
+models"_https://openkim.org/kim-items/models/by-model-drivers
+
+See the list of "example KIM models"_https://openkim.org/kim-api which
+are included in the KIM library by default, in the "What is in the KIM
+API source package?" section.
+
+To use this pair style, you must first download and install the KIM
+API library from the "OpenKIM website"_https://openkim.org. The "KIM
+section of Section packages"_Section_packages.html#kim-package has
+instructions on how to do this with a simple make command, when
+building LAMMPS.
+
+See the examples/kim dir for an input script that uses a KIM model
+(potential) for Lennard-Jones.
+
+:line
The argument {virialmode} determines how the global virial is
calculated. If {KIMvirial} is specified, the KIM model performs the
diff --git a/examples/COUPLE/README b/examples/COUPLE/README
index c8c9e0e31b0e350a4ef9af6478bf973b11cb9493..83e7463531de47c29b81883ff74493682139c3eb 100644
--- a/examples/COUPLE/README
+++ b/examples/COUPLE/README
@@ -41,8 +41,8 @@ fortran a simple wrapper on the LAMMPS library API that
can be called from Fortran
fortran2 a more sophisticated wrapper on the LAMMPS library API that
can be called from Fortran
-fortran3 wrapper written by Nir Goldman (LLNL), as an
+fortran_dftb wrapper written by Nir Goldman (LLNL), as an
extension to fortran2, used for calling LAMMPS
- from Fortran DFTB+ code
+ from Fortran DFTB+ tight-binding code
Each sub-directory has its own README with more details.
diff --git a/examples/COUPLE/fortran3/LAMMPS-wrapper.cpp b/examples/COUPLE/fortran_dftb/LAMMPS-wrapper.cpp
similarity index 100%
rename from examples/COUPLE/fortran3/LAMMPS-wrapper.cpp
rename to examples/COUPLE/fortran_dftb/LAMMPS-wrapper.cpp
diff --git a/examples/COUPLE/fortran3/LAMMPS-wrapper.h b/examples/COUPLE/fortran_dftb/LAMMPS-wrapper.h
similarity index 100%
rename from examples/COUPLE/fortran3/LAMMPS-wrapper.h
rename to examples/COUPLE/fortran_dftb/LAMMPS-wrapper.h
diff --git a/examples/COUPLE/fortran3/LAMMPS-wrapper2.cpp b/examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.cpp
similarity index 71%
rename from examples/COUPLE/fortran3/LAMMPS-wrapper2.cpp
rename to examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.cpp
index f245c44d79c26fd13266b8b5e301c427b114cb73..d16b49cc50e68d484a03eb994bca2d2704a5b749 100644
--- a/examples/COUPLE/fortran3/LAMMPS-wrapper2.cpp
+++ b/examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.cpp
@@ -47,11 +47,35 @@ void lammps_set_callback (void *ptr) {
return;
}
+void lammps_set_external_vector_length (void *ptr, int n) {
+ class LAMMPS *lmp = (class LAMMPS *) ptr;
+ int ifix = lmp->modify->find_fix_by_style("external");
+ FixExternal *fix = (FixExternal *) lmp->modify->fix[ifix];
+ fix->set_vector_length(n);
+ return;
+}
+
+void lammps_set_external_vector (void *ptr, int n, double val) {
+ class LAMMPS *lmp = (class LAMMPS *) ptr;
+ int ifix = lmp->modify->find_fix_by_style("external");
+ FixExternal *fix = (FixExternal *) lmp->modify->fix[ifix];
+ fix->set_vector (n, val);
+ return;
+}
+
void lammps_set_user_energy (void *ptr, double energy) {
class LAMMPS *lmp = (class LAMMPS *) ptr;
int ifix = lmp->modify->find_fix_by_style("external");
FixExternal *fix = (FixExternal *) lmp->modify->fix[ifix];
- fix->set_energy(energy);
+ fix->set_energy_global(energy);
+ return;
+}
+
+void lammps_set_user_virial (void *ptr, double *virial) {
+ class LAMMPS *lmp = (class LAMMPS *) ptr;
+ int ifix = lmp->modify->find_fix_by_style("external");
+ FixExternal *fix = (FixExternal *) lmp->modify->fix[ifix];
+ fix->set_virial_global(virial);
return;
}
diff --git a/examples/COUPLE/fortran3/LAMMPS-wrapper2.h b/examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.h
