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Merge pull request #1465 from akohlmey/collected-minor-changes

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Collected small changes and bugfixes
This commit is contained in:
Axel Kohlmeyer
2019-05-21 16:55:19 -04:00
committed by GitHub
parent bd05228c71 d0c6484fb0
commit cfad0634ac
11 changed files with 59 additions and 90 deletions
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2
doc/Makefile
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@ -211,7 +211,7 @@ $(VENV):
@( \
$(VIRTUALENV) -p $(PYTHON) $(VENV); \
. $(VENV)/bin/activate; \
pip install Sphinx==1.7.6; \
pip install Sphinx; \
deactivate;\
)

44
doc/src/Build_extras.txt
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@ -30,7 +30,6 @@ This is the list of packages that may require additional steps.
"KIM"_#kim,
"KOKKOS"_#kokkos,
"LATTE"_#latte,
"MEAM"_#meam,
"MESSAGE"_#message,
"MSCG"_#mscg,
"OPT"_#opt,
@ -351,49 +350,6 @@ the compiler you use on your system to build LATTE.
:line
MEAM package :h4,link(meam)
NOTE: the use of the MEAM package is discouraged, as it has been
superseded by the USER-MEAMC package, which is a direct translation of
the Fortran code in the MEAM library to C++. The code in USER-MEAMC
should be functionally equivalent to the MEAM package, fully supports
use of "pair_style hybrid"_pair_hybrid.html (the MEAM package does
not), and has optimizations that make it significantly faster than the
MEAM package.
[CMake build]:
No additional settings are needed besides "-D PKG_MEAM=yes".
[Traditional make]:
Before building LAMMPS, you must build the MEAM library in lib/meam.
You can build the MEAM library manually if you prefer; follow the
instructions in lib/meam/README. You can also do it in one step from
the lammps/src dir, using a command like these, which simply invoke
the lib/meam/Install.py script with the specified args:
make lib-meam # print help message
make lib-meam args="-m mpi" # build with default Fortran compiler compatible with your MPI library
make lib-meam args="-m serial" # build with compiler compatible with "make serial" (GNU Fortran)
make lib-meam args="-m ifort" # build with Intel Fortran compiler using Makefile.ifort :pre
NOTE: You should test building the MEAM library with both the Intel
and GNU compilers to see if a simulation runs faster with one versus
the other on your system.
The build should produce two files: lib/meam/libmeam.a and
lib/meam/Makefile.lammps. The latter is copied from an existing
Makefile.lammps.* and has settings needed to link C++ (LAMMPS) with
Fortran (MEAM library). Typically the two compilers used for LAMMPS
and the MEAM library need to be consistent (e.g. both Intel or both
GNU compilers). If necessary, you can edit/create a new
lib/meam/Makefile.machine file for your system, which should define an
EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
file.
:line
MESSAGE package :h4,link(message)
This package can optionally include support for messaging via sockets,

1
doc/src/Build_package.txt
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@ -41,7 +41,6 @@ packages:
"KIM"_Build_extras.html#kim,
"KOKKOS"_Build_extras.html#kokkos,
"LATTE"_Build_extras.html#latte,
"MEAM"_Build_extras.html#meam,
"MESSAGE"_Build_extras.html#message,
"MSCG"_Build_extras.html#mscg,
"OPT"_Build_extras.html#opt,

20
doc/src/Errors_messages.txt
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@ -9990,25 +9990,25 @@ quote. :dd
Self-explanatory. :dd
{Unexpected end of AngleCoeffs section} :dt
{Unexpected empty line in AngleCoeffs section} :dt
Read a blank line. :dd
Read a blank line where there should be coefficient data. :dd
{Unexpected end of BondCoeffs section} :dt
{Unexpected empty line in BondCoeffs section} :dt
Read a blank line. :dd
Read a blank line where there should be coefficient data. :dd
{Unexpected end of DihedralCoeffs section} :dt
{Unexpected empty line in DihedralCoeffs section} :dt
Read a blank line. :dd
Read a blank line where there should be coefficient data. :dd
{Unexpected end of ImproperCoeffs section} :dt
{Unexpected empty line in ImproperCoeffs section} :dt
Read a blank line. :dd
Read a blank line where there should be coefficient data. :dd
{Unexpected end of PairCoeffs section} :dt
{Unexpected empty line in PairCoeffs section} :dt
Read a blank line. :dd
Read a blank line where there should be coefficient data. :dd
{Unexpected end of custom file} :dt

