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Merge pull request #665 from akohlmey/collected-small-fixes

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Collected small fixes
This commit is contained in:
Steve Plimpton
2017-10-05 16:58:49 -06:00
committed by GitHub
parent 4b7ca0383a c522b1b7a9
commit 