diff --git a/doc/src/Section_accelerate.txt b/doc/src/Section_accelerate.txt
index 8812358886e5f867e7fa3e002130c74ad828d877..bb0c93b8aa2b744dcd4ad0e1ec650138defee9d0 100644
--- a/doc/src/Section_accelerate.txt
+++ b/doc/src/Section_accelerate.txt
@@ -233,8 +233,8 @@ set any needed options for the package via "-pk" "command-line switch"_Section_s
use accelerated styles in your input via "-sf" "command-line switch"_Section_start.html#start_6 or "suffix"_suffix.html command | lmp_machine -in in.script -sf gpu
:tb(c=2,s=|)
-Note that the first 4 steps can be done as a single command, using the
-src/Make.py tool. This tool is discussed in "Section
+Note that the first 4 steps can be done as a single command with
+suitable make command invocations. This is discussed in "Section
4"_Section_packages.html of the manual, and its use is
illustrated in the individual accelerator sections. Typically these
steps only need to be done once, to create an executable that uses one
diff --git a/doc/src/Section_example.txt b/doc/src/Section_example.txt
index 26dc3b96985afbf2c3fe7956d7f395b66be07229..f8b39be1738c46a31ba27d37bbb1af62ab3d9bf9 100644
--- a/doc/src/Section_example.txt
+++ b/doc/src/Section_example.txt
@@ -49,6 +49,7 @@ Lists of both kinds of directories are given below.
Lowercase directories :h4
accelerate: run with various acceleration options (OpenMP, GPU, Phi)
+airebo: polyethylene with AIREBO potential
balance: dynamic load balancing, 2d system
body: body particles, 2d system
cmap: CMAP 5-body contributions to CHARMM force field
diff --git a/doc/src/Section_packages.txt b/doc/src/Section_packages.txt
index 6afcb2758d95bfe7fc25000b64337bf4e32b0ea4..ea7b41b0affe15ad12f2c1c6606888d1ea988cf3 100644
--- a/doc/src/Section_packages.txt
+++ b/doc/src/Section_packages.txt
@@ -80,7 +80,7 @@ Package, Description, Doc page, Example, Library
"DIPOLE"_#DIPOLE, point dipole particles, "pair_style dipole/cut"_pair_dipole.html, dipole, -
"GPU"_#GPU, GPU-enabled styles, "Section 5.3.1"_accelerate_gpu.html, WWW bench, int
"GRANULAR"_#GRANULAR, granular systems, "Section 6.6.6"_Section_howto.html#howto_6, pour, -
-"KIM"_#KIM, openKIM wrapper, "pair_style kim"_pair_kim.html, kim, ext
+"KIM"_#KIM, OpenKIM wrapper, "pair_style kim"_pair_kim.html, kim, ext
"KOKKOS"_#KOKKOS, Kokkos-enabled styles, "Section 5.3.3"_accelerate_kokkos.html, WWW bench, -
"KSPACE"_#KSPACE, long-range Coulombic solvers, "kspace_style"_kspace_style.html, peptide, -
"MANYBODY"_#MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, -
@@ -1438,7 +1438,7 @@ lib/linalg. In the latter case you also need to build the library
in lib/linalg with a command like these:
make lib-linalg # print help message
-make lib-atc args="-m gfortran" # build with GNU Fortran compiler
+make lib-linalg args="-m gfortran" # build with GNU Fortran compiler
You can then install/un-install the package and build LAMMPS in the
usual manner:
@@ -2493,8 +2493,8 @@ step from the lammps/src dir, using a command like these, which simply
invoke the lib/smd/Install.py script with the specified args:
make lib-smd # print help message
-make lib-smd args="-g -l" # download in default lib/smd/eigen-eigen-*
-make lib-smd args="-h . eigen -g -l" # download in lib/smd/eigen
+make lib-smd args="-g -l" # download and build in default lib/smd/eigen-eigen-*
+make lib-smd args="-h . eigen -g -l" # download and build in lib/smd/eigen
make lib-smd args="-h ~ eigen -g -l" # download and build in ~/eigen :pre
Note that the final -l switch is to create a symbolic (soft) link
diff --git a/doc/src/accelerate_gpu.txt b/doc/src/accelerate_gpu.txt
index 68e9fa477a2a6d52e4ab8db10f50b935bab37adf..2723b6e971972e0147c57072ffb559f1f2a42f9d 100644
--- a/doc/src/accelerate_gpu.txt
+++ b/doc/src/accelerate_gpu.txt
@@ -74,13 +74,8 @@ Run lammps/lib/gpu/nvc_get_devices (after building the GPU library, see below) t
This requires two steps (a,b): build the GPU library, then build
LAMMPS with the GPU package.
-You can do both these steps in one line, using the src/Make.py script,
-described in "Section 4"_Section_packages.html of the manual.
-Type "Make.py -h" for help. If run from the src directory, this
-command will create src/lmp_gpu using src/MAKE/Makefile.mpi as the
-starting Makefile.machine:
-
-Make.py -p gpu -gpu mode=single arch=31 -o gpu -a lib-gpu file mpi :pre
+You can do both these steps in one line as described in
+"Section 4"_Section_packages.html of the manual.
Or you can follow these two (a,b) steps:
diff --git a/doc/src/accelerate_intel.txt b/doc/src/accelerate_intel.txt
index 74ae9d9a4249d825922d36d38ba71b798fbc1b95..9eb295e0d08d022201149b2cc2912cae7f78dcf5 100644
--- a/doc/src/accelerate_intel.txt
+++ b/doc/src/accelerate_intel.txt
@@ -225,11 +225,9 @@ source /opt/intel/parallel_studio_xe_2016.3.067/psxevars.sh
# or psxevars.csh for C-shell
make intel_cpu_intelmpi :pre
-Alternatively, the build can be accomplished with the src/Make.py
-script, described in "Section 4"_Section_packages.html of the
-manual. Type "Make.py -h" for help. For an example:
-
-Make.py -v -p intel omp -intel cpu -a file intel_cpu_intelmpi :pre
+Alternatively this can be done as a single command with
+suitable make command invocations. This is discussed in "Section
+4"_Section_packages.html of the manual.
Note that if you build with support for a Phi coprocessor, the same
binary can be used on nodes with or without coprocessors installed.
@@ -244,8 +242,7 @@ highly recommended for CCFLAGS and LINKFLAGS. LIB should include
is required for CCFLAGS and "-qoffload" is required for LINKFLAGS.
Other recommended CCFLAG options for best performance are
"-O2 -fno-alias -ansi-alias -qoverride-limits fp-model fast=2
--no-prec-div". The Make.py command will add all of these
-automatically.
+-no-prec-div".
NOTE: The vectorization and math capabilities can differ depending on
the CPU. For Intel compilers, the "-x" flag specifies the type of
diff --git a/doc/src/accelerate_kokkos.txt b/doc/src/accelerate_kokkos.txt
index 6ccd6958411523d0a6b958eab78b88ff4a32f72c..712a05300c7a90230db0ea601a64eba504d05272 100644
--- a/doc/src/accelerate_kokkos.txt
+++ b/doc/src/accelerate_kokkos.txt
@@ -60,8 +60,7 @@ More details follow.
use a C++11 compatible compiler
make yes-kokkos
make mpi KOKKOS_DEVICES=OpenMP # build with the KOKKOS package
-make kokkos_omp # or Makefile.kokkos_omp already has variable set
-Make.py -v -p kokkos -kokkos omp -o mpi -a file mpi # or one-line build via Make.py :pre
+make kokkos_omp # or Makefile.kokkos_omp already has variable set :pre
mpirun -np 16 lmp_mpi -k on -sf kk -in in.lj # 1 node, 16 MPI tasks/node, no threads
mpirun -np 2 -ppn 1 lmp_mpi -k on t 16 -sf kk -in in.lj # 2 nodes, 1 MPI task/node, 16 threads/task
@@ -82,8 +81,7 @@ use a C++11 compatible compiler
KOKKOS_DEVICES = Cuda, OpenMP
KOKKOS_ARCH = Kepler35
make yes-kokkos
-make machine
-Make.py -p kokkos -kokkos cuda arch=31 -o kokkos_cuda -a file kokkos_cuda :pre
+make machine :pre
mpirun -np 1 lmp_cuda -k on t 6 -sf kk -in in.lj # one MPI task, 6 threads on CPU
mpirun -np 4 -ppn 1 lmp_cuda -k on t 6 -sf kk -in in.lj # ditto on 4 nodes :pre
@@ -98,8 +96,7 @@ use a C++11 compatible compiler
KOKKOS_DEVICES = OpenMP
KOKKOS_ARCH = KNC
make yes-kokkos
-make machine
-Make.py -p kokkos -kokkos phi -o kokkos_phi -a file mpi :pre
+make machine :pre
host=MIC, Intel Phi with 61 cores (240 threads/phi via 4x hardware threading):
mpirun -np 1 lmp_g++ -k on t 240 -sf kk -in in.lj # 1 MPI task on 1 Phi, 1*240 = 240
@@ -135,9 +132,9 @@ mode like the USER-INTEL package supports.
You must choose at build time whether to build for CPUs (OpenMP),
GPUs, or Phi.
-You can do any of these in one line, using the src/Make.py script,
-described in "Section 4"_Section_packages.html of the manual.
-Type "Make.py -h" for help. If run from the src directory, these
+You can do any of these in one line, using the suitable make command
+line flags as described in "Section 4"_Section_packages.html of the
+manual. If run from the src directory, these
commands will create src/lmp_kokkos_omp, lmp_kokkos_cuda, and
lmp_kokkos_phi. Note that the OMP and PHI options use
src/MAKE/Makefile.mpi as the starting Makefile.machine. The CUDA
diff --git a/doc/src/accelerate_omp.txt b/doc/src/accelerate_omp.txt
index 81b7a5adc28ac9740edea7b0f084e7547bf25fcc..fa7bef1a520bd867b4d3cf610d50b5ea8614c865 100644
--- a/doc/src/accelerate_omp.txt
+++ b/doc/src/accelerate_omp.txt
@@ -23,8 +23,7 @@ one or more 16-core nodes. More details follow.
use -fopenmp with CCFLAGS and LINKFLAGS in Makefile.machine
make yes-user-omp
make mpi # build with USER-OMP package, if settings added to Makefile.mpi
-make omp # or Makefile.omp already has settings
-Make.py -v -p omp -o mpi -a file mpi # or one-line build via Make.py :pre
+make omp # or Makefile.omp already has settings :pre
lmp_mpi -sf omp -pk omp 16 < in.script # 1 MPI task, 16 threads
mpirun -np 4 lmp_mpi -sf omp -pk omp 4 -in in.script # 4 MPI tasks, 4 threads/task
@@ -40,14 +39,11 @@ each MPI task running on a CPU.
The lines above illustrate how to include/build with the USER-OMP
package in two steps, using the "make" command. Or how to do it with
-one command via the src/Make.py script, described in "Section
-4"_Section_packages.html of the manual. Type "Make.py -h" for
-help.
+one command as described in "Section 4"_Section_packages.html of the manual.
Note that the CCFLAGS and LINKFLAGS settings in Makefile.machine must
include "-fopenmp". Likewise, if you use an Intel compiler, the
-CCFLAGS setting must include "-restrict". The Make.py command will
-add these automatically.
+CCFLAGS setting must include "-restrict".
[Run with the USER-OMP package from the command line:]
diff --git a/doc/src/accelerate_opt.txt b/doc/src/accelerate_opt.txt
index 5a2a5eac0a971be2ba5e2b0fc8a418bdba550d2b..845264b5227ca31493cb582eac91ab5c216427ae 100644
--- a/doc/src/accelerate_opt.txt
+++ b/doc/src/accelerate_opt.txt
@@ -21,8 +21,7 @@ Here is a quick overview of how to use the OPT package. More details
follow.
make yes-opt
-make mpi # build with the OPT package
-Make.py -v -p opt -o mpi -a file mpi # or one-line build via Make.py :pre
+make mpi # build with the OPT package :pre
lmp_mpi -sf opt -in in.script # run in serial
mpirun -np 4 lmp_mpi -sf opt -in in.script # run in parallel :pre
@@ -35,13 +34,10 @@ None.
The lines above illustrate how to build LAMMPS with the OPT package in
two steps, using the "make" command. Or how to do it with one command
-via the src/Make.py script, described in "Section
-4"_Section_packages.html of the manual. Type "Make.py -h" for
-help.
+as described in "Section 4"_Section_packages.html of the manual.
Note that if you use an Intel compiler to build with the OPT package,
the CCFLAGS setting in your Makefile.machine must include "-restrict".
-The Make.py command will add this automatically.
[Run with the OPT package from the command line:]
diff --git a/doc/src/compute_voronoi_atom.txt b/doc/src/compute_voronoi_atom.txt
index d084fcee66e7edbe1c794fb88e537b7621c1a0b5..a280b2b151d7e7656a421e8007f04c1eed464c90 100644
--- a/doc/src/compute_voronoi_atom.txt
+++ b/doc/src/compute_voronoi_atom.txt
@@ -217,7 +217,7 @@ This compute is part of the VORONOI package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
-It also requiers you have a copy of the Voro++ library built and
+It also requires you have a copy of the Voro++ library built and
installed on your system. See instructions on obtaining and
installing the Voro++ software in the src/VORONOI/README file.
diff --git a/doc/src/fix_msst.txt b/doc/src/fix_msst.txt
index 025c733897a6ec7a14ff21edbeafbeeb7536c073..310692669abb39aaebb7e3596ee7f0b9e8cdf865 100644
--- a/doc/src/fix_msst.txt
+++ b/doc/src/fix_msst.txt
@@ -75,7 +75,7 @@ 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
+thermostat. See "(Reed)"_#Reed and "(Goldman)"_#Goldman2 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.
@@ -108,7 +108,7 @@ 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,
+"(Goldman)"_#Goldman2 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.
@@ -188,6 +188,6 @@ timestep.
:link(Reed2)
[(Reed2)] Reed, J. Phys. Chem. C, 116, 2205 (2012).