10
doc/src/Examples.txt
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@ -52,13 +52,14 @@ Lowercase directories :h4
accelerate: run with various acceleration options (OpenMP, GPU, Phi)
airebo: polyethylene with AIREBO potential
atm: Axilrod-Teller-Muto potential example
balance: dynamic load balancing, 2d system
body: body particles, 2d system
cmap: CMAP 5-body contributions to CHARMM force field
colloid: big colloid particles in a small particle solvent, 2d system
comb: models using the COMB potential
coreshell: core/shell model using CORESHELL package
controller: use of fix controller as a thermostat
coreshell: core/shell model using CORESHELL package
crack: crack propagation in a 2d solid
deposit: deposit atoms and molecules on a surface
dipole: point dipolar particles, 2d system
@ -70,10 +71,13 @@ friction: frictional contact of spherical asperities between 2d surfaces
gcmc: Grand Canonical Monte Carlo (GCMC) via the fix gcmc command
granregion: use of fix wall/region/gran as boundary on granular particles
hugoniostat: Hugoniostat shock dynamics
hyper: global and local hyperdynamics of diffusion on Pt surface
indent: spherical indenter into a 2d solid
kim: use of potentials in Knowledge Base for Interatomic Models (KIM)
latte: examples for using fix latte for DFTB via the LATTE library
meam: MEAM test for SiC and shear (same as shear examples)
melt: rapid melt of 3d LJ system
message: demos for LAMMPS client/server coupling with the MESSAGE package
micelle: self-assembly of small lipid-like molecules into 2d bilayers
min: energy minimization of 2d LJ melt
mscg: parameterize a multi-scale coarse-graining (MSCG) model
@ -88,6 +92,7 @@ pour: pouring of granular particles into a 3d box, then chute flow
prd: parallel replica dynamics of vacancy diffusion in bulk Si
python: using embedded Python in a LAMMPS input script
qeq: use of the QEQ package for charge equilibration
rdf-adf: computing radial and angle distribution functions for water
reax: RDX and TATB models using the ReaxFF
rigid: rigid bodies modeled as independent or coupled
shear: sideways shear applied to 2d solid, with and without a void
@ -95,6 +100,7 @@ snap: NVE dynamics for BCC tantalum crystal using SNAP potential
srd: stochastic rotation dynamics (SRD) particles as solvent
streitz: use of Streitz/Mintmire potential with charge equilibration
tad: temperature-accelerated dynamics of vacancy diffusion in bulk Si
threebody: regression test input for a variety of manybody potentials
vashishta: use of the Vashishta potential
voronoi: Voronoi tesselation via compute voronoi/atom command :tb(s=:)
@ -131,8 +137,10 @@ COUPLE: examples of how to use LAMMPS as a library
DIFFUSE: compute diffusion coefficients via several methods
ELASTIC: compute elastic constants at zero temperature
ELASTIC_T: compute elastic constants at finite temperature
HEAT: compute thermal conductivity for LJ and water via fix ehex
KAPPA: compute thermal conductivity via several methods
MC: using LAMMPS in a Monte Carlo mode to relax the energy of a system
SPIN: examples for features of the SPIN package
USER: examples for USER packages and USER-contributed commands
VISCOSITY: compute viscosity via several methods :tb(s=:)

1
doc/utils/sphinx-config/false_positives.txt
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@ -2708,6 +2708,7 @@ Thiaville
Thibaudeau
Thijsse
Thirumalai
threebody
thrid
ThunderX
thylakoid

2
examples/HEAT/README
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@ -1,6 +1,6 @@
This directory contains 4 input scripts for carrying out NEMD
simulations of thermal gradients for a Lennard-Jones fluid and SPC/E
water using the HEX/a (fix heat) and eHEX/a (fix ehex) algorithms.
water using the HEX/a (fix ehex w/ hex option) and eHEX/a (fix ehex) algorithms.
All input scripts are part of the supplementary (open access) material
supporting the publication of Wirnsberger et al. [J. Chem. Phys. 143,