similarity index 89%
rename from examples/COUPLE/fortran3/LAMMPS-wrapper2.h
rename to examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.h
index 794006e3afac4919d33cf1d0080b1d4a0a22dc49..ed79015e78851f57af3e90203436f89d4b1dcdd1 100644
--- a/examples/COUPLE/fortran3/LAMMPS-wrapper2.h
+++ b/examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.h
@@ -26,6 +26,9 @@ extern "C" {
/* Prototypes for auxiliary functions */
void lammps_set_callback (void *);
void lammps_set_user_energy (void*, double);
+void lammps_set_user_virial (void*, double*);
+void lammps_set_external_vector_length (void*, int);
+void lammps_set_external_vector (void*, int, double);
#ifdef __cplusplus
}
diff --git a/examples/COUPLE/fortran3/LAMMPS.F90 b/examples/COUPLE/fortran_dftb/LAMMPS.F90
similarity index 97%
rename from examples/COUPLE/fortran3/LAMMPS.F90
rename to examples/COUPLE/fortran_dftb/LAMMPS.F90
index eb5b7f825becfb54fd80c2400c3f4ef52fd94b82..9b18bbfa5fc4330ba46a2aba8e2f7fda87c5d65e 100644
--- a/examples/COUPLE/fortran3/LAMMPS.F90
+++ b/examples/COUPLE/fortran_dftb/LAMMPS.F90
@@ -52,12 +52,16 @@ module LAMMPS
C_NULL_CHAR, C_loc, C_F_pointer, lammps_instance => C_ptr
implicit none
private
+ public :: lammps_set_user_virial
+ public :: lammps_set_external_vector_length
+ public :: lammps_set_external_vector
+ public :: lammps_set_user_energy
public :: lammps_open, lammps_open_no_mpi, lammps_close, lammps_file, &
lammps_command, lammps_free, lammps_extract_global, &
lammps_extract_atom, lammps_extract_compute, lammps_extract_fix, &
lammps_extract_variable, lammps_get_natoms, lammps_gather_atoms, &
- lammps_scatter_atoms, lammps_set_callback, lammps_set_user_energy
- public :: lammps_instance, C_ptr, C_double, C_int
+ lammps_set_callback
+ public :: lammps_scatter_atoms, lammps_instance, C_ptr, C_double, C_int
!! Functions supplemental to the prototypes in library.h. {{{1
!! The function definitions (in C++) are contained in LAMMPS-wrapper.cpp.
@@ -218,6 +222,28 @@ module LAMMPS
real(C_double), value :: energy
end subroutine lammps_set_user_energy
+ subroutine lammps_set_user_virial (ptr, virial) &
+ bind (C, name='lammps_set_user_virial')
+ import :: C_ptr, C_double
+ type (C_ptr), value :: ptr
+ real(C_double) :: virial(6)
+ end subroutine lammps_set_user_virial
+
+ subroutine lammps_set_external_vector_length (ptr, n) &
+ bind (C, name='lammps_set_external_vector_length')
+ import :: C_ptr, C_double, C_int
+ type(C_ptr), value :: ptr
+ integer (C_int), value :: n
+ end subroutine lammps_set_external_vector_length
+
+ subroutine lammps_set_external_vector (ptr, n, val) &
+ bind (C, name='lammps_set_external_vector')
+ import :: C_ptr, C_int, C_double
+ type (C_ptr), value :: ptr
+ integer (C_int), value :: n
+ real(C_double), value :: val
+ end subroutine lammps_set_external_vector
+
subroutine lammps_actual_gather_atoms (ptr, name, type, count, data) &
bind (C, name='lammps_gather_atoms')
import :: C_ptr, C_int, C_char
diff --git a/examples/COUPLE/fortran3/README b/examples/COUPLE/fortran_dftb/README
similarity index 78%
rename from examples/COUPLE/fortran3/README
rename to examples/COUPLE/fortran_dftb/README
index 9effa35ec4e0040bcfca794be6757aad05e28fd2..39a2f1816976500f27e337272462aee653ddec98 100644
--- a/examples/COUPLE/fortran3/README
+++ b/examples/COUPLE/fortran_dftb/README
@@ -3,8 +3,9 @@ forces from a fortran code for a LAMMPS simulation. The reader should
refer to the README file in COUPLE/fortran2 before proceeding. Here,
the LAMMPS.F90 file has been modified slightly and additional files
named LAMMPS-wrapper2.h and LAMMPS-wrapper2.cpp have been included in
-order to supply wrapper functions to set the LAMMPS callback function
-and total energy.