-:link(Goldman)
+:link(Goldman2)
[(Goldman)] Goldman, Srinivasan, Hamel, Fried, Gaus, and Elstner,
J. Phys. Chem. C, 117, 7885 (2013).
diff --git a/doc/src/fix_qbmsst.txt b/doc/src/fix_qbmsst.txt
index 468206a57bba711708efb746111fb780dc89974f..2c116fb0f8cf34f6e29143035d0c9cc7414e2750 100644
--- a/doc/src/fix_qbmsst.txt
+++ b/doc/src/fix_qbmsst.txt
@@ -78,7 +78,7 @@ especially when the temperature of the initial state is below the
classical limit or there is a great change in the zero point energies
between the initial and final states. Theoretical post processing
quantum corrections of shock compressed water and methane have been
-reported as much as 30% of the temperatures "(Goldman)"_#Goldman. A
+reported as much as 30% of the temperatures "(Goldman)"_#Goldman1. A
self-consistent method that couples the shock to a quantum thermal
bath described by a colored noise Langevin thermostat has been
developed by Qi et al "(Qi)"_#Qi and applied to shocked methane. The
@@ -212,7 +212,7 @@ T_init=300.0. e0, p0, and v0 are calculated on the first step.
:line
-:link(Goldman)
+:link(Goldman1)
[(Goldman)] Goldman, Reed and Fried, J. Chem. Phys. 131, 204103 (2009)
:link(Qi)
diff --git a/doc/src/neigh_modify.txt b/doc/src/neigh_modify.txt
index 5c149d892ddbbc2d35be8af744d1beab3f812e27..c4544cb29bde3ccf25b708e7d2ad552fc97e7eea 100644
--- a/doc/src/neigh_modify.txt
+++ b/doc/src/neigh_modify.txt
@@ -109,7 +109,8 @@ atoms in the specified group. This can be useful for models where a
large portion of the simulation is particles that do not interact with
other particles or with each other via pairwise interactions. The
group specified with this option must also be specified via the
-"atom_modify first"_atom_modify.html command.
+"atom_modify first"_atom_modify.html command. Note that specifying
+"all" as the group-ID effectively turns off the {include} option.
The {exclude} option turns off pairwise interactions between certain
pairs of atoms, by not including them in the neighbor list. These are
@@ -213,5 +214,5 @@ space.
[Default:]
The option defaults are delay = 10, every = 1, check = yes, once = no,
-cluster = no, include = all, exclude = none, page = 100000, one =
-2000, and binsize = 0.0.
+cluster = no, include = all (same as no include option defined),
+exclude = none, page = 100000, one = 2000, and binsize = 0.0.
diff --git a/doc/src/pair_kim.txt b/doc/src/pair_kim.txt
index 5a623e5ece39d4b482b9fa11a40921639df4b938..c5d910e27c841f9d71e5e6dfd160bfce0a949b46 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 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/README b/examples/README
index 0b037f5c387b58226ebf47c708800b08044374bb..dc622ef7c4945b50f773c6347c16956a9273c109 100644
--- a/examples/README
+++ b/examples/README
@@ -58,7 +58,7 @@ These are the sample problems and their output in the various
sub-directories:
accelerate: use of all the various accelerator packages
-airebo: example for using AIREBO and AIREBO-M
+airebo: polyethylene with AIREBO potential
balance: dynamic load balancing, 2d system
body: body particles, 2d system
cmap: CMAP 5-body contributions to CHARMM force field
diff --git a/examples/USER/quip/in.gap b/examples/USER/quip/in.gap
index 37667e39b94bc041381ab7510f1c0e28a955ecb2..dd049a473704dbef392095746bdc1578e4bec736 100644
--- a/examples/USER/quip/in.gap
+++ b/examples/USER/quip/in.gap
@@ -17,6 +17,6 @@ fix 1 all nve
thermo 10
timestep 0.001
-dump 1 all custom 10 dump.gap id fx fy fz
+#dump 1 all custom 10 dump.gap id fx fy fz
run 40
diff --git a/examples/USER/quip/in.molecular b/examples/USER/quip/in.molecular
index 24d21d6762d8aa010e2edc13708f3ca5d0852c78..4253399d7c7c517160b06061c500c1cd4e1a715c 100644
--- a/examples/USER/quip/in.molecular
+++ b/examples/USER/quip/in.molecular
@@ -1,7 +1,6 @@
units metal
atom_style full
boundary p p p
-processors 1 1 1
timestep 0.0001 # 0.1 fs
read_data methane-box-8.data
@@ -28,7 +27,7 @@ pair_modify pair lj/cut special lj/coul 0.0 0.0 0.0
# Intramolecular
# Tell QUIP to pretend this is silane (which is covered by the parameter file)
-pair_coeff * * quip ip.parms.SW.xml "IP SW" 14 1
+pair_coeff * * quip sw_example.xml "IP SW" 14 1
bond_style none
angle_style none
diff --git a/examples/USER/quip/in.sw b/examples/USER/quip/in.sw
index c1367ac8055e2452632dabbc6a3c7b60b0e31483..aaa4217b2ff81f1bff71e86eba7d0fb3138a4c7e 100644
--- a/examples/USER/quip/in.sw
+++ b/examples/USER/quip/in.sw
@@ -10,6 +10,7 @@ read_data data_sw
pair_style quip
pair_coeff * * sw_example.xml "IP SW" 14
+velocity all create 10.0 355311
neighbor 0.3 bin
neigh_modify delay 10
@@ -17,6 +18,6 @@ fix 1 all nve
thermo 10
timestep 0.001
-dump 1 all custom 10 dump.sw id fx fy fz
+#dump 1 all custom 10 dump.sw id fx fy fz
-run 1
+run 100
diff --git a/examples/USER/quip/log.24Jul17.gap.g++.1 b/examples/USER/quip/log.24Jul17.gap.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..348f2ae0ccf1d7fc63fd5fb817703d52a2d35101
--- /dev/null
+++ b/examples/USER/quip/log.24Jul17.gap.g++.1
@@ -0,0 +1,76 @@
+LAMMPS (24 Jul 2017)
+ using 1 OpenMP thread(s) per MPI task
+# Test of GAP potential for Si system
+
+units metal
+boundary p p p
+
+atom_style atomic
+
+read_data data_gap
+ orthogonal box = (0 0 0) to (10.9685 10.9685 10.9685)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 64 atoms
+
+pair_style quip
+pair_coeff * * gap_example.xml "Potential xml_label=GAP_2015_2_20_0_10_54_35_765" 14
+
+neighbor 0.3 bin
+neigh_modify delay 10
+
+fix 1 all nve
+thermo 10
+timestep 0.001
+
+#dump 1 all custom 10 dump.gap id fx fy fz
+
+run 40
+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
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair quip, perpetual
+ attributes: full, newton on
+ pair build: full/bin/atomonly
+ stencil: full/bin/3d
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.689 | 2.689 | 2.689 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 0 -10412.677 0 -10412.677 -107490.01
+ 10 173.98393 -10414.096 0 -10412.679 -91270.969
+ 20 417.38493 -10416.08 0 -10412.681 -42816.133
+ 30 434.34789 -10416.217 0 -10412.68 2459.83
+ 40 423.05899 -10416.124 0 -10412.679 22936.209
+Loop time of 1.83555 on 1 procs for 40 steps with 64 atoms
+
+Performance: 1.883 ns/day, 12.747 hours/ns, 21.792 timesteps/s
+98.1% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 1.8349 | 1.8349 | 1.8349 | 0.0 | 99.96
+Neigh | 0.00022817 | 0.00022817 | 0.00022817 | 0.0 | 0.01
+Comm | 0.00013709 | 0.00013709 | 0.00013709 | 0.0 | 0.01
+Output | 9.8228e-05 | 9.8228e-05 | 9.8228e-05 | 0.0 | 0.01
+Modify | 8.6308e-05 | 8.6308e-05 | 8.6308e-05 | 0.0 | 0.00
+Other | | 0.0001223 | | | 0.01
+
+Nlocal: 64 ave 64 max 64 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 303 ave 303 max 303 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
+FullNghs: 1080 ave 1080 max 1080 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1080
+Ave neighs/atom = 16.875
+Neighbor list builds = 2
+Dangerous builds = 0
+Total wall time: 0:00:01
diff --git a/examples/USER/quip/log.24Jul17.gap.g++.4 b/examples/USER/quip/log.24Jul17.gap.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..a8127148b5a3e39e112b370658c4f192ea68a4b0
--- /dev/null
+++ b/examples/USER/quip/log.24Jul17.gap.g++.4
@@ -0,0 +1,76 @@
+LAMMPS (24 Jul 2017)
+ using 1 OpenMP thread(s) per MPI task
+# Test of GAP potential for Si system
+
+units metal
+boundary p p p
+
+atom_style atomic
+
+read_data data_gap
+ orthogonal box = (0 0 0) to (10.9685 10.9685 10.9685)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 64 atoms
+
+pair_style quip
+pair_coeff * * gap_example.xml "Potential xml_label=GAP_2015_2_20_0_10_54_35_765" 14
+
+neighbor 0.3 bin
+neigh_modify delay 10
+
+fix 1 all nve
+thermo 10
+timestep 0.001
+
+#dump 1 all custom 10 dump.gap id fx fy fz
+
+run 40
+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
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair quip, perpetual
+ attributes: full, newton on
+ pair build: full/bin/atomonly
+ stencil: full/bin/3d
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.685 | 2.779 | 3.06 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 0 -10412.677 0 -10412.677 -107490.01
+ 10 173.98393 -10414.096 0 -10412.679 -91270.969
+ 20 417.38493 -10416.08 0 -10412.681 -42816.133
+ 30 434.34789 -10416.217 0 -10412.68 2459.83
+ 40 423.05899 -10416.124 0 -10412.679 22936.209
+Loop time of 0.837345 on 4 procs for 40 steps with 64 atoms
+
+Performance: 4.127 ns/day, 5.815 hours/ns, 47.770 timesteps/s
+96.0% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.73144 | 0.79214 | 0.83586 | 4.3 | 94.60
+Neigh | 5.7936e-05 | 6.5327e-05 | 7.1049e-05 | 0.0 | 0.01
+Comm | 0.00085807 | 0.044631 | 0.10532 | 18.0 | 5.33
+Output | 0.00013208 | 0.00013494 | 0.00013733 | 0.0 | 0.02
+Modify | 6.0558e-05 | 7.8678e-05 | 9.5129e-05 | 0.0 | 0.01
+Other | | 0.0002971 | | | 0.04
+
+Nlocal: 16 ave 18 max 14 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+Nghost: 174 ave 182 max 167 min
+Histogram: 1 0 0 0 2 0 0 0 0 1
+Neighs: 0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs: 270 ave 294 max 237 min
+Histogram: 1 0 0 0 1 0 0 0 1 1
+
+Total # of neighbors = 1080
+Ave neighs/atom = 16.875
+Neighbor list builds = 2
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/USER/quip/log.24Jul17.molecular.g++.1 b/examples/USER/quip/log.24Jul17.molecular.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..28fc63579b8dfb43e02b2cd36152157c12afad0b
--- /dev/null
+++ b/examples/USER/quip/log.24Jul17.molecular.g++.1
@@ -0,0 +1,130 @@
+LAMMPS (24 Jul 2017)
+ using 1 OpenMP thread(s) per MPI task
+units metal
+atom_style full
+boundary p p p
+timestep 0.0001 # 0.1 fs
+
+read_data methane-box-8.data
+ orthogonal box = (-0.499095 -0.270629 0.131683) to (8.4109 8.63937 9.04168)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 40 atoms
+ scanning bonds ...
+ 4 = max bonds/atom
+ scanning angles ...
+ 6 = max angles/atom
+ reading bonds ...
+ 32 bonds
+ reading angles ...
+ 48 angles
+ 4 = max # of 1-2 neighbors
+ 3 = max # of 1-3 neighbors
+ 3 = max # of 1-4 neighbors
+ 4 = max # of special neighbors
+
+# DISCLAIMER: This potential mixes parameters from methane and silane
+# potentials and is NOT intended to be a realistic representation of either
+# system. It is meant to demonstrate the use of hybrid QUIP/LAMMPS potentials,
+# including the use of separate 'special_bonds' settings.