27
examples/README
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@ -64,37 +64,37 @@ balance: dynamic load balancing, 2d system
body: body particles, 2d system
cmap: CMAP 5-body contributions to CHARMM force field
colloid: big colloid particles in a small particle solvent, 2d system
comb: models using the COMB potential
comb: models using the COMB potential
coreshell: adiabatic core/shell model
controller: use of fix controller as a thermostat
crack: crack propagation in a 2d solid
crack: crack propagation in a 2d solid
deposit: deposition of atoms and molecules onto a 3d substrate
dipole: point dipolar particles, 2d system
dreiding: methanol via Dreiding FF
eim: NaCl using the EIM potential
ellipse: ellipsoidal particles in spherical solvent, 2d system
flow: Couette and Poiseuille flow in a 2d channel
flow: Couette and Poiseuille flow in a 2d channel
friction: frictional contact of spherical asperities between 2d surfaces
gcmc: Grand Canonical Monte Carlo (GCMC) via the fix gcmc command
granregion: use of fix wall/region/gran as boundary on granular particles
hugoniostat: Hugoniostat shock dynamics
hyper: global and local hyperdynamics of diffusion on Pt surface
indent: spherical indenter into a 2d solid
indent: spherical indenter into a 2d solid
kim: use of potentials in Knowledge Base for Interatomic Models (KIM)
latte: use of LATTE density-functional tight-binding quantum code
meam: MEAM test for SiC and shear (same as shear examples)
melt: rapid melt of 3d LJ system
meam: MEAM test for SiC and shear (same as shear examples)
melt: rapid melt of 3d LJ system
message: client/server coupling of 2 codes
micelle: self-assembly of small lipid-like molecules into 2d bilayers
min: energy minimization of 2d LJ melt
min: energy minimization of 2d LJ melt
mscg: parameterize a multi-scale coarse-graining (MSCG) model
msst: MSST shock dynamics
msst: MSST shock dynamics
nb3b: use of nonbonded 3-body harmonic pair style
neb: nudged elastic band (NEB) calculation for barrier finding
nemd: non-equilibrium MD of 2d sheared system
neb: nudged elastic band (NEB) calculation for barrier finding
nemd: non-equilibrium MD of 2d sheared system
obstacle: flow around two voids in a 2d channel
peptide: dynamics of a small solvated peptide chain (5-mer)
peri: Peridynamic model of cylinder impacted by indenter
peri: Peridynamic model of cylinder impacted by indenter
pour: pouring of granular particles into a 3d box, then chute flow
prd: parallel replica dynamics of vacancy diffusion in bulk Si
python: use of PYTHON package to invoke Python code from input script
@ -107,6 +107,7 @@ srd: stochastic rotation dynamics (SRD) particles as solvent
snap: NVE dynamics for BCC tantalum crystal using SNAP potential
streitz: Streitz-Mintmire potential for Al2O3
tad: temperature-accelerated dynamics of vacancy diffusion in bulk Si
threebody: regression test input for a variety of manybody potentials
vashishta: models using the Vashishta potential
voronoi: Voronoi tesselation via compute voronoi/atom command
@ -117,9 +118,7 @@ cp ../../src/lmp_mpi . # copy LAMMPS executable to this dir
lmp_mpi -in in.indent # run the problem
Running the simulation produces the files {dump.indent} and
{log.lammps}. You can visualize the dump file as follows:
../../tools/xmovie/xmovie -scale dump.indent
{log.lammps}.
If you uncomment the dump image line(s) in the input script a series
of JPG images will be produced by the run. These can be viewed

2
src/USER-OMP/pair_rebo_omp.cpp
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@ -41,8 +41,6 @@ void PairREBOOMP::settings(int narg, char ** /* arg */)
void PairREBOOMP::spline_init() {
PairAIREBO::spline_init();
int i,j,k;
PCCf[0][2] = 0.007860700254745;
PCCf[0][3] = 0.016125364564267;
PCCf[1][1] = 0.003026697473481;

20
src/read_data.cpp
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@ -1768,7 +1768,8 @@ void ReadData::paircoeffs()
next = strchr(buf,'\n');
*next = '\0';
parse_coeffs(buf,NULL,1,2,toffset);
if (narg == 0) error->all(FLERR,"Unexpected end of PairCoeffs section");
if (narg == 0)
error->all(FLERR,"Unexpected empty line in PairCoeffs section");
force->pair->coeff(narg,arg);
buf = next + 1;
}
@ -1794,7 +1795,8 @@ void ReadData::pairIJcoeffs()
next = strchr(buf,'\n');
*next = '\0';
parse_coeffs(buf,NULL,0,2,toffset);
if (narg == 0) error->all(FLERR,"Unexpected end of PairCoeffs section");
if (narg == 0)
error->all(FLERR,"Unexpected empty line in PairCoeffs section");
force->pair->coeff(narg,arg);
buf = next + 1;
}
@ -1818,7 +1820,8 @@ void ReadData::bondcoeffs()
next = strchr(buf,'\n');
*next = '\0';
parse_coeffs(buf,NULL,0,1,boffset);
if (narg == 0) error->all(FLERR,"Unexpected end of BondCoeffs section");
if (narg == 0)
error->all(FLERR,"Unexpected empty line in BondCoeffs section");
force->bond->coeff(narg,arg);
buf = next + 1;
}
@ -1844,7 +1847,7 @@ void ReadData::anglecoeffs(int which)
if (which == 0) parse_coeffs(buf,NULL,0,1,aoffset);
else if (which == 1) parse_coeffs(buf,"bb",0,1,aoffset);
else if (which == 2) parse_coeffs(buf,"ba",0,1,aoffset);
if (narg == 0) error->all(FLERR,"Unexpected end of AngleCoeffs section");
if (narg == 0) error->all(FLERR,"Unexpected empty line in AngleCoeffs section");
force->angle->coeff(narg,arg);
buf = next + 1;
}
@ -1873,7 +1876,8 @@ void ReadData::dihedralcoeffs(int which)
else if (which == 3) parse_coeffs(buf,"at",0,1,doffset);
else if (which == 4) parse_coeffs(buf,"aat",0,1,doffset);
else if (which == 5) parse_coeffs(buf,"bb13",0,1,doffset);
if (narg == 0) error->all(FLERR,"Unexpected end of DihedralCoeffs section");
if (narg == 0)
error->all(FLERR,"Unexpected empty line in DihedralCoeffs section");
force->dihedral->coeff(narg,arg);
buf = next + 1;
}
@ -1898,7 +1902,7 @@ void ReadData::impropercoeffs(int which)
*next = '\0';
if (which == 0) parse_coeffs(buf,NULL,0,1,ioffset);
else if (which == 1) parse_coeffs(buf,"aa",0,1,ioffset);
if (narg == 0) error->all(FLERR,"Unexpected end of ImproperCoeffs section");
if (narg == 0) error->all(FLERR,"Unexpected empty line in ImproperCoeffs section");
force->improper->coeff(narg,arg);
buf = next + 1;
}
@ -2092,6 +2096,10 @@ void ReadData::parse_coeffs(char *line, const char *addstr,
word = strtok(NULL," \t\n\r\f");
}
// to avoid segfaults on empty lines
if (narg == 0) return;
if (noffset) {
int value = force->inumeric(FLERR,arg[0]);
sprintf(argoffset1,"%d",value+offset);

20
src/read_data.h
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@ -533,25 +533,25 @@ E: Too many lines in one body in data file - boost MAXBODY
MAXBODY is a setting at the top of the src/read_data.cpp file.
Set it larger and re-compile the code.
E: Unexpected end of PairCoeffs section
E: Unexpected empty line in PairCoeffs section
Read a blank line.
Read a blank line where there should be coefficient data.
E: Unexpected end of BondCoeffs section
E: Unexpected empty line in BondCoeffs section
Read a blank line.
Read a blank line where there should be coefficient data.
E: Unexpected end of AngleCoeffs section
E: Unexpected empty line in AngleCoeffs section
Read a blank line.
Read a blank line where there should be coefficient data.
E: Unexpected end of DihedralCoeffs section
E: Unexpected empty line in DihedralCoeffs section
Read a blank line.
Read a blank line where there should be coefficient data.
E: Unexpected end of ImproperCoeffs section
E: Unexpected empty line in ImproperCoeffs section
Read a blank line.
Read a blank line where there should be coefficient data.
E: Cannot open gzipped file