+order to supply wrapper functions to set the LAMMPS callback function,
+total energy, virial, and electronic entropy contribution (needed for
+MSST simulations with a quantum code).
In this example, the callback function is set to run the
semi-empirical quantum code DFTB+ in serial and then read in the total
@@ -20,11 +21,14 @@ etc.
A few more important notes:
--The stress tensor from DFTB+ is passed in to LAMMPS via pointer.
-Calling the subroutine lammps_set_callback() is required in order to set
a pointer to the callback function in LAMMPS.
-The subroutine lammps_set_user_energy() passes in the potential energy
- from DFTB+ to LAMMPS.
+ from DFTB+ to LAMMPS. Similarly, lammps_set_user_virial passes the stress tensor.
+
+-The electronic entropy contribution is set via lammps_set_external_vector(). Their needs
+ to be a call to lammps_set_external_vector_length() before this value can be
+ passed to LAMMPS.
This example was created by Nir Goldman, whom you can contact with
questions:
diff --git a/examples/COUPLE/fortran3/data.diamond b/examples/COUPLE/fortran_dftb/data.diamond
similarity index 100%
rename from examples/COUPLE/fortran3/data.diamond
rename to examples/COUPLE/fortran_dftb/data.diamond
diff --git a/examples/COUPLE/fortran_dftb/dftb_in.hsd b/examples/COUPLE/fortran_dftb/dftb_in.hsd
new file mode 100644
index 0000000000000000000000000000000000000000..104a4c04ce9bd8d66d67537c376ba0a437b37f2c
--- /dev/null
+++ b/examples/COUPLE/fortran_dftb/dftb_in.hsd
@@ -0,0 +1,40 @@
+#sample DFTB+ script to run this test code
+Geometry = GenFormat {
+<<< "lammps.gen"
+}
+
+Driver = {
+}
+
+Hamiltonian = DFTB {
+ LAMMPS = Yes # keyword to print energy, forces, and stress tensor to file(results.out)
+ SCC = No
+ MaxAngularMomentum = {
+ C = "p"
+ }
+ Charge = 0.0
+ Eigensolver = Standard {}
+ Filling = Fermi {
+ Temperature [Kelvin] = 298.0
+ }
+ SlaterKosterFiles = Type2FileNames {
+ Prefix = "~/slako/mio-1-1/" # the user must define the location of the skf files
+ Separator = "-"
+ Suffix = ".skf"
+ LowerCaseTypeName = No
+ }
+ KPointsAndWeights = {
+ 0.0000000000000 0.0000000000000 0.0000000000000 1.00000000000000
+ }
+}
+
+Options = {
+ CalculateForces = Yes
+ WriteDetailedOut = No
+ WriteBandOut = No
+ RandomSeed = 12345
+}
+
+ParserOptions = {
+ ParserVersion = 3
+}
diff --git a/examples/COUPLE/fortran_dftb/dftb_pin.hsd b/examples/COUPLE/fortran_dftb/dftb_pin.hsd
new file mode 100644
index 0000000000000000000000000000000000000000..6d9dea4a1574f38d4676060a864369086687ff40
--- /dev/null
+++ b/examples/COUPLE/fortran_dftb/dftb_pin.hsd
@@ -0,0 +1,129 @@
+Geometry = GenFormat {
+64 S
+C
+1 1 7.099007 7.117657 7.119139
+2 1 0.858709 0.867233 0.882294
+3 1 1.772527 1.811776 7.120239
+4 1 2.702145 2.681271 0.901362
+5 1 0.017539 1.794455 1.788454
+6 1 0.885593 2.694118 2.707994
+7 1 1.795055 7.120787 1.777896
+8 1 2.642849 0.868278 2.670699
+9 1 0.016060 0.017156 3.568644
+10 1 0.891891 0.896406 4.439286
+11 1 1.766086 1.764402 3.550134
+12 1 2.677349 2.648926 4.427174
+13 1 0.010133 1.771283 5.342173
+14 1 0.858153 2.653565 6.241596
+15 1 1.804087 0.020636 5.353268
+16 1 2.689680 0.907188 6.224575
+17 1 0.017845 3.577563 7.113016
+18 1 0.910027 4.459286 0.910286
+19 1 1.766394 5.376046 0.015526
+20 1 2.683727 6.220728 0.898553
+21 1 0.003357 5.363423 1.774139
+22 1 0.856735 6.238324 2.660213
+23 1 1.761079 3.549776 1.797054
+24 1 2.667227 4.463441 2.646074
+25 1 7.132499 3.551558 3.599764
+26 1 0.920387 4.482191 4.479257
+27 1 1.772194 5.337132 3.555569
+28 1 2.675010 6.251629 4.483124
+29 1 0.005702 5.371095 5.351147
+30 1 0.880807 6.249819 6.264231
+31 1 1.793177 3.592396 5.369939
+32 1 2.653179 4.463595 6.274044
+33 1 3.557243 7.118913 0.026006
+34 1 4.458971 0.889331 0.904950
+35 1 5.367903 1.759757 7.104941
+36 1 6.271565 2.658454 0.890168
+37 1 3.591915 1.768681 1.793880
+38 1 4.435612 2.662184 2.676722
+39 1 5.371040 0.000196 1.783464
+40 1 6.226453 0.886640 2.653384
+41 1 3.583339 0.005449 3.600177
+42 1 4.453692 0.909417 4.459713
+43 1 5.314554 1.805409 3.584215
+44 1 6.210181 2.642660 4.486206
+45 1 3.545704 1.802745 5.365369
+46 1 4.476660 2.701226 6.220451
+47 1 5.332820 0.029557 5.347965
+48 1 6.215725 0.915081 6.230289
+49 1 3.536446 3.551469 7.106600
+50 1 4.451181 4.426439 0.900180
+51 1 5.368735 5.377996 7.109524
+52 1 6.230666 6.220985 0.862175
+53 1 3.596626 5.372822 1.797613
+54 1 4.485613 6.221252 2.699652
+55 1 5.364421 3.549838 1.796281
+56 1 6.261739 4.459046 2.648152
+57 1 3.588752 3.581054 3.581755
+58 1 4.462342 4.467270 4.478800
+59 1 5.355202 5.318323 3.556531
+60 1 6.268570 6.259831 4.465795
+61 1 3.588636 5.354278 5.362327
+62 1 4.475747 6.263866 6.227803
+63 1 5.331158 3.554349 5.318368
+64 1 6.254581 4.436344 6.209681
+0.0 0.0 0.0
+7.13400000000000 0 0
+0 7.13400000000000 0
+0 0 7.13400000000000
+}
+Driver = {}
+Hamiltonian = DFTB {
+ LAMMPS = Yes
+ SCC = No
+ MaxAngularMomentum = {
+ C = "p"
+ }
+ Charge = 0.0
+ Eigensolver = Standard {}
+ Filling = Fermi {
+ Temperature [Kelvin] = 298.0
+ IndependentKFilling = No
+ }
+ SlaterKosterFiles = Type2FileNames {
+ Prefix = "~/slako/mio-1-1/"
+ Separator = "-"
+ Suffix = ".skf"
+ LowerCaseTypeName = No
+ }
+ KPointsAndWeights = {
+0.0000000000000 0.0000000000000 0.0000000000000 1.00000000000000
+ }
+ PolynomialRepulsive = {}
+ OldRepulsiveSum = No
+ OrbitalResolvedSCC = No
+ OldSKInterpolation = No
+ NoErep = No
+ Dispersion = {}
+ ThirdOrder = No
+ ThirdOrderFull = No
+}
+Options = {
+ CalculateForces = Yes
+ WriteDetailedOut = No
+ WriteBandOut = No
+ RandomSeed = 12345
+ MullikenAnalysis = No
+ WriteEigenvectors = No
+ WriteAutotestTag = No
+ WriteDetailedXML = No
+ WriteResultsTag = No
+ AtomResolvedEnergies = No
+ WriteHS = No
+ WriteRealHS = No
+ MinimiseMemoryUsage = No
+ ShowFoldedCoords = No
+}
+ParserOptions = {
+ ParserVersion = 3
+ WriteHSDInput = Yes
+ WriteXMLInput = No
+ StopAfterParsing = No
+ IgnoreUnprocessedNodes = No
+}
+Analysis = {
+ ProjectStates = {}
+}
diff --git a/examples/COUPLE/fortran3/in.simple b/examples/COUPLE/fortran_dftb/in.simple
similarity index 100%
rename from examples/COUPLE/fortran3/in.simple
rename to examples/COUPLE/fortran_dftb/in.simple
diff --git a/examples/COUPLE/fortran_dftb/log.simple b/examples/COUPLE/fortran_dftb/log.simple
new file mode 100644
index 0000000000000000000000000000000000000000..3496e94ebea30edfabf2c716d96beac482cc10a5
--- /dev/null
+++ b/examples/COUPLE/fortran_dftb/log.simple
@@ -0,0 +1,71 @@
+LAMMPS (6 Jul 2017)
+units real
+atom_style charge
+atom_modify map array
+atom_modify sort 0 0.0
+read_data data.diamond
+ triclinic box = (0 0 0) to (7.134 7.134 7.134) with tilt (0 0 0)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 64 atoms
+ reading velocities ...
+ 64 velocities
+neighbor 1.0 bin
+neigh_modify delay 0 every 5 check no
+fix 1 all nve
+fix 2 all external pf/callback 1 1
+
+fix_modify 2 energy yes
+thermo_style custom step temp etotal ke pe lx ly lz pxx pyy pzz press
+
+thermo 1
+timestep 0.5
+
+run 10
+Neighbor list info ...
+ update every 5 steps, delay 0 steps, check no
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 0
+ ghost atom cutoff = 0
+ binsize = 7.134, bins = 1 1 1
+ 0 neighbor lists, perpetual/occasional/extra = 0 0 0
+Per MPI rank memory allocation (min/avg/max) = 2.3 | 2.3 | 2.3 Mbytes
+Step Temp TotEng KinEng PotEng Lx Ly Lz Pxx Pyy Pzz Press
+ 0 298.24835 -69593.587 56.008365 -69649.595 7.134 7.134 7.134 -19980.19 -21024.038 -21097.458 -20700.562
+ 1 295.24358 -69593.585 55.444098 -69649.029 7.134 7.134 7.134 -19778.833 -20799.657 -20854.156 -20477.549
+ 2 286.37211 -69593.58 53.778115 -69647.358 7.134 7.134 7.134 -19227.52 -20177.28 -20176.12 -19860.306
+ 3 272.062 -69593.572 51.090804 -69644.663 7.134 7.134 7.134 -18360.869 -19189.684 -19100.021 -18883.525
+ 4 253.01834 -69593.561 47.514575 -69641.075 7.134 7.134 7.134 -17198.143 -17855.03 -17652.036 -17568.403
+ 5 230.19242 -69593.547 43.228073 -69636.775 7.134 7.134 7.134 -15750.247 -16183.764 -15854.145 -15929.386
+ 6 204.71787 -69593.533 38.44418 -69631.977 7.134 7.134 7.134 -14083.498 -14247.434 -13789.835 -14040.256
+ 7 177.82397 -69593.518 33.393748 -69626.911 7.134 7.134 7.134 -12340.963 -12202.878 -11623.171 -12055.671
+ 8 150.76736 -69593.503 28.312758 -69621.816 7.134 7.134 7.134 -10637.824 -10180.827 -9495.0496 -10104.567
+ 9 124.7737 -69593.49 23.431383 -69616.921 7.134 7.134 7.134 -9113.3842 -8339.0492 -7572.8076 -8341.747
+ 10 100.98183 -69593.478 18.963481 -69612.442 7.134 7.134 7.134 -7833.9349 -6756.9749 -5945.8968 -6845.6022
+Loop time of 2.20497 on 1 procs for 10 steps with 64 atoms
+
+Performance: 0.196 ns/day, 122.499 hours/ns, 4.535 timesteps/s
+0.2% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 1.4305e-06 | 1.4305e-06 | 1.4305e-06 | 0.0 | 0.00
+Comm | 4.22e-05 | 4.22e-05 | 4.22e-05 | 0.0 | 0.00
+Output | 0.00067687 | 0.00067687 | 0.00067687 | 0.0 | 0.03
+Modify | 2.2042 | 2.2042 | 2.2042 | 0.0 | 99.96
+Other | | 6.533e-05 | | | 0.00
+
+Nlocal: 64 ave 64 max 64 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 2
+Dangerous builds not checked
+Total wall time: 0:00:02
diff --git a/examples/COUPLE/fortran3/makefile b/examples/COUPLE/fortran_dftb/makefile
similarity index 95%
rename from examples/COUPLE/fortran3/makefile
rename to examples/COUPLE/fortran_dftb/makefile
index 86dea30850676c3a58fee935ca6da612e7c2476d..225bd0025a5de954e3f4cde904f5d87bb875d76e 100644
--- a/examples/COUPLE/fortran3/makefile
+++ b/examples/COUPLE/fortran_dftb/makefile
@@ -21,7 +21,7 @@ liblammps_fortran.so : LAMMPS.o LAMMPS-wrapper.o LAMMPS-wrapper2.o
$(FC) $(FFLAGS) -shared -o $@ $^
simpleF.x: simple.o LAMMPS.o LAMMPS-wrapper.o LAMMPS-wrapper2.o
- $(FC) $(FFLAGS) simple.o -o simpleF.x liblammps_fortran.a $(LAMMPS_SRC)/liblammps_mvapich.a -lstdc++ /usr/local/tools/fftw/lib/libfftw.a
+ $(FC) $(FFLAGS) simple.o -o simpleF.x liblammps_fortran.a $(LAMMPS_SRC)/liblammps_mvapich.a -lstdc++ /usr/lib64/libfftw3.a
liblammps_fortran.a : LAMMPS.o LAMMPS-wrapper.o LAMMPS-wrapper2.o
$(AR) rs $@ $^
diff --git a/examples/COUPLE/fortran3/simple.f90 b/examples/COUPLE/fortran_dftb/simple.f90
similarity index 91%
rename from examples/COUPLE/fortran3/simple.f90
rename to examples/COUPLE/fortran_dftb/simple.f90
index 40f8bf8b86dedb840becd448ad367df30a56a5b0..4604b4e4a989b6d595208a60c22cc554d675d370 100644
--- a/examples/COUPLE/fortran3/simple.f90
+++ b/examples/COUPLE/fortran_dftb/simple.f90
@@ -13,7 +13,7 @@
type(c_ptr) :: c_pos, c_fext, c_ids
double precision, pointer :: fext(:,:), pos(:,:)
integer, intent(in) :: ids(nlocal)
- real (C_double), dimension(:), pointer :: virial => NULL()
+ real(C_double) :: virial(6)
real (C_double) :: etot
real(C_double), pointer :: ts_lmp
double precision :: stress(3,3), ts_dftb
@@ -61,26 +61,21 @@
read(10,*)stress(i,:)
enddo
stress (:,:) = stress(:,:)*autoatm
+ virial(1) = stress(1,1)/(nktv2p/volume)
+ virial(2) = stress(2,2)/(nktv2p/volume)
+ virial(3) = stress(3,3)/(nktv2p/volume)
+ virial(4) = stress(1,2)/(nktv2p/volume)
+ virial(5) = stress(1,3)/(nktv2p/volume)
+ virial(6) = stress(2,3)/(nktv2p/volume)
etot = etot*econv
- call lammps_extract_global(ts_lmp, lmp, 'TS_dftb')
- ts_lmp = ts_dftb
+ call lammps_set_external_vector(lmp,1,ts_dftb*econv)
do i = 1, nlocal
read(10,*)fext(:,ids(i))
fext(:,ids(i)) = fext(:,ids(i))*fconv
enddo
close(10)
call lammps_set_user_energy (lmp, etot)
- call lammps_extract_atom (virial, lmp, 'virial')
- if (.not. associated(virial)) then
- print*,'virial pointer not associated.'
- STOP
- endif
- virial(1) = stress(1,1)/(nktv2p/volume)
- virial(2) = stress(2,2)/(nktv2p/volume)
- virial(3) = stress(3,3)/(nktv2p/volume)
- virial(4) = stress(1,2)/(nktv2p/volume)
- virial(5) = stress(1,3)/(nktv2p/volume)
- virial(6) = stress(2,3)/(nktv2p/volume)
+ call lammps_set_user_virial (lmp, virial)
end subroutine
end module callback
@@ -103,6 +98,7 @@ program simple_fortran_callback
call lammps_open_no_mpi ('lmp -log log.simple', lmp)
call lammps_file (lmp, 'in.simple')
call lammps_set_callback(lmp)
+ call lammps_set_external_vector_length(lmp,2)
call lammps_command (lmp, 'run 10')
call lammps_close (lmp)
diff --git a/lib/colvars/Install.py b/lib/colvars/Install.py
index af658fa26cef42b3658bbdb0868cb8d2efc1ec30..18b426f9282819ce196b6cf030aef477e3769d66 100644
--- a/lib/colvars/Install.py
+++ b/lib/colvars/Install.py
@@ -1,34 +1,27 @@
#!/usr/bin/env python
-# Install.py tool to do automate build of Colvars
+# install.py tool to do a generic build of a library
+# soft linked to by many of the lib/Install.py files
+# used to automate the steps described in the corresponding lib/README
-from __future__ import print_function
-import sys,os,subprocess
+import sys,commands,os
# help message
help = """
-Syntax from src dir: make lib-colvars args="-m machine -e suffix"
-Syntax from lib/colvars dir: python Install.py -m machine -e suffix
-
-specify -m and optionally -e, order does not matter
-
+Syntax: python Install.py -m machine -e suffix
+ specify -m and optionally -e, order does not matter
-m = peform a clean followed by "make -f Makefile.machine"
- machine = suffix of a lib/colvars/Makefile.* or of a
- src/MAKE/MACHINES/Makefile.* file
+ machine = suffix of a lib/Makefile.* file
-e = set EXTRAMAKE variable in Makefile.machine to Makefile.lammps.suffix
does not alter existing Makefile.machine
-
-Examples:
-
-make lib-colvars args="-m g++" # build COLVARS lib with GNU g++ compiler
"""
# print error message or help
def error(str=None):
- if not str: print(help)
- else: print("ERROR"),str
+ if not str: print help
+ else: print "ERROR",str
sys.exit()
# parse args
@@ -38,17 +31,17 @@ nargs = len(args)
if nargs == 0: error()
machine = None
-extraflag = False
+extraflag = 0
iarg = 0
while iarg < nargs:
if args[iarg] == "-m":
- if iarg+2 > len(args): error()
+ if iarg+2 > nargs: error()
machine = args[iarg+1]
iarg += 2
elif args[iarg] == "-e":
- if iarg+2 > len(args): error()
- extraflag = True
+ if iarg+2 > nargs: error()
+ extraflag = 1
suffix = args[iarg+1]
iarg += 2
else: error()
@@ -58,85 +51,32 @@ while iarg < nargs:
cwd = os.getcwd()
lib = os.path.basename(cwd)
-def get_lammps_machine_flags(machine):
- """Parse Makefile.machine from LAMMPS, return dictionary of compiler flags"""
- if not os.path.exists("../../src/MAKE/MACHINES/Makefile.%s" % machine):
- error("Cannot locate src/MAKE/MACHINES/Makefile.%s" % machine)
- lines = open("../../src/MAKE/MACHINES/Makefile.%s" % machine,
- 'r').readlines()
- machine_flags = {}
- for line in lines:
- line = line.partition('#')[0]
- line = line.rstrip()
- words = line.split()
- if (len(words) > 2):
- if ((words[0] == 'CC') or (words[0] == 'CCFLAGS') or
- (words[0] == 'SHFLAGS') or (words[0] == 'ARCHIVE') or
- (words[0] == 'ARFLAGS') or (words[0] == 'SHELL')):
- machine_flags[words[0]] = ' '.join(words[2:])
- return machine_flags
-
-def gen_colvars_makefile_machine(machine, machine_flags):
- """Generate Makefile.machine for Colvars given the compiler flags"""
- machine_makefile = open("Makefile.%s" % machine, 'w')
- machine_makefile.write('''# -*- makefile -*- to build Colvars module with %s
-
-COLVARS_LIB = libcolvars.a
-COLVARS_OBJ_DIR =
-
-CXX = %s
-CXXFLAGS = %s %s
-AR = %s
-ARFLAGS = %s
-SHELL = %s
-
-include Makefile.common
-
-.PHONY: default clean
-
-default: $(COLVARS_LIB) Makefile.lammps
-
-clean:
- -rm -f $(COLVARS_OBJS) $(COLVARS_LIB)
-''' % (machine, machine_flags['CC'],
- machine_flags['CCFLAGS'], machine_flags['SHFLAGS'] ,
- machine_flags['ARCHIVE'], machine_flags['ARFLAGS'],
- machine_flags['SHELL']))
-
-if not os.path.exists("Makefile.%s" % machine):
- machine_flags = get_lammps_machine_flags(machine)
- gen_colvars_makefile_machine(machine, machine_flags)
-if not os.path.exists("Makefile.%s" % machine):
- error("lib/%s/Makefile.%s does not exist" % (lib,machine))
-
# create Makefile.auto as copy of Makefile.machine
# reset EXTRAMAKE if requested
+
+if not os.path.exists("Makefile.%s" % machine):
+ error("lib/%s/Makefile.%s does not exist" % (lib,machine))
lines = open("Makefile.%s" % machine,'r').readlines()
fp = open("Makefile.auto",'w')
+
for line in lines:
words = line.split()
if len(words) == 3 and extraflag and \
words[0] == "EXTRAMAKE" and words[1] == '=':
line = line.replace(words[2],"Makefile.lammps.%s" % suffix)
- fp.write(line)
+ print >>fp,line,
+
fp.close()
# make the library via Makefile.auto
-try:
- import multiprocessing
- n_cpus = multiprocessing.cpu_count()
-except:
- n_cpus = 1
-
-print("Building lib%s.a ..." % lib)
-cmd = ["make -f Makefile.auto clean"]
-print(subprocess.check_output(cmd, shell=True).decode())
-cmd = ["make -f Makefile.auto -j%d" % n_cpus]
-print(subprocess.check_output(cmd, shell=True).decode())
+print "Building lib%s.a ..." % lib
+cmd = "make -f Makefile.auto clean; make -f Makefile.auto"
+txt = commands.getoutput(cmd)
+print txt
-if os.path.exists("lib%s.a" % lib): print("Build was successful")
+if os.path.exists("lib%s.a" % lib): print "Build was successful"
else: error("Build of lib/%s/lib%s.a was NOT successful" % (lib,lib))
if not os.path.exists("Makefile.lammps"):
- print("lib/%s/Makefile.lammps was NOT created" % lib)
+ print "lib/%s/Makefile.lammps was NOT created" % lib