+
+pair_style hybrid/overlay lj/cut 8.0 quip
+
+# exclusion setting for quip; cannot be exactly 1.0 1.0 1.0,
+# since that would not flag 1-2, 1-3, and 1-4 pairs in lj/cut
+special_bonds lj/coul 0.999999999 0.999999999 0.999999999
+ 4 = max # of 1-2 neighbors
+ 3 = max # of 1-3 neighbors
+ 3 = max # of 1-4 neighbors
+ 4 = max # of special neighbors
+
+# Intermolecular: OPLS (JACS 118 (45), p. 11225 (1996))
+# Coulomb interactions ommitted for simplicity
+pair_coeff 1 1 lj/cut 0.0028619844 3.5 # CT
+pair_coeff 2 2 lj/cut 0.0013009018 2.5 # HC
+pair_coeff 1 2 lj/cut 0.0019295487 2.95
+pair_modify shift no
+# change exclusion settings for lj/cut only: exclude bonded pairs
+pair_modify pair lj/cut special lj/coul 0.0 0.0 0.0
+
+# Intramolecular
+# Tell QUIP to pretend this is silane (which is covered by the parameter file)
+pair_coeff * * quip sw_example.xml "IP SW" 14 1
+bond_style none
+angle_style none
+
+fix 1 all nve
+
+# Include diagnostics that allow us to compare to a pure QUIP run
+compute equip all pair quip
+compute evdw all pair lj/cut
+compute vir all pressure NULL virial
+
+thermo_style custom step epair ke etotal temp press c_vir c_evdw c_equip
+thermo 1
+
+# dump 1 all custom 1 dump.molecular id type x y z fx fy fz
+# dump_modify 1 sort id
+
+run 10
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 10
+ ghost atom cutoff = 10
+ binsize = 5, bins = 2 2 2
+ 2 neighbor lists, perpetual/occasional/extra = 2 0 0
+ (1) pair lj/cut, perpetual, half/full from (2)
+ attributes: half, newton on
+ pair build: halffull/newton
+ stencil: none
+ bin: none
+ (2) pair quip, perpetual
+ attributes: full, newton on
+ pair build: full/bin
+ stencil: full/bin/3d
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 8.288 | 8.288 | 8.288 Mbytes
+Step E_pair KinEng TotEng Temp Press c_vir c_evdw c_equip
+ 0 -5.3530213 0 -5.3530213 0 518847.56 518847.56 -0.10904079 -5.2439805
+ 1 -5.9384459 0.58384822 -5.3545977 115.81657 517370.5 516488.87 -0.10783656 -5.8306093
+ 2 -7.669616 2.3104051 -5.3592109 458.30954 512986.36 509497.58 -0.10422283 -7.5653932
+ 3 -10.473314 5.1069211 -5.3663924 1013.0477 505833.04 498121.43 -0.098049469 -10.375264
+ 4 -14.234705 8.859182 -5.3755227 1757.3747 496127.44 482749.79 -0.089147485 -14.145557
+ 5 -18.806851 13.420941 -5.3859098 2662.28 484148.76 463882.72 -0.077305196 -18.729546
+ 6 -24.021727 18.625147 -5.3965797 3694.6259 470219.95 442095.39 -0.06194509 -23.959782
+ 7 -29.702647 24.295529 -5.4071176 4819.446 454683.57 417996.56 -0.042859727 -29.659787
+ 8 -35.67405 30.257258 -5.4167913 6002.0599 437887.03 392197.62 -0.019248651 -35.654801
+ 9 -41.771047 36.345757 -5.4252893 7209.8209 420163.51 365280.27 0.0096063065 -41.780653
+ 10 -47.845522 42.413161 -5.4323614 8413.3973 401821.91 337776.7 0.044743702 -47.890266
+Loop time of 0.0537777 on 1 procs for 10 steps with 40 atoms
+
+Performance: 1.607 ns/day, 14.938 hours/ns, 185.951 timesteps/s
+90.3% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.053478 | 0.053478 | 0.053478 | 0.0 | 99.44
+Bond | 1.9073e-06 | 1.9073e-06 | 1.9073e-06 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 7.7724e-05 | 7.7724e-05 | 7.7724e-05 | 0.0 | 0.14
+Output | 0.00018263 | 0.00018263 | 0.00018263 | 0.0 | 0.34
+Modify | 1.5974e-05 | 1.5974e-05 | 1.5974e-05 | 0.0 | 0.03
+Other | | 2.122e-05 | | | 0.04
+
+Nlocal: 40 ave 40 max 40 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1175 ave 1175 max 1175 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 4768 ave 4768 max 4768 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 9536 ave 9536 max 9536 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 9536
+Ave neighs/atom = 238.4
+Ave special neighs/atom = 4
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/USER/quip/log.24Jul17.molecular.g++.4 b/examples/USER/quip/log.24Jul17.molecular.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..a8be8e77bb4b2452eda764f00f5085d7209dbd53
--- /dev/null
+++ b/examples/USER/quip/log.24Jul17.molecular.g++.4
@@ -0,0 +1,130 @@
+LAMMPS (24 Jul 2017)
+ using 1 OpenMP thread(s) per MPI task
+units metal
+atom_style full
+boundary p p p
+timestep 0.0001 # 0.1 fs
+
+read_data methane-box-8.data
+ orthogonal box = (-0.499095 -0.270629 0.131683) to (8.4109 8.63937 9.04168)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 40 atoms
+ scanning bonds ...
+ 4 = max bonds/atom
+ scanning angles ...
+ 6 = max angles/atom
+ reading bonds ...
+ 32 bonds
+ reading angles ...
+ 48 angles
+ 4 = max # of 1-2 neighbors
+ 3 = max # of 1-3 neighbors
+ 3 = max # of 1-4 neighbors
+ 4 = max # of special neighbors
+
+# DISCLAIMER: This potential mixes parameters from methane and silane
+# potentials and is NOT intended to be a realistic representation of either
+# system. It is meant to demonstrate the use of hybrid QUIP/LAMMPS potentials,
+# including the use of separate 'special_bonds' settings.
+
+pair_style hybrid/overlay lj/cut 8.0 quip
+
+# exclusion setting for quip; cannot be exactly 1.0 1.0 1.0,
+# since that would not flag 1-2, 1-3, and 1-4 pairs in lj/cut
+special_bonds lj/coul 0.999999999 0.999999999 0.999999999
+ 4 = max # of 1-2 neighbors
+ 3 = max # of 1-3 neighbors
+ 3 = max # of 1-4 neighbors
+ 4 = max # of special neighbors
+
+# Intermolecular: OPLS (JACS 118 (45), p. 11225 (1996))
+# Coulomb interactions ommitted for simplicity
+pair_coeff 1 1 lj/cut 0.0028619844 3.5 # CT
+pair_coeff 2 2 lj/cut 0.0013009018 2.5 # HC
+pair_coeff 1 2 lj/cut 0.0019295487 2.95
+pair_modify shift no
+# change exclusion settings for lj/cut only: exclude bonded pairs
+pair_modify pair lj/cut special lj/coul 0.0 0.0 0.0
+
+# Intramolecular
+# Tell QUIP to pretend this is silane (which is covered by the parameter file)
+pair_coeff * * quip sw_example.xml "IP SW" 14 1
+bond_style none
+angle_style none
+
+fix 1 all nve
+
+# Include diagnostics that allow us to compare to a pure QUIP run
+compute equip all pair quip
+compute evdw all pair lj/cut
+compute vir all pressure NULL virial
+
+thermo_style custom step epair ke etotal temp press c_vir c_evdw c_equip
+thermo 1
+
+# dump 1 all custom 1 dump.molecular id type x y z fx fy fz
+# dump_modify 1 sort id
+
+run 10
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 10
+ ghost atom cutoff = 10
+ binsize = 5, bins = 2 2 2
+ 2 neighbor lists, perpetual/occasional/extra = 2 0 0
+ (1) pair lj/cut, perpetual, half/full from (2)
+ attributes: half, newton on
+ pair build: halffull/newton
+ stencil: none
+ bin: none
+ (2) pair quip, perpetual
+ attributes: full, newton on
+ pair build: full/bin
+ stencil: full/bin/3d
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 8.26 | 8.386 | 8.762 Mbytes
+Step E_pair KinEng TotEng Temp Press c_vir c_evdw c_equip
+ 0 -5.3530213 0 -5.3530213 0 518847.56 518847.56 -0.10904079 -5.2439805
+ 1 -5.9384459 0.58384822 -5.3545977 115.81657 517370.5 516488.87 -0.10783656 -5.8306093
+ 2 -7.669616 2.3104051 -5.3592109 458.30954 512986.36 509497.58 -0.10422283 -7.5653932
+ 3 -10.473314 5.1069211 -5.3663924 1013.0477 505833.04 498121.43 -0.098049469 -10.375264
+ 4 -14.234705 8.859182 -5.3755227 1757.3747 496127.44 482749.79 -0.089147485 -14.145557
+ 5 -18.806851 13.420941 -5.3859098 2662.28 484148.76 463882.72 -0.077305196 -18.729546
+ 6 -24.021727 18.625147 -5.3965797 3694.6259 470219.95 442095.39 -0.06194509 -23.959782
+ 7 -29.702647 24.295529 -5.4071176 4819.446 454683.57 417996.56 -0.042859727 -29.659787
+ 8 -35.67405 30.257258 -5.4167913 6002.0599 437887.03 392197.62 -0.019248651 -35.654801
+ 9 -41.771047 36.345757 -5.4252893 7209.8209 420163.51 365280.27 0.0096063065 -41.780653
+ 10 -47.845522 42.413161 -5.4323614 8413.3973 401821.91 337776.7 0.044743702 -47.890266
+Loop time of 0.0506847 on 4 procs for 10 steps with 40 atoms
+
+Performance: 1.705 ns/day, 14.079 hours/ns, 197.298 timesteps/s
+94.4% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.04216 | 0.045656 | 0.049349 | 1.2 | 90.08
+Bond | 1.9073e-06 | 2.4438e-06 | 2.861e-06 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.00068545 | 0.004438 | 0.0079191 | 3.9 | 8.76
+Output | 0.00048304 | 0.00053334 | 0.00060964 | 0.0 | 1.05
+Modify | 1.1444e-05 | 1.4424e-05 | 1.9312e-05 | 0.0 | 0.03
+Other | | 4.047e-05 | | | 0.08
+
+Nlocal: 10 ave 15 max 6 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+Nghost: 878 ave 948 max 812 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+Neighs: 1192 ave 1764 max 731 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+FullNghs: 2384 ave 3527 max 1439 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+
+Total # of neighbors = 9536
+Ave neighs/atom = 238.4
+Ave special neighs/atom = 4
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/USER/quip/log.24Jul17.sw.g++.1 b/examples/USER/quip/log.24Jul17.sw.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..c8115f4cfc3ecd0d1da9731f213debd007438039
--- /dev/null
+++ b/examples/USER/quip/log.24Jul17.sw.g++.1
@@ -0,0 +1,83 @@
+LAMMPS (24 Jul 2017)
+ using 1 OpenMP thread(s) per MPI task
+# Test of SW potential for Si system
+
+units metal
+boundary p p p
+
+atom_style atomic
+
+read_data data_sw
+ orthogonal box = (0 0 0) to (5.431 5.431 5.431)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 8 atoms
+
+pair_style quip
+pair_coeff * * sw_example.xml "IP SW" 14
+
+velocity all create 10.0 355311
+neighbor 0.3 bin
+neigh_modify delay 10
+
+fix 1 all nve
+thermo 10
+timestep 0.001
+
+#dump 1 all custom 10 dump.sw id fx fy fz
+
+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 = 4.2258
+ ghost atom cutoff = 4.2258
+ binsize = 2.1129, bins = 3 3 3
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair quip, perpetual
+ attributes: full, newton on
+ pair build: full/bin/atomonly
+ stencil: full/bin/3d
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.684 | 2.684 | 2.684 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 10 -34.68 0 -34.670952 32.206289
+ 10 4.5659178 -34.675073 0 -34.670942 46.253731
+ 20 1.606683 -34.672391 0 -34.670937 44.736892
+ 30 6.7007748 -34.677011 0 -34.670948 16.403049
+ 40 5.682757 -34.676087 0 -34.670945 18.696408
+ 50 2.2140716 -34.672942 0 -34.670939 37.592282
+ 60 5.0475382 -34.675512 0 -34.670944 37.331666
+ 70 7.0990979 -34.677369 0 -34.670946 40.533757
+ 80 5.7306189 -34.676128 0 -34.670943 47.748813
+ 90 5.0895648 -34.675549 0 -34.670944 38.092721
+ 100 4.1070919 -34.674659 0 -34.670943 28.737864
+Loop time of 0.384233 on 1 procs for 100 steps with 8 atoms
+
+Performance: 22.486 ns/day, 1.067 hours/ns, 260.259 timesteps/s
+94.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.38365 | 0.38365 | 0.38365 | 0.0 | 99.85
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.00017333 | 0.00017333 | 0.00017333 | 0.0 | 0.05
+Output | 0.00014162 | 0.00014162 | 0.00014162 | 0.0 | 0.04
+Modify | 7.081e-05 | 7.081e-05 | 7.081e-05 | 0.0 | 0.02
+Other | | 0.0001957 | | | 0.05
+
+Nlocal: 8 ave 8 max 8 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 162 ave 162 max 162 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
+FullNghs: 128 ave 128 max 128 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 128
+Ave neighs/atom = 16
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/USER/quip/log.24Jul17.sw.g++.4 b/examples/USER/quip/log.24Jul17.sw.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..d7306c705564395c5f8f820c92190d6e0b6fe12f
--- /dev/null
+++ b/examples/USER/quip/log.24Jul17.sw.g++.4
@@ -0,0 +1,83 @@
+LAMMPS (24 Jul 2017)
+ using 1 OpenMP thread(s) per MPI task
+# Test of SW potential for Si system
+
+units metal
+boundary p p p
+
+atom_style atomic
+
+read_data data_sw
+ orthogonal box = (0 0 0) to (5.431 5.431 5.431)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 8 atoms
+
+pair_style quip
+pair_coeff * * sw_example.xml "IP SW" 14
+
+velocity all create 10.0 355311
+neighbor 0.3 bin
+neigh_modify delay 10
+
+fix 1 all nve
+thermo 10
+timestep 0.001
+
+#dump 1 all custom 10 dump.sw id fx fy fz
+
+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 = 4.2258
+ ghost atom cutoff = 4.2258
+ binsize = 2.1129, bins = 3 3 3
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair quip, perpetual
+ attributes: full, newton on
+ pair build: full/bin/atomonly
+ stencil: full/bin/3d
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.698 | 2.698 | 2.698 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 10 -34.68 0 -34.670952 32.206289
+ 10 4.5659178 -34.675073 0 -34.670942 46.253731
+ 20 1.606683 -34.672391 0 -34.670937 44.736892
+ 30 6.7007748 -34.677011 0 -34.670948 16.403049
+ 40 5.682757 -34.676087 0 -34.670945 18.696408
+ 50 2.2140716 -34.672942 0 -34.670939 37.592282
+ 60 5.0475382 -34.675512 0 -34.670944 37.331666
+ 70 7.0990979 -34.677369 0 -34.670946 40.533757
+ 80 5.7306189 -34.676128 0 -34.670943 47.748813
+ 90 5.0895648 -34.675549 0 -34.670944 38.092721
+ 100 4.1070919 -34.674659 0 -34.670943 28.737864
+Loop time of 0.423803 on 4 procs for 100 steps with 8 atoms
+
+Performance: 20.387 ns/day, 1.177 hours/ns, 235.959 timesteps/s
+90.6% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.39332 | 0.40011 | 0.40704 | 0.8 | 94.41
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.015632 | 0.022605 | 0.029425 | 3.3 | 5.33
+Output | 0.00025702 | 0.00028491 | 0.00035429 | 0.0 | 0.07
+Modify | 7.3671e-05 | 8.1897e-05 | 8.9884e-05 | 0.0 | 0.02
+Other | | 0.0007259 | | | 0.17
+
+Nlocal: 2 ave 2 max 2 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 113 ave 113 max 113 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs: 32 ave 32 max 32 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 128
+Ave neighs/atom = 16
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/lib/.gitignore b/lib/.gitignore
index e153da2c3434ac54cb27ac2773936dfc900834f1..cbeae7705e8c95436cc956bd01e60ca0cd1caff7 100644
--- a/lib/.gitignore
+++ b/lib/.gitignore
@@ -1 +1,2 @@
Makefile.lammps
+.depend
diff --git a/lib/Install.py b/lib/Install.py
index 18b426f9282819ce196b6cf030aef477e3769d66..6b90254336b6b54adee6453a2ed249e576329640 100644
--- a/lib/Install.py
+++ b/lib/Install.py
@@ -4,24 +4,34 @@
# soft linked to by many of the lib/Install.py files
# used to automate the steps described in the corresponding lib/README
-import sys,commands,os
+from __future__ import print_function
+import sys,os,subprocess
# help message
help = """
-Syntax: python Install.py -m machine -e suffix
- specify -m and optionally -e, order does not matter
+Syntax from src dir: make lib-libname args="-m machine -e suffix"
+Syntax from lib dir: python Install.py -m machine -e suffix
+
+libname = name of lib dir (e.g. atc, h5md, meam, poems, etc)
+specify -m and optionally -e, order does not matter
+
-m = peform a clean followed by "make -f Makefile.machine"
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-poems args="-m g++" # build COLVARS lib with GNU g++ compiler
+make lib-meam args="-m ifort" # build MEAM lib with Intel ifort 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
@@ -38,12 +48,12 @@ while iarg < nargs:
if args[iarg] == "-m":
if iarg+2 > nargs: error()
machine = args[iarg+1]
- iarg += 2
+ iarg += 2
elif args[iarg] == "-e":
if iarg+2 > nargs: error()
extraflag = 1
suffix = args[iarg+1]
- iarg += 2
+ iarg += 2
else: error()
# set lib from working dir
@@ -53,7 +63,7 @@ lib = os.path.basename(cwd)
# 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))
@@ -71,12 +81,12 @@ fp.close()
# make the library via Makefile.auto
-print "Building lib%s.a ..." % lib
+print("Building lib%s.a ..." % lib)
cmd = "make -f Makefile.auto clean; make -f Makefile.auto"
-txt = commands.getoutput(cmd)
-print txt
+txt = subprocess.check_output(cmd,shell=True,stderr=subprocess.STDOUT)
+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)
diff --git a/lib/atc/Install.py b/lib/atc/Install.py
index 37041d2ea1a2c903edce5c2c15e14149ae7bf3aa..ffe709d44c22d2060ad41538d1f8fc0df2b09b30 120000
--- a/lib/atc/Install.py
+++ b/lib/atc/Install.py
@@ -1 +1 @@
-Install.py
\ No newline at end of file
+../Install.py
\ No newline at end of file
diff --git a/lib/atc/Makefile.g++ b/lib/atc/Makefile.g++
index d15e6cb3b87dc509591e013e43496e6c6d1ff68c..bb3028392a631b002c040fb72ad581b608d62f89 100644
--- a/lib/atc/Makefile.g++
+++ b/lib/atc/Makefile.g++
@@ -1,3 +1,4 @@
+# library build -*- makefile -*-
SHELL = /bin/sh
# which file will be copied to Makefile.lammps
@@ -5,6 +6,7 @@ SHELL = /bin/sh
EXTRAMAKE = Makefile.lammps.installed
# ------ FILES ------
+
SRC = $(wildcard *.cpp)
INC = $(wildcard *.h)
@@ -47,5 +49,9 @@ DEPENDS = $(OBJ:.o=.d)
# ------ CLEAN ------
+.PHONY: clean lib
+
clean:
-rm *.o *.d *~ $(LIB)
+
+sinclude $(DEPENDS)
diff --git a/lib/atc/Makefile.lammps b/lib/atc/Makefile.lammps
deleted file mode 100644
index c8cd66af26957af7143783f533aa30683df0c3d9..0000000000000000000000000000000000000000
--- a/lib/atc/Makefile.lammps
+++ /dev/null
@@ -1,5 +0,0 @@
-# Settings that the LAMMPS build will import when this package library is used
-
-user-atc_SYSINC =
-user-atc_SYSLIB = -lblas -llapack
-user-atc_SYSPATH =
diff --git a/lib/atc/Makefile.mingw32-cross b/lib/atc/Makefile.mingw32-cross
deleted file mode 100644
index 8b335409813f98834b78dd9a894ec9a29ed284e8..0000000000000000000000000000000000000000
--- a/lib/atc/Makefile.mingw32-cross
+++ /dev/null
@@ -1,67 +0,0 @@
-# library build -*- makefile -*-
-SHELL = /bin/sh
-
-# which file will be copied to Makefile.lammps
-EXTRAMAKE = Makefile.lammps.linalg
-
-# ------ FILES ------
-
-SRC = $(wildcard *.cpp)
-INC = $(wildcard *.h)
-
-# ------ DEFINITIONS ------
-
-DIR = Obj_mingw32/
-LIB = $(DIR)libatc.a
-OBJ = $(SRC:%.cpp=$(DIR)%.o)
-
-# ------ SETTINGS ------
-
-# include any MPI settings needed for the ATC library to build with
-# the same MPI library that LAMMPS is built with
-
-CC = i686-w64-mingw32-g++
-CCFLAGS = -I../../src -I../../src/STUBS -DMPICH_IGNORE_CXX_SEEK \
- -O3 -march=i686 -mtune=generic -mfpmath=387 -mpc64 \
- -ffast-math -funroll-loops -fstrict-aliasing \
- -DLAMMPS_SMALLSMALL -Wno-uninitialized
-ARCHIVE = i686-w64-mingw32-ar
-ARCHFLAG = -rcs
-DEPFLAGS = -M
-LINK = $(CC)
-LINKFLAGS = -O
-USRLIB =
-SYSLIB =
-
-# ------ MAKE PROCEDURE ------
-
-default: $(DIR) $(LIB) Makefile.lammps
-
-$(DIR):
- mkdir $(DIR)
-
-Makefile.lammps:
- @cp $(EXTRAMAKE) Makefile.lammps
-
-$(LIB): $(OBJ)
- $(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
- @cp $(EXTRAMAKE) Makefile.lammps
-
-# ------ COMPILE RULES ------
-
-$(DIR)%.o:%.cpp
- $(CC) $(CCFLAGS) -c $< -o $@
-$(DIR)%.d:%.cpp
- $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
-
-# ------ DEPENDENCIES ------
-
-DEPENDS = $(OBJ:.o=.d)
-
-# ------ CLEAN ------
-
-clean:
- -rm $(DIR)*.o $(DIR)*.d *~ $(LIB)
-
-$(DEPENDS) : $(DIR)
-sinclude $(DEPENDS)
diff --git a/lib/atc/Makefile.mingw32-cross-mpi b/lib/atc/Makefile.mingw32-cross-mpi
deleted file mode 100644
index c5feeca81adf660c29113f7cf4376d8271c11299..0000000000000000000000000000000000000000
--- a/lib/atc/Makefile.mingw32-cross-mpi
+++ /dev/null
@@ -1,68 +0,0 @@
-# library build -*- makefile -*-
-SHELL = /bin/sh
-
-# which file will be copied to Makefile.lammps
-EXTRAMAKE = Makefile.lammps.linalg
-
-# ------ FILES ------
-
-SRC = $(wildcard *.cpp)
-INC = $(wildcard *.h)
-
-# ------ DEFINITIONS ------
-
-DIR = Obj_mingw32-mpi/
-LIB = $(DIR)libatc.a
-OBJ = $(SRC:%.cpp=$(DIR)%.o)
-
-# ------ SETTINGS ------
-
-# include any MPI settings needed for the ATC library to build with
-# the same MPI library that LAMMPS is built with
-
-CC = i686-w64-mingw32-g++
-CCFLAGS = -I../../tools/mingw-cross/mpich2-win32/include/ \
- -I../../src -DMPICH_IGNORE_CXX_SEEK \
- -O3 -march=i686 -mtune=generic -mfpmath=387 -mpc64 \
- -ffast-math -funroll-loops -fstrict-aliasing \
- -DLAMMPS_SMALLSMALL -Wno-uninitialized
-ARCHIVE = i686-w64-mingw32-ar
-ARCHFLAG = -rcs
-DEPFLAGS = -M
-LINK = $(CC)
-LINKFLAGS = -O
-USRLIB =
-SYSLIB =
-
-# ------ MAKE PROCEDURE ------
-
-default: $(DIR) $(LIB) Makefile.lammps
-
-$(DIR):
- mkdir $(DIR)
-
-Makefile.lammps:
- @cp $(EXTRAMAKE) Makefile.lammps
-
-$(LIB): $(OBJ)
- $(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
- @cp $(EXTRAMAKE) Makefile.lammps
-
-# ------ COMPILE RULES ------
-
-$(DIR)%.o:%.cpp
- $(CC) $(CCFLAGS) -c $< -o $@
-$(DIR)%.d:%.cpp
- $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
-
-# ------ DEPENDENCIES ------
-
-DEPENDS = $(OBJ:.o=.d)
-
-# ------ CLEAN ------
-
-clean:
- -rm $(DIR)*.o $(DIR)*.d *~ $(LIB)
-
-$(DEPENDS) : $(DIR)
-sinclude $(DEPENDS)
diff --git a/lib/atc/Makefile.mingw64-cross b/lib/atc/Makefile.mingw64-cross
deleted file mode 100644
index fbd3a02610a80275c934e8f8c962bcb7ccb7e7ff..0000000000000000000000000000000000000000
--- a/lib/atc/Makefile.mingw64-cross
+++ /dev/null
@@ -1,67 +0,0 @@
-# library build -*- makefile -*-
-SHELL = /bin/sh
-
-# which file will be copied to Makefile.lammps
-EXTRAMAKE = Makefile.lammps.linalg
-
-# ------ FILES ------
-
-SRC = $(wildcard *.cpp)
-INC = $(wildcard *.h)
-
-# ------ DEFINITIONS ------
-
-DIR = Obj_mingw64/
-LIB = $(DIR)libatc.a
-OBJ = $(SRC:%.cpp=$(DIR)%.o)
-
-# ------ SETTINGS ------
-
-# include any MPI settings needed for the ATC library to build with
-# the same MPI library that LAMMPS is built with
-
-CC = x86_64-w64-mingw32-g++
-CCFLAGS = -I../../src -I../../src/STUBS -DMPICH_IGNORE_CXX_SEEK \
- -O3 -march=core2 -mtune=core2 -mpc64 -msse2 \
- -ffast-math -funroll-loops -fstrict-aliasing \
- -DLAMMPS_SMALLBIG -Wno-uninitialized
-ARCHIVE = x86_64-w64-mingw32-ar
-ARCHFLAG = -rcs
-DEPFLAGS = -M
-LINK = $(CC)
-LINKFLAGS = -O
-USRLIB =
-SYSLIB =
-
-# ------ MAKE PROCEDURE ------
-
-default: $(DIR) $(LIB) Makefile.lammps
-
-$(DIR):
- mkdir $(DIR)
-
-Makefile.lammps:
- @cp $(EXTRAMAKE) Makefile.lammps
-
-$(LIB): $(OBJ)
- $(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
- @cp $(EXTRAMAKE) Makefile.lammps
-
-# ------ COMPILE RULES ------
-
-$(DIR)%.o:%.cpp
- $(CC) $(CCFLAGS) -c $< -o $@
-$(DIR)%.d:%.cpp
- $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
-
-# ------ DEPENDENCIES ------
-
-DEPENDS = $(OBJ:.o=.d)
-
-# ------ CLEAN ------
-
-clean:
- -rm $(DIR)*.o $(DIR)*.d *~ $(LIB)
-
-$(DEPENDS) : $(DIR)
-sinclude $(DEPENDS)
diff --git a/lib/atc/Makefile.mingw64-cross-mpi b/lib/atc/Makefile.mingw64-cross-mpi
deleted file mode 100644
index f8dd64eae376692dfb1c8cd8594ce564fcc7a08e..0000000000000000000000000000000000000000
--- a/lib/atc/Makefile.mingw64-cross-mpi
+++ /dev/null
@@ -1,68 +0,0 @@
-# library build -*- makefile -*-
-SHELL = /bin/sh
-
-# which file will be copied to Makefile.lammps
-EXTRAMAKE = Makefile.lammps.linalg
-
-# ------ FILES ------
-
-SRC = $(wildcard *.cpp)
-INC = $(wildcard *.h)
-
-# ------ DEFINITIONS ------
-
-DIR = Obj_mingw64-mpi/
-LIB = $(DIR)libatc.a
-OBJ = $(SRC:%.cpp=$(DIR)%.o)
-
-# ------ SETTINGS ------
-
-# include any MPI settings needed for the ATC library to build with
-# the same MPI library that LAMMPS is built with
-
-CC = x86_64-w64-mingw32-g++
-CCFLAGS = -I../../tools/mingw-cross/mpich2-win64/include/ \
- -I../../src -DMPICH_IGNORE_CXX_SEEK \
- -O3 -march=core2 -mtune=core2 -mpc64 -msse2 \
- -ffast-math -funroll-loops -fstrict-aliasing \
- -DLAMMPS_SMALLBIG -Wno-uninitialized
-ARCHIVE = x86_64-w64-mingw32-ar
-ARCHFLAG = -rcs
-DEPFLAGS = -M
-LINK = $(CC)
-LINKFLAGS = -O
-USRLIB =
-SYSLIB =
-
-# ------ MAKE PROCEDURE ------
-
-default: $(DIR) $(LIB) Makefile.lammps
-
-$(DIR):
- mkdir $(DIR)
-
-Makefile.lammps:
- @cp $(EXTRAMAKE) Makefile.lammps
-
-$(LIB): $(OBJ)
- $(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
- @cp $(EXTRAMAKE) Makefile.lammps
-
-# ------ COMPILE RULES ------
-
-$(DIR)%.o:%.cpp
- $(CC) $(CCFLAGS) -c $< -o $@
-$(DIR)%.d:%.cpp
- $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
-
-# ------ DEPENDENCIES ------
-
-DEPENDS = $(OBJ:.o=.d)
-
-# ------ CLEAN ------
-
-clean:
- -rm $(DIR)*.o $(DIR)*.d *~ $(LIB)
-
-$(DEPENDS) : $(DIR)
-sinclude $(DEPENDS)
diff --git a/lib/atc/Makefile.mpic++ b/lib/atc/Makefile.mpi
similarity index 59%
rename from lib/atc/Makefile.mpic++
rename to lib/atc/Makefile.mpi
index c9dfdb79c9594a76d66d1eaf924f9db811d51a96..ec941efdcb6c0b0171440306653fa9522b8b65cf 100644
--- a/lib/atc/Makefile.mpic++
+++ b/lib/atc/Makefile.mpi
@@ -2,38 +2,54 @@
SHELL = /bin/sh
# which file will be copied to Makefile.lammps
-EXTRAMAKE = Makefile.lammps.installed
+EXTRAMAKE = Makefile.lammps.linalg
+
# ------ FILES ------
+
SRC = $(wildcard *.cpp)
INC = $(wildcard *.h)
+
# ------ DEFINITIONS ------
+
LIB = libatc.a
OBJ = $(SRC:.cpp=.o)
+
+default: lib
+
# ------ SETTINGS ------
+.PHONY: clean lib depend
+
# include any MPI settings needed for the ATC library to build with
# must be the same MPI library that LAMMPS is built with
-CC = mpic++
-CCFLAGS = -O3 -Wall -g -I../../src -fPIC -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1
+CC = mpicxx
+CCFLAGS = -O3 -Wall -g -fPIC
+CPPFLAGS = -I../../src -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1
ARCHIVE = ar
ARCHFLAG = -rc
-DEPFLAGS = -M
-LINK = $(CC)
-LINKFLAGS = -O
# ------ MAKE PROCEDURE ------
+
lib: $(OBJ)
$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
@cp $(EXTRAMAKE) Makefile.lammps
+
# ------ COMPILE RULES ------
+
%.o:%.cpp
- $(CC) $(CCFLAGS) -c $<
-%.d:%.cpp
- $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
+ $(CC) $(CPPFLAGS) $(CCFLAGS) -c $<
+
# ------ DEPENDENCIES ------
-DEPENDS = $(OBJ:.o=.d)
+
+depend .depend : fastdep.exe $(SRC)
+ @./fastdep.exe $(INCFLAGS) -- $^ > .depend || exit 1
+
+fastdep.exe: ../../src/DEPEND/fastdep.c
+ @cc -O -o $@ $<
+
# ------ CLEAN ------
+
clean:
- -rm *.o *.d *~ $(LIB)
+ -rm -f *.o *~ .depend $(LIB) fastdep.exe
sinclude $(DEPENDS)
diff --git a/lib/atc/Makefile.serial b/lib/atc/Makefile.serial
index 44ce5fd3416015d7cc02ba6dfed0c82c2c4b7a58..70b786a6b8fa2a028315fe054d5fd7c8f5f1c14c 100644
--- a/lib/atc/Makefile.serial
+++ b/lib/atc/Makefile.serial
@@ -14,18 +14,20 @@ INC = $(wildcard *.h)
LIB = libatc.a
OBJ = $(SRC:.cpp=.o)
+default: lib
+
# ------ SETTINGS ------
+.PHONY: clean lib depend
+
# include any MPI settings needed for the ATC library to build with
# must be the same MPI library that LAMMPS is built with
CC = g++
-CCFLAGS = -O -g -fPIC -I../../src -I../../src/STUBS
+CCFLAGS = -O3 -g -fPIC
+CPPFLAGS = -I../../src -I../../src/STUBS
ARCHIVE = ar
ARCHFLAG = -rc
-DEPFLAGS = -M
-LINK = $(CC)
-LINKFLAGS = -O
# ------ MAKE PROCEDURE ------
lib: $(OBJ)
@@ -35,17 +37,19 @@ lib: $(OBJ)
# ------ COMPILE RULES ------
%.o:%.cpp
- $(CC) $(CCFLAGS) -c $<
-%.d:%.cpp
- $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
+ $(CC) $(CPPFLAGS) $(CCFLAGS) -c $<
# ------ DEPENDENCIES ------
-DEPENDS = $(OBJ:.o=.d)
+depend .depend : fastdep.exe $(SRC)
+ @./fastdep.exe $(INCFLAGS) -- $^ > .depend || exit 1
+
+fastdep.exe: ../../src/DEPEND/fastdep.c
+ @cc -O -o $@ $<
# ------ CLEAN ------
clean:
- -rm *.o *.d *~ $(LIB)
+ -rm -f *.o *~ .depend $(LIB) fastdep.exe
-sinclude $(DEPENDS)
+sinclude .depend
diff --git a/lib/awpmd/Install.py b/lib/awpmd/Install.py
index 37041d2ea1a2c903edce5c2c15e14149ae7bf3aa..ffe709d44c22d2060ad41538d1f8fc0df2b09b30 120000
--- a/lib/awpmd/Install.py
+++ b/lib/awpmd/Install.py
@@ -1 +1 @@
-Install.py
\ No newline at end of file
+../Install.py
\ No newline at end of file
diff --git a/lib/awpmd/Makefile.mingw32-cross b/lib/awpmd/Makefile.mingw32-cross
deleted file mode 100644
index 6a93987173b24819770b636d37749893e10f4977..0000000000000000000000000000000000000000
--- a/lib/awpmd/Makefile.mingw32-cross
+++ /dev/null
@@ -1,80 +0,0 @@
-# library build -*- makefile -*-
-SHELL = /bin/sh
-
-# which file will be copied to Makefile.lammps
-
-EXTRAMAKE = Makefile.lammps.linalg
-
-# ------ FILES ------
-
-SRC = logexc.cpp wpmd.cpp wpmd_split.cpp
-vpath %.cpp ivutils/src
-vpath %.cpp systems/interact/TCP
-
-INC = \
- cerf.h \
- cerf2.h \
- cerf_octave.h \
- cvector_3.h \
- lapack_inter.h \
- logexc.h \
- pairhash.h \
- refobj.h \
- tcpdefs.h \
- vector_3.h \
- wavepacket.h \
- wpmd.h \
- wpmd_split.h
-
-# ------ DEFINITIONS ------
-DIR = Obj_mingw32/
-LIB = $(DIR)libawpmd.a
-OBJ = $(SRC:%.cpp=$(DIR)%.o)
-
-# ------ SETTINGS ------
-
-# include any MPI settings needed for the ATC library to build with
-# the same MPI library that LAMMPS is built with
-
-CC = i686-w64-mingw32-g++
-CCFLAGS = -O2 -march=i686 -mtune=generic -mfpmath=387 -mpc64 \
- -finline-functions \
- -ffast-math -funroll-loops -fstrict-aliasing \
- -Wall -W -Wno-uninitialized -Isystems/interact/TCP/ -Isystems/interact -Iivutils/include
-ARCHIVE = i686-w64-mingw32-ar
-ARCHFLAG = -rscv
-DEPFLAGS = -M
-#LINK =
-#LINKFLAGS =
-USRLIB =
-SYSLIB =
-
-# ------ MAKE PROCEDURE ------
-
-default: $(DIR) $(LIB) Makefile.lammps
-
-$(DIR):
- mkdir $(DIR)
-
-Makefile.lammps:
- @cp $(EXTRAMAKE) Makefile.lammps
-
-$(LIB): $(OBJ)
- $(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
- @cp $(EXTRAMAKE) Makefile.lammps
-
-# ------ COMPILE RULES ------
-
-$(DIR)%.o:%.cpp
- $(CC) $(CCFLAGS) -c $< -o $@
-$(DIR)%.d:%.cpp
- $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
-
-# ------ DEPENDENCIES ------
-
-DEPENDS = $(OBJ:.o=.d)
-
-# ------ CLEAN ------
-
-clean:
- -rm *.d *~ $(OBJ) $(LIB)
diff --git a/lib/awpmd/Makefile.mingw32-cross-mpi b/lib/awpmd/Makefile.mingw32-cross-mpi
deleted file mode 100644
index cc2a76111a555bb51d002be8c286b1823f745284..0000000000000000000000000000000000000000
--- a/lib/awpmd/Makefile.mingw32-cross-mpi
+++ /dev/null
@@ -1,13 +0,0 @@
-# -*- makefile -*- wrapper for non-MPI libraries
-
-SHELL=/bin/sh
-
-all:
- $(MAKE) $(MFLAGS) mingw32-cross
- rm -f Obj_mingw32-mpi
- ln -s Obj_mingw32 Obj_mingw32-mpi
-
-clean:
- $(MAKE) $(MFLAGS) clean-mingw32-cross
- rm -f Obj_mingw32-mpi
-
diff --git a/lib/awpmd/Makefile.mingw64-cross b/lib/awpmd/Makefile.mingw64-cross
deleted file mode 100644
index 1f3e608129709660f0a5efb95838178d05212780..0000000000000000000000000000000000000000
--- a/lib/awpmd/Makefile.mingw64-cross
+++ /dev/null
@@ -1,79 +0,0 @@
-# library build -*- makefile -*-
-SHELL = /bin/sh
-
-# which file will be copied to Makefile.lammps
-
-EXTRAMAKE = Makefile.lammps.linalg
-
-# ------ FILES ------
-
-SRC = logexc.cpp wpmd.cpp wpmd_split.cpp
-vpath %.cpp ivutils/src
-vpath %.cpp systems/interact/TCP
-
-INC = \
- cerf.h \
- cerf2.h \
- cerf_octave.h \
- cvector_3.h \
- lapack_inter.h \
- logexc.h \
- pairhash.h \
- refobj.h \
- tcpdefs.h \
- vector_3.h \
- wavepacket.h \
- wpmd.h \
- wpmd_split.h
-
-# ------ DEFINITIONS ------
-DIR = Obj_mingw64/
-LIB = $(DIR)libawpmd.a
-OBJ = $(SRC:%.cpp=$(DIR)%.o)
-
-# ------ SETTINGS ------
-
-# include any MPI settings needed for the ATC library to build with
-# the same MPI library that LAMMPS is built with
-
-CC = x86_64-w64-mingw32-g++
-CCFLAGS = -O3 -march=core2 -mtune=core2 -mpc64 -msse2 \
- -ffast-math -funroll-loops -fstrict-aliasing \
- -Wall -W -Wno-uninitialized -Isystems/interact/TCP/ -Isystems/interact -Iivutils/include
-ARCHIVE = x86_64-w64-mingw32-ar
-ARCHFLAG = -rscv
-DEPFLAGS = -M
-#LINK =
-#LINKFLAGS =
-USRLIB =
-SYSLIB =
-
-# ------ MAKE PROCEDURE ------
-
-default: $(DIR) $(LIB) Makefile.lammps
-
-$(DIR):
- mkdir $(DIR)
-
-Makefile.lammps:
- @cp $(EXTRAMAKE) Makefile.lammps
-
-$(LIB): $(OBJ)
- $(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
- @cp $(EXTRAMAKE) Makefile.lammps
-
-# ------ COMPILE RULES ------
-
-$(DIR)%.o:%.cpp
- $(CC) $(CCFLAGS) -c $< -o $@
-$(DIR)%.d:%.cpp
- $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
-
-# ------ DEPENDENCIES ------
-
-DEPENDS = $(OBJ:.o=.d)
-
-# ------ CLEAN ------
-
-clean:
- -rm *.d *~ $(OBJ) $(LIB)
diff --git a/lib/awpmd/Makefile.mingw64-cross-mpi b/lib/awpmd/Makefile.mingw64-cross-mpi
deleted file mode 100644
index 1ec1a0995b1a8180c0ea3ba35cce6a66252495aa..0000000000000000000000000000000000000000
--- a/lib/awpmd/Makefile.mingw64-cross-mpi
+++ /dev/null
@@ -1,13 +0,0 @@
-# -*- makefile -*- wrapper for non-MPI libraries
-
-SHELL=/bin/sh
-
-all:
- $(MAKE) $(MFLAGS) mingw64-cross
- rm -f Obj_mingw64-mpi
- ln -s Obj_mingw64 Obj_mingw64-mpi
-
-clean:
- $(MAKE) $(MFLAGS) clean-mingw64-cross
- rm -f Obj_mingw64-mpi
-
diff --git a/lib/colvars/Install.py b/lib/colvars/Install.py
index af658fa26cef42b3658bbdb0868cb8d2efc1ec30..2fc207710c54e4303dc1ffc9c589be977219b3e9 100644
--- a/lib/colvars/Install.py
+++ b/lib/colvars/Install.py
@@ -28,7 +28,7 @@ make lib-colvars args="-m g++" # build COLVARS lib with GNU g++ compiler
def error(str=None):
if not str: print(help)
- else: print("ERROR"),str
+ else: print("ERROR",str)
sys.exit()
# parse args
diff --git a/lib/gpu/Install.py b/lib/gpu/Install.py
index d396be5e1a00fdbc296d711faaafbd46a3e3a811..c6cd1f3021b117ec7bf0986e685f840cd59e998c 100644
--- a/lib/gpu/Install.py
+++ b/lib/gpu/Install.py
@@ -8,14 +8,17 @@ import sys,os,re,commands
# help message
help = """
-Syntax: python Install.py -i isuffix -h hdir -a arch -p precision -e esuffix -m -o osuffix
- specify one or more options, order does not matter
- copies an existing Makefile.isuffix in lib/gpu to Makefile.auto
- optionally edits these variables in Makefile.auto:
- CUDA_HOME, CUDA_ARCH, CUDA_PRECISION, EXTRAMAKE
- optionally uses Makefile.auto to build the GPU library -> libgpu.a
- and to copy a Makefile.lammps.esuffix -> Makefile.lammps
- optionally copies Makefile.auto to a new Makefile.osuffix
+Syntax from src dir: make lib-gpu args="-i isuffix -h hdir -a arch -p precision -e esuffix -m -o osuffix"
+Syntax from lib dir: python Install.py -i isuffix -h hdir -a arch -p precision -e esuffix -m -o osuffix
+
+specify one or more options, order does not matter
+
+copies an existing Makefile.isuffix in lib/gpu to Makefile.auto
+optionally edits these variables in Makefile.auto:
+ CUDA_HOME, CUDA_ARCH, CUDA_PRECISION, EXTRAMAKE
+optionally uses Makefile.auto to build the GPU library -> libgpu.a
+ and to copy a Makefile.lammps.esuffix -> Makefile.lammps
+optionally copies Makefile.auto to a new Makefile.osuffix
-i = use Makefile.isuffix as starting point, copy to Makefile.auto
default isuffix = linux
@@ -34,6 +37,12 @@ Syntax: python Install.py -i isuffix -h hdir -a arch -p precision -e esuffix -m
also copies EXTRAMAKE file -> Makefile.lammps
-e can set which Makefile.lammps.esuffix file is copied
-o = copy final Makefile.auto to Makefile.osuffix
+
+Examples:
+
+make lib-gpu args="-m" # build GPU lib with default Makefile.linux
+make lib-gpu args="-i xk7 -p single -o xk7.single" # create new Makefile.xk7.single, altered for single-precision
+make lib-gpu args="-i xk7 -p single -o xk7.single -m" # ditto, also build GPU lib
"""
# print error message or help
diff --git a/lib/h5md/Install.py b/lib/h5md/Install.py
index 37041d2ea1a2c903edce5c2c15e14149ae7bf3aa..ffe709d44c22d2060ad41538d1f8fc0df2b09b30 120000
--- a/lib/h5md/Install.py
+++ b/lib/h5md/Install.py
@@ -1 +1 @@
-Install.py
\ No newline at end of file
+../Install.py
\ No newline at end of file
diff --git a/lib/h5md/Makefile.mpi b/lib/h5md/Makefile.mpi
new file mode 120000
index 0000000000000000000000000000000000000000..df682a9547c6500dad7e1280fce33a049e6294b7
--- /dev/null
+++ b/lib/h5md/Makefile.mpi
@@ -0,0 +1 @@
+Makefile.h5cc
\ No newline at end of file
diff --git a/lib/h5md/Makefile.serial b/lib/h5md/Makefile.serial
new file mode 120000
index 0000000000000000000000000000000000000000..df682a9547c6500dad7e1280fce33a049e6294b7
--- /dev/null
+++ b/lib/h5md/Makefile.serial
@@ -0,0 +1 @@
+Makefile.h5cc
\ No newline at end of file
diff --git a/lib/kim/.gitignore b/lib/kim/.gitignore
index 3be8ecbdd6bf8a02dbd89a1e9b07cc6bf2718d4a..c1f57fe64c60c0837e5d004e3b11998bc09e6079 100644
--- a/lib/kim/.gitignore
+++ b/lib/kim/.gitignore
@@ -1,2 +1,3 @@
/Makefile.KIM_DIR
/Makefile.KIM_Config
+/installed-kim-api-*
diff --git a/lib/kim/Install.py b/lib/kim/Install.py
index bcd22dcbb3dc80300cdd4754bc2064bb7e5d452b..315bb4e11c47cd41ec28935255fa9e76c9bedbc2 100644
--- a/lib/kim/Install.py
+++ b/lib/kim/Install.py
@@ -2,149 +2,275 @@
# install.py tool to setup the kim-api library
# used to automate the steps described in the README file in this dir
+from __future__ import print_function
+import sys,os,re,subprocess
-import sys,os,re,urllib,commands
+# transparently use either urllib or an external tool
+try:
+ import ssl
+ try: from urllib.request import urlretrieve as geturl
+ except: from urllib import urlretrieve as geturl
+except:
+ def geturl(url,fname):
+ cmd = "curl -o %s %s" % (fname,url)
+ txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+ return txt
help = """
-Syntax: install.py -v version -c kim-dir -b kim-model-name -a kim-name
- specify one or more options, order does not matter
- -v = version of kim-api to download and work with
- default = kim-api-v1.8.2 (current as of June 2017)
- -c = create Makefile.KIM_DIR within lammps lib/kim to configure lammps
- for use with the kim-api library installed at "kim-dir" (absolute
- path). default = this dir
- -b = build kim-api and kim model where kim-model-name can be a specific
- openkim.org model name (such as
- "EAM_Dynamo_Ackland_W__MO_141627196590_002") or the keyword
- "OpenKIM" to install all compatible models from the openkim.org
- site.
- -a = add kim-name openkim.org item (model driver or model) to existing
- kim-api instalation.
+Syntax from src dir: make lib-kim args="-v version -a kim-name"
+Syntax from lib dir: python Install.py -v version -a kim-name
+
+specify one or more options, order does not matter
+
+ -v = version of KIM API library to use
+ default = kim-api-v1.8.2 (current as of June 2017)
+ -b = download and build base KIM API library with example Models (default)
+ this will delete any previous installation in the current folder
+ -n = do NOT download and build base KIM API library. Use an existing installation
+ -p = specify location of KIM API installation (implies -n)
+ -a = add single KIM model or model driver with kim-name
+ to existing KIM API lib (see example below).
+ If kim-name = everything, then rebuild KIM API library with
+ all available OpenKIM Models (this implies -b).
+ -vv = be more verbose about what is happening while the script runs
+
+Examples:
+
+make lib-kim # install KIM API lib with only example models
+make lib-kim args="-a Glue_Ercolessi_Adams_Al__MO_324507536345_001" # Ditto plus one model
+make lib-kim args="-a everything" # install KIM API lib with all models
+make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # only add one model or model driver
+
+See the list of KIM model drivers here:
+https://openkim.org/kim-items/model-drivers/alphabetical
+
+See the list of all KIM models here:
+https://openkim.org/kim-items/models/by-model-drivers
+
+See the list of example KIM models included by default here:
+https://openkim.org/kim-api
+in the "What is in the KIM API source package?" section
"""
def error():
- print help
+ print(help)
sys.exit()
+# expand to full path name
+# process leading '~' or relative path
+
+def fullpath(path):
+ return os.path.abspath(os.path.expanduser(path))
+
# parse args
-args = sys.argv
+args = sys.argv[1:]
+nargs = len(args)
thisdir = os.environ['PWD']
-dir = thisdir
version = "kim-api-v1.8.2"
-dirflag = 0
-buildflag = 0
-addflag = 0
+buildflag = True
+everythingflag = False
+addflag = False
+verboseflag = False
+pathflag = False
-iarg = 1
+iarg = 0
while iarg < len(args):
if args[iarg] == "-v":
if iarg+2 > len(args): error()
version = args[iarg+1]
iarg += 2
- elif args[iarg] == "-c":
- dirflag = 1
- if iarg+2 > len(args): error()
- dir = args[iarg+1]
- iarg += 2
elif args[iarg] == "-b":
- buildflag = 1
+ buildflag = True
+ iarg += 1
+ elif args[iarg] == "-n":
+ buildflag = False
+ iarg += 1
+ elif args[iarg] == "-p":
if iarg+2 > len(args): error()
- modelname = args[iarg+1]
+ kimdir = fullpath(args[iarg+1])
+ pathflag = True
+ buildflag = False
iarg += 2
elif args[iarg] == "-a":
- addflag = 1
+ addflag = True
if iarg+2 > len(args): error()
addmodelname = args[iarg+1]
+ if addmodelname == "everything":
+ buildflag = True
+ everythingflag = True
+ addflag = False
iarg += 2
+ elif args[iarg] == "-vv":
+ verboseflag = True
+ iarg += 1
else: error()
thisdir = os.path.abspath(thisdir)
-dir = os.path.abspath(dir)
url = "https://s3.openkim.org/kim-api/%s.tgz" % version
-# download and unpack tarball
+# set KIM API directory
+if pathflag:
+ if not os.path.isdir(kimdir):
+ print("\nkim-api is not installed at %s" % kimdir)
+ error()
-if not os.path.isfile("%s/Makefile.KIM_DIR" % thisdir):
- open("%s/Makefile.KIM_DIR" % thisdir, 'w').write("KIM_INSTALL_DIR=%s" % dir)
- open("%s/Makefile.KIM_Config" % thisdir, 'w').write("include %s/lib/kim-api/Makefile.KIM_Config" % dir)
- print "Created %s/Makefile.KIM_DIR : using %s" % (thisdir,dir)
+ # configure LAMMPS to use existing kim-api installation
+ with open("%s/Makefile.KIM_DIR" % thisdir, 'w') as mkfile:
+ mkfile.write("KIM_INSTALL_DIR=%s\n\n" % kimdir)
+ mkfile.write(".DUMMY: print_dir\n\n")
+ mkfile.write("print_dir:\n")
+ mkfile.write(" @printf $(KIM_INSTALL_DIR)\n")
+
+ with open("%s/Makefile.KIM_Config" % thisdir, 'w') as cfgfile:
+ cfgfile.write("include %s/lib/kim-api/Makefile.KIM_Config" % kimdir)
+
+ print("Created %s/Makefile.KIM_DIR\n using %s" % (thisdir,kimdir))
else:
- if dirflag == 1:
- open("%s/Makefile.KIM_DIR" % thisdir, 'w').write("KIM_INSTALL_DIR=%s" % dir)
- open("%s/Makefile.KIM_Config" % thisdir, 'w').write("include %s/lib/kim-api/Makefile.KIM_Config" % dir)
- print "Updated %s/Makefile.KIM_DIR : using %s" % (thisdir,dir)
+ kimdir = os.path.join(os.path.abspath(thisdir), "installed-" + version)
+
+# download KIM tarball, unpack, build KIM
+if buildflag:
+
+ # check to see if an installed kim-api already exists and wipe it out.
+
+ if os.path.isdir(kimdir):
+ print("kim-api is already installed at %s.\nRemoving it for re-install" % kimdir)
+ cmd = "rm -rf %s" % kimdir
+ subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+ # configure LAMMPS to use kim-api to be installed
-if buildflag == 1:
- # download kim-api
- print "Downloading kim-api tarball ..."
- urllib.urlretrieve(url,"%s/%s.tgz" % (thisdir,version))
- print "Unpacking kim-api tarball ..."
+ with open("%s/Makefile.KIM_DIR" % thisdir, 'w') as mkfile:
+ mkfile.write("KIM_INSTALL_DIR=%s\n\n" % kimdir)
+ mkfile.write(".DUMMY: print_dir\n\n")
+ mkfile.write("print_dir:\n")
+ mkfile.write(" @printf $(KIM_INSTALL_DIR)\n")
+
+ with open("%s/Makefile.KIM_Config" % thisdir, 'w') as cfgfile:
+ cfgfile.write("include %s/lib/kim-api/Makefile.KIM_Config" % kimdir)
+
+ print("Created %s/Makefile.KIM_DIR\n using %s" % (thisdir,kimdir))
+
+ # download entire kim-api tarball
+
+ print("Downloading kim-api tarball ...")
+ geturl(url,"%s/%s.tgz" % (thisdir,version))
+ print("Unpacking kim-api tarball ...")
cmd = "cd %s; rm -rf %s; tar zxvf %s.tgz" % (thisdir,version,version)
- txt = commands.getstatusoutput(cmd)
- if txt[0] != 0: error()
+ subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
# configure kim-api
- print "Configuring kim-api ..."
- cmd = "cd %s/%s; ./configure --prefix='%s'" % (thisdir,version,dir)
- txt = commands.getstatusoutput(cmd)
- print txt[1]
- if txt[0] != 0: error()
+
+ print("Configuring kim-api ...")
+ cmd = "cd %s/%s; ./configure --prefix='%s'" % (thisdir,version,kimdir)
+ subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
# build kim-api
- print "Configuring model : %s" % modelname
- cmd = "cd %s/%s; make add-%s" % (thisdir,version,modelname)
- txt = commands.getstatusoutput(cmd)
- print txt[1]
- if txt[0] != 0: error()
- #
- print "Building kim-api ..."
+
+ print("Configuring example Models")
+ cmd = "cd %s/%s; make add-examples" % (thisdir,version)
+ txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+ if verboseflag: print (txt.decode("UTF-8"))
+
+ if everythingflag:
+ print("Configuring all OpenKIM models, this will take a while ...")
+ cmd = "cd %s/%s; make add-OpenKIM" % (thisdir,version)
+ txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+ if verboseflag: print(txt.decode("UTF-8"))
+
+ print("Building kim-api ...")
cmd = "cd %s/%s; make" % (thisdir,version)
- txt = commands.getstatusoutput(cmd)
- print txt[1]
- if txt[0] != 0: error()
+ txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+ if verboseflag: print(txt.decode("UTF-8"))
# install kim-api
- print "Installing kim-api ..."
+
+ print("Installing kim-api ...")
cmd = "cd %s/%s; make install" % (thisdir,version)
- txt = commands.getstatusoutput(cmd)
- print txt[1]
- if txt[0] != 0: error()
- #
+ txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+ if verboseflag: print(txt.decode("UTF-8"))
+
cmd = "cd %s/%s; make install-set-default-to-v1" %(thisdir,version)
- txt = commands.getstatusoutput(cmd)
- print txt[1]
- if txt[0] != 0: error()
+ txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+ if verboseflag: print(txt.decode("UTF-8"))
# remove source files
- print "Removing kim-api source and build files ..."
+
+ print("Removing kim-api source and build files ...")
cmd = "cd %s; rm -rf %s; rm -rf %s.tgz" % (thisdir,version,version)
- txt = commands.getstatusoutput(cmd)
- print txt[1]
- if txt[0] != 0: error()
+ subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
-if addflag == 1:
- # download model
+# add a single model (and possibly its driver) to existing KIM installation
+
+if addflag:
+
+ if not os.path.isdir(kimdir):
+ print("\nkim-api is not installed")
+ error()
+
+ # download single model
+
+ print("Downloading tarball for %s..." % addmodelname)
url = "https://openkim.org/download/%s.tgz" % addmodelname
- print "Downloading item tarball ..."
- urllib.urlretrieve(url,"%s/%s.tgz" % (thisdir,addmodelname))
- print "Unpacking item tarball ..."
+ geturl(url,"%s/%s.tgz" % (thisdir,addmodelname))
+
+ print("Unpacking item tarball ...")
cmd = "cd %s; tar zxvf %s.tgz" % (thisdir,addmodelname)
- txt = commands.getstatusoutput(cmd)
- if txt[0] != 0: error()
- #
- print "Building item ..."
+ subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+
+ print("Building item ...")
cmd = "cd %s/%s; make; make install" %(thisdir,addmodelname)
- txt = commands.getstatusoutput(cmd)
- print txt[1]
- if txt[0] != 0: error()
- #
- print "Removing kim item source and build files ..."
+ try:
+ txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+ except subprocess.CalledProcessError as e:
+
+ # Error: but first, check to see if it needs a driver
+ firstRunOutput = e.output.decode("UTF-8")
+
+ cmd = "cd %s/%s; make kim-item-type" % (thisdir,addmodelname)
+ txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+ txt = txt.decode("UTF-8")
+ if txt == "ParameterizedModel":
+
+ # Get and install driver
+
+ cmd = "cd %s/%s; make model-driver-name" % (thisdir,addmodelname)
+ txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+ adddrivername = txt.decode("UTF-8").strip()
+ print("First installing model driver: %s..." % adddrivername)
+ cmd = "cd %s; python Install.py -n -a %s" % (thisdir,adddrivername)
+ try:
+ txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+ except subprocess.CalledProcessError as e:
+ print(e.output)
+ sys.exit()
+
+ if verboseflag: print(txt.decode("UTF-8"))
+
+ # now install the model that needed the driver
+
+ print("Now installing model : %s" % addmodelname)
+ cmd = "cd %s; python Install.py -n -a %s" % (thisdir,addmodelname)
+ try:
+ txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+ except subprocess.CalledProcessError as e:
+ print(e.output)
+ sys.exit()
+ print(txt.decode("UTF-8"))
+ sys.exit()
+ else:
+ print(firstRunOutput)
+ print("Error, unable to build and install OpenKIM item: %s" \
+ % addmodelname)
+ sys.exit()
+
+ # success the first time
+
+ if verboseflag: print(txt.decode("UTF-8"))
+ print("Removing kim item source and build files ...")
cmd = "cd %s; rm -rf %s; rm -rf %s.tgz" %(thisdir,addmodelname,addmodelname)
- txt = commands.getstatusoutput(cmd)
- print txt[1]
- if txt[0] != 0: error()
+ subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
diff --git a/lib/kim/README b/lib/kim/README
index 00d6ea8fadc296b24a15c41ff831bcec8d6ca698..7a4230dc25e99a282b5ba9b8e439d0b0250da058 100644
--- a/lib/kim/README
+++ b/lib/kim/README
@@ -8,14 +8,16 @@ James Sethna (Cornell U). Ryan Elliott is the main developer for the
KIM API and he also maintains the code that implements the pair_style
kim command.
-To download, build, and install the KIM API on your system, follow
-these steps. You can use the install.py script to automate these steps.
+You can type "make lib-kim" from the src directory to see help on
+how to download and 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.
-----------------
Instructions:
-
1. Configure lammps for use with the kim-api library installed in this directory
$ printf "KIM_INSTALL_DIR=${PWD}\n" > ./Makefile.KIM_DIR
@@ -65,7 +67,7 @@ $ rm -rf EAM_Johnson_NearestNeighbor_Cu__MO_887933271505_001.tgz
When these steps are complete you can build LAMMPS with the KIM
package installed:
-$ cd ../../src
+$ cd lammpos/src
$ make yes-kim
$ make g++ (or whatever target you wish)
diff --git a/lib/linalg/Install.py b/lib/linalg/Install.py
index c7076ca52f28dd63d09dae244f8491110d4a7891..560afecec42a844184b6723f1f87c55177cfd768 100644
--- a/lib/linalg/Install.py
+++ b/lib/linalg/Install.py
@@ -8,9 +8,15 @@ import sys,commands,os
# help message
help = """
-Syntax: python Install.py -m machine
+Syntax from src dir: make lib-linalg args="-m machine"
+Syntax from lib dir: python Install.py -m machine
+
-m = peform a clean followed by "make -f Makefile.machine"
machine = suffix of a lib/Makefile.* file
+
+Example:
+
+make lib-linalg args="-m gfortran" # build with GNU Fortran compiler
"""
# print error message or help
diff --git a/lib/meam/Install.py b/lib/meam/Install.py
index 37041d2ea1a2c903edce5c2c15e14149ae7bf3aa..ffe709d44c22d2060ad41538d1f8fc0df2b09b30 120000
--- a/lib/meam/Install.py
+++ b/lib/meam/Install.py
@@ -1 +1 @@
-Install.py
\ No newline at end of file
+../Install.py
\ No newline at end of file
diff --git a/lib/mscg/Install.py b/lib/mscg/Install.py
index e54723261452d1af2ddf1c837985089fd71aa2cd..7b10be189fee9b5c60fb84d318dcf388fb510926 100644
--- a/lib/mscg/Install.py
+++ b/lib/mscg/Install.py
@@ -8,8 +8,11 @@ import sys,os,re,commands
# help message
help = """
-Syntax: python Install.py -h hpath hdir -g -b [suffix] -l
- specify one or more options, order does not matter
+Syntax from src dir: make lib-mscg args="-h hpath hdir -g -b [suffix] -l"
+Syntax from lib dir: python Install.py -h hpath hdir -g -b [suffix] -l
+
+specify one or more options, order does not matter
+
-h = set home dir of MS-CG to be hpath/hdir
hpath can be full path, contain '~' or '.' chars
default hpath = . = lib/mscg
@@ -22,6 +25,10 @@ Syntax: python Install.py -h hpath hdir -g -b [suffix] -l
optional suffix specifies which src/Make/Makefile.suffix to use
default suffix = g++_simple
-l = create 2 softlinks (includelink,liblink) in lib/mscg to MS-CG src dir
+
+Example:
+
+make lib-mscg args="-g -b -l" # download/build in lib/mscg/MSCG-release-master
"""
# settings
diff --git a/lib/poems/Install.py b/lib/poems/Install.py
index 37041d2ea1a2c903edce5c2c15e14149ae7bf3aa..ffe709d44c22d2060ad41538d1f8fc0df2b09b30 120000
--- a/lib/poems/Install.py
+++ b/lib/poems/Install.py
@@ -1 +1 @@
-Install.py
\ No newline at end of file
+../Install.py
\ No newline at end of file
diff --git a/lib/qmmm/Install.py b/lib/qmmm/Install.py
index 37041d2ea1a2c903edce5c2c15e14149ae7bf3aa..ffe709d44c22d2060ad41538d1f8fc0df2b09b30 120000
--- a/lib/qmmm/Install.py
+++ b/lib/qmmm/Install.py
@@ -1 +1 @@
-Install.py
\ No newline at end of file
+../Install.py
\ No newline at end of file
diff --git a/lib/quip/.gitignore b/lib/quip/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..d6797a67febc6f223196111f75004b9dfa248898
--- /dev/null
+++ b/lib/quip/.gitignore
@@ -0,0 +1 @@
+/QUIP
diff --git a/lib/quip/Makefile.lammps b/lib/quip/Makefile.lammps
index 19ff20b073b30925d67e783f93ef8308a7a4ad54..e471d3f6f45b5a48252545b3af0f1a4cf86cf835 100644
--- a/lib/quip/Makefile.lammps
+++ b/lib/quip/Makefile.lammps
@@ -1,17 +1,26 @@
# Settings that the LAMMPS build will import when this package library is used
-# include ${QUIP_ROOT}/Makefiles/Makefile.${QUIP_ARCH}
-
-F95=$(shell egrep 'F95[ ]*=' ${QUIP_ROOT}/arch/Makefile.${QUIP_ARCH} | sed 's/.*F95[ ]*=[ ]*//')
-
+# try to guess settings assuming there is a configured QUIP git checkout inside the lib/quip directory
+QUIPDIR=$(abspath ../../lib/quip/QUIP)
ifeq (${QUIP_ROOT},)
-$(error Environment variable QUIP_ROOT must be set.)
+ QUIP_ROOT=$(shell test -d $(QUIPDIR) && echo $(QUIPDIR))
+ ifeq (${QUIP_ARCH},)
+ QUIP_ARCH=$(notdir $(wildcard $(QUIP_ROOT)/build/*))
+ endif
+else
+# uncomment and set manually or set the corresponding environment variables
+# QUIP_ROOT=
+# QUIP_ARCH=
endif
+ifeq (${QUIP_ROOT},)
+$(error Environment or make variable QUIP_ROOT must be set.)
+endif
ifeq (${QUIP_ARCH},)
-$(error Environment variable QUIP_ARCH must be set.)
+$(error Environment or make variable QUIP_ARCH must be set.)
endif
+F95=$(shell egrep 'F95[ ]*=' ${QUIP_ROOT}/arch/Makefile.${QUIP_ARCH} | sed 's/.*F95[ ]*=[ ]*//')
include ${QUIP_ROOT}/build/${QUIP_ARCH}/Makefile.inc
include ${QUIP_ROOT}/Makefile.rules
@@ -28,3 +37,4 @@ $(error fortran compiler >>${F95}<< not recognised. Edit lib/quip/Makefile.lammp
endif
quip_SYSPATH = -L${QUIP_ROOT}/build/${QUIP_ARCH}
+
diff --git a/lib/quip/README b/lib/quip/README
index 94039cfa179c8c23819f47296e32578ff3196942..e6cc3903bdeb71a612c3af3440218c5fc994013f 100644
--- a/lib/quip/README
+++ b/lib/quip/README
@@ -17,7 +17,7 @@ Building LAMMPS with QUIP support:
1) Building QUIP
1.1) Obtaining QUIP
-The most current release of QUIP can be obtained from github:
+The most current release of QUIP can be obtained from github:
$ git clone https://github.com/libAtoms/QUIP.git QUIP
@@ -59,7 +59,7 @@ necessary libraries will be built.
for example:
$ cd QUIP
-$ export QUIP_ROOT=/path/to/QUIP
+$ export QUIP_ROOT=${PWD}
$ export QUIP_ARCH=linux_x86_64_gfortran
$ make config
$ make libquip
@@ -70,21 +70,32 @@ to run a test suite.
2) Building LAMMPS
-LAMMPS is now shipped with the interface necessary to use QUIP potentials, but
-it should be enabled first. Enter the LAMMPS directory:
+Edit Makefile.lammps in the lib/quip folder, if necessary. If you
+have cloned, configured, and built QUIP inside this folder, QUIP_ROOT
+and QUIP_ARCH should be autodetected, even without having to set
+the environment variables. Otherwise export the environment variables
+as shown above or edit Makefile.lammps
+
+LAMMPS ships with a user package containing the interface necessary
+to use QUIP potentials, but it needs to be added to the compilation
+first. To do that, enter the LAMMPS source directory and type:
-$ cd LAMMPS
-$ cd src
$ make yes-user-quip
2.2) Build LAMMPS according to the instructions on the LAMMPS website.
-3) There are two example sets in examples/USER/quip:
+3) There are three example sets in examples/USER/quip:
- a set of input files to compute the energy of an 8-atom cubic
diamond cell of silicon with the Stillinger-Weber potential. Use
this to benchmark that the interface is working correctly.
+- a set of input files demonstrating the use of the QUIP pair style
+ for a molecular system with pair style hybrid/overlay and different
+ exclusion settings for different pair styles. This input is
+ for DEMONSTRATION purposes only, and does not simulate a physically
+ meaningful system.
+
- a set of input files to demonstrate how GAP potentials are specified
in a LAMMPS input file to run a short MD. The GAP parameter file
gap_example.xml is intended for TESTING purposes only. Potentials can be
diff --git a/lib/reax/Install.py b/lib/reax/Install.py
index 37041d2ea1a2c903edce5c2c15e14149ae7bf3aa..ffe709d44c22d2060ad41538d1f8fc0df2b09b30 120000
--- a/lib/reax/Install.py
+++ b/lib/reax/Install.py
@@ -1 +1 @@
-Install.py
\ No newline at end of file
+../Install.py
\ No newline at end of file
diff --git a/lib/smd/.gitignore b/lib/smd/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..4ab7a789ec5d0bbad7ced0d7f7e0977f667ef031
--- /dev/null
+++ b/lib/smd/.gitignore
@@ -0,0 +1,5 @@
+# ignore these entries with git
+/eigen.tar.gz
+/eigen-eigen-*
+/includelink
+/eigen3
diff --git a/lib/smd/Install.py b/lib/smd/Install.py
index dc0a3187ce546e81176d780297588a91b04dccce..337f993be5d192623996aa2f1cf361f0ff54eba2 100644
--- a/lib/smd/Install.py
+++ b/lib/smd/Install.py
@@ -3,101 +3,115 @@
# Install.py tool to download, unpack, and point to the Eigen library
# used to automate the steps described in the README file in this dir
-import sys,os,re,glob,commands
+from __future__ import print_function
+import sys,os,re,glob,subprocess
+try: from urllib.request import urlretrieve as geturl
+except: from urllib import urlretrieve as geturl
# help message
help = """
-Syntax: python Install.py -h hpath hdir -g -l
- specify one or more options, order does not matter
- -h = set home dir of Eigen to be hpath/hdir
- hpath can be full path, contain '~' or '.' chars
- default hpath = . = lib/smd
- default hdir = "ee" = what tarball unpacks to (eigen-eigen-*)
- -g = grab (download) tarball from http://eigen.tuxfamily.org website
- unpack it to hpath/hdir
- hpath must already exist
- if hdir already exists, it will be deleted before unpack
- -l = create softlink (includelink) in lib/smd to Eigen src dir
+Syntax from src dir: make lib-smd
+ or: make lib-smd args="-p /usr/include/eigen3"
+
+Syntax from lib dir: python Install.py
+ or: python Install.py -p /usr/include/eigen3"
+ or: python Install.py -v 3.3.4 -b
+
+specify one or more options, order does not matter
+
+ -b = download and unpack/configure the Eigen library (default)
+ -p = specify folder holding an existing installation of Eigen
+ -v = set version of Eigen library to download and set up (default = 3.3.4)
+
+
+Example:
+
+make lib-smd args="-b" # download/build in default lib/smd/eigen-eigen-*
"""
# settings
-url = "http://bitbucket.org/eigen/eigen/get/3.3.3.tar.gz"
+version = '3.3.4'
tarball = "eigen.tar.gz"
# 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()
# expand to full path name
# process leading '~' or relative path
-
+
def fullpath(path):
return os.path.abspath(os.path.expanduser(path))
-
+
# parse args
args = sys.argv[1:]
nargs = len(args)
-if nargs == 0: error()
homepath = "."
-homedir = "ee"
+homedir = "eigen3"
-grabflag = 0
-linkflag = 0
+grabflag = True
+buildflag = True
+pathflag = False
+linkflag = True
iarg = 0
while iarg < nargs:
- if args[iarg] == "-h":
- if iarg+3 > nargs: error()
- homepath = args[iarg+1]
- homedir = args[iarg+2]
- iarg += 3
- elif args[iarg] == "-g":
- grabflag = 1
- iarg += 1
- elif args[iarg] == "-l":
- linkflag = 1
+ if args[iarg] == "-v":
+ if iarg+2 > nargs: error()
+ version = args[iarg+1]
+ iarg += 2
+ elif args[iarg] == "-p":
+ if iarg+2 > nargs: error()
+ eigenpath = fullpath(args[iarg+1])
+ pathflag = True
+ buildflag = False
+ iarg += 2
+ elif args[iarg] == "-b":
+ buildflag = True
iarg += 1
else: error()
homepath = fullpath(homepath)
-if not os.path.isdir(homepath): error("Eigen path does not exist")
+
+if (pathflag):
+ if not os.path.isdir(eigenpath): error("Eigen path does not exist")
+
+if (buildflag and pathflag):
+ error("Cannot use -b and -p flag at the same time")
# download and unpack Eigen tarball
-# glob to find name of dir it unpacks to
+# use glob to find name of dir it unpacks to
-if grabflag:
- print "Downloading Eigen ..."
- cmd = "curl -L %s > %s/%s" % (url,homepath,tarball)
- print cmd
- print commands.getoutput(cmd)
+if buildflag:
+ print("Downloading Eigen ...")
+ url = "http://bitbucket.org/eigen/eigen/get/%s.tar.gz" % version
+ geturl(url,"%s/%s" % (homepath,tarball))
- print "Unpacking Eigen tarball ..."
+ print("Unpacking Eigen tarball ...")
edir = glob.glob("%s/eigen-eigen-*" % homepath)
for one in edir:
- if os.path.isdir(one): commands.getoutput("rm -rf %s" % one)
- cmd = "cd %s; tar zxvf %s" % (homepath,tarball)
- commands.getoutput(cmd)
- if homedir != "ee":
- if os.path.exists(homedir): commands.getoutput("rm -rf %s" % homedir)
- edir = glob.glob("%s/eigen-eigen-*" % homepath)
- os.rename(edir[0],"%s/%s" % (homepath,homedir))
+ if os.path.isdir(one):
+ subprocess.check_output("rm -rf %s" % one,stderr=subprocess.STDOUT,shell=True)
+ cmd = 'cd "%s"; tar -xzvf %s' % (homepath,tarball)
+ subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+ edir = glob.glob("%s/eigen-eigen-*" % homepath)
+ os.rename(edir[0],"%s/%s" % (homepath,homedir))
+ os.remove(tarball)
# create link in lib/smd to Eigen src dir
if linkflag:
- print "Creating link to Eigen files"
+ print("Creating link to Eigen files")
if os.path.isfile("includelink") or os.path.islink("includelink"):
os.remove("includelink")
- if homedir == "ee":
- edir = glob.glob("%s/eigen-eigen-*" % homepath)
- linkdir = edir[0]
+ if pathflag: linkdir = eigenpath
else: linkdir = "%s/%s" % (homepath,homedir)
cmd = "ln -s %s includelink" % linkdir
- commands.getoutput(cmd)
+ subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
diff --git a/lib/voronoi/.gitignore b/lib/voronoi/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..6ca01c094f57a17dd29df3d78128897b4fcf9854
--- /dev/null
+++ b/lib/voronoi/.gitignore
@@ -0,0 +1,4 @@
+# files to ignore
+/liblink
+/includelink
+/voro++-*
diff --git a/lib/voronoi/Install.py b/lib/voronoi/Install.py
index 7d847183b38fb3e0733df56f33a4ccffcf479bbc..17bba5e8eb5cdfe0e0cd013c74433c894c4f4038 100644
--- a/lib/voronoi/Install.py
+++ b/lib/voronoi/Install.py
@@ -3,25 +3,30 @@
# Install.py tool to download, unpack, build, and link to the Voro++ library
# used to automate the steps described in the README file in this dir
-import sys,os,re,urllib,commands
+from __future__ import print_function
+import sys,os,re,subprocess
+try: from urllib.request import urlretrieve as geturl
+except: from urllib import urlretrieve as geturl
# help message
help = """
-Syntax: python Install.py -v version -h hpath hdir -g -b -l
- specify one or more options, order does not matter
- -v = version of Voro++ to download and build
- default version = voro++-0.4.6 (current as of Jan 2015)
- -h = set home dir of Voro++ to be hpath/hdir
- hpath can be full path, contain '~' or '.' chars
- default hpath = . = lib/voronoi
- default hdir = voro++-0.4.6 = what tarball unpacks to
- -g = grab (download) tarball from math.lbl.gov/voro++ website
- unpack it to hpath/hdir
- hpath must already exist
- if hdir already exists, it will be deleted before unpack
- -b = build Voro++ library in its src dir
- -l = create 2 softlinks (includelink,liblink) in lib/voronoi to Voro++ src dir
+Syntax from src dir: make lib-voronoi
+ or: make lib-voronoi args="-p /usr/local/voro++-0.4.6"
+ or: make lib-voronoi args="-v voro++-0.4.6 -b"
+Syntax from lib dir: python Install.py -v voro++-0.4.6 -b
+ or: python Install.py
+ or: python Install.py -p /usr/local/voro++-0.4.6
+
+specify one or more options, order does not matter
+
+ -b = download and build the Voro++ library (default)
+ -p = specify folder of existing Voro++ installation
+ -v = set version of Voro++ to download and build (default voro++-0.4.6)
+
+Example:
+
+make lib-voronoi args="-b" # download/build in lib/voronoi/voro++-0.4.6
"""
# settings
@@ -32,28 +37,28 @@ url = "http://math.lbl.gov/voro++/download/dir/%s.tar.gz" % version
# 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()
# expand to full path name
# process leading '~' or relative path
-
+
def fullpath(path):
return os.path.abspath(os.path.expanduser(path))
-
+
# parse args
args = sys.argv[1:]
nargs = len(args)
-if nargs == 0: error()
homepath = "."
homedir = version
-grabflag = 0
-buildflag = 0
-linkflag = 0
+grabflag = True
+buildflag = True
+pathflag = False
+linkflag = True
iarg = 0
while iarg < nargs:
@@ -61,58 +66,63 @@ while iarg < nargs:
if iarg+2 > nargs: error()
version = args[iarg+1]
iarg += 2
- elif args[iarg] == "-h":
- if iarg+3 > nargs: error()
- homepath = args[iarg+1]
- homedir = args[iarg+2]
- iarg += 3
- elif args[iarg] == "-g":
- grabflag = 1
- iarg += 1
+ elif args[iarg] == "-p":
+ if iarg+2 > nargs: error()
+ voropath = fullpath(args[iarg+1])
+ pathflag = True
+ buildflag = False
+ iarg += 2
elif args[iarg] == "-b":
- buildflag = 1
- iarg += 1
- elif args[iarg] == "-l":
- linkflag = 1
+ buildflag = True
iarg += 1
else: error()
homepath = fullpath(homepath)
-if not os.path.isdir(homepath): error("Voro++ path does not exist")
-homedir = "%s/%s" % (homepath,homedir)
+homedir = "%s/%s" % (homepath,version)
+
+if (pathflag):
+ if not os.path.isdir(voropath): error("Voro++ path does not exist")
+ homedir = voropath
+
+if (buildflag and pathflag):
+ error("Cannot use -b and -p flag at the same time")
# download and unpack Voro++ tarball
if grabflag:
- print "Downloading Voro++ ..."
- urllib.urlretrieve(url,"%s/%s.tar.gz" % (homepath,version))
-
- print "Unpacking Voro++ tarball ..."
+ print("Downloading Voro++ ...")
+ geturl(url,"%s/%s.tar.gz" % (homepath,version))
+
+ print("Unpacking Voro++ tarball ...")
if os.path.exists("%s/%s" % (homepath,version)):
- commands.getoutput("rm -rf %s/%s" % (homepath,version))
- cmd = "cd %s; tar zxvf %s.tar.gz" % (homepath,version)
- commands.getoutput(cmd)
+ cmd = 'rm -rf "%s/%s"' % (homepath,version)
+ subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+ cmd = 'cd "%s"; tar -xzvf %s.tar.gz' % (homepath,version)
+ subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+ os.remove("%s/%s.tar.gz" % (homepath,version))
if os.path.basename(homedir) != version:
- if os.path.exists(homedir): commands.getoutput("rm -rf %s" % homedir)
+ if os.path.exists(homedir):
+ cmd = 'rm -rf "%s"' % homedir
+ subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
os.rename("%s/%s" % (homepath,version),homedir)
# build Voro++
if buildflag:
- print "Building Voro++ ..."
- cmd = "cd %s; make" % homedir
- txt = commands.getoutput(cmd)
- print txt
+ print("Building Voro++ ...")
+ cmd = 'cd "%s"; make' % homedir
+ txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+ print(txt.decode('UTF-8'))
# create 2 links in lib/voronoi to Voro++ src dir
if linkflag:
- print "Creating links to Voro++ include and lib files"
+ print("Creating links to Voro++ include and lib files")
if os.path.isfile("includelink") or os.path.islink("includelink"):
os.remove("includelink")
if os.path.isfile("liblink") or os.path.islink("liblink"):
os.remove("liblink")
- cmd = "ln -s %s/src includelink" % homedir
- commands.getoutput(cmd)
- cmd = "ln -s %s/src liblink" % homedir
- commands.getoutput(cmd)
+ cmd = ['ln -s "%s/src" includelink' % homedir, 'includelink']
+ subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+ cmd = ['ln -s "%s/src" liblink' % homedir]
+ subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
diff --git a/lib/voronoi/README b/lib/voronoi/README
index 9863632be0d1ea7e3f5c4158197291a5cd43ab30..2ca11c9221a9f4751b739b9a71f484ba9b88bf1a 100644
--- a/lib/voronoi/README
+++ b/lib/voronoi/README
@@ -22,7 +22,7 @@ Instructions:
or somewhere else on your system.
2. compile Voro++ from within its home directory
- % make
+ % make
3. There is no need to install Voro++ if you only wish
to use it from LAMMPS. You can install it if you
diff --git a/src/.gitignore b/src/.gitignore
index e26f3c6ca0e5bad2eb3021268ab83a7c9316f229..80166e260e42c40c435c86d01aa254e1baeb3f17 100644
--- a/src/.gitignore
+++ b/src/.gitignore
@@ -790,6 +790,8 @@
/pair_peri_pmb.h
/pair_peri_ves.cpp
/pair_peri_ves.h
+/pair_quip.cpp
+/pair_quip.h
/pair_reax.cpp
/pair_reax.h
/pair_reax_fortran.h
diff --git a/src/Makefile b/src/Makefile
index c7b20dcb1301803f84b4baabf62e1004ea670d5f..3d1085e0be5c0a5bda16580dc60a0a6ce5474f8c 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -116,7 +116,8 @@ help:
@echo 'make package-overwrite replace package files with src files'
@echo 'make package-diff (pd) diff src files against package files'
@echo ''
- @echo 'make lib-package download/build/install a package library'
+ @echo 'make lib-package help for download/build/install a package library'
+ @echo 'make lib-package args="..." download/build/install a package library'
@echo 'make purge purge obsolete copies of source files'
@echo ''
@echo 'make machine build LAMMPS for machine'
diff --git a/src/balance.cpp b/src/balance.cpp
index c184a72d3278807cccc25d110bd813f4a810bd1b..8f994466ad8e18cd30658f92108ff6648fade083 100644
--- a/src/balance.cpp
+++ b/src/balance.cpp
@@ -782,7 +782,7 @@ void Balance::shift_setup(char *str, int nitermax_in, double thresh_in)
int Balance::shift()
{
- int i,j,k,m,np,max;
+ int i,j,k,m,np;
double mycost,totalcost;
double *split;
diff --git a/src/variable.cpp b/src/variable.cpp
index 6e16597c636b9e9e07f9f484cdbcb8721b8c5352..a8f195dbc886fa4e1da538e973f7504175879efd 100644
--- a/src/variable.cpp
+++ b/src/variable.cpp
@@ -2148,8 +2148,10 @@ double Variable::evaluate(char *str, Tree **tree)
argstack[nargstack++] = fmod(value1,value2);
} else if (opprevious == CARAT) {
if (value2 == 0.0)
- error->all(FLERR,"Power by 0 in variable formula");
- argstack[nargstack++] = pow(value1,value2);
+ argstack[nargstack++] = 1.0;
+ else if ((value1 == 0.0) && (value2 < 0.0))
+ error->all(FLERR,"Invalid power expression in variable formula");
+ else argstack[nargstack++] = pow(value1,value2);
} else if (opprevious == UNARY) {
argstack[nargstack++] = -value2;
} else if (opprevious == NOT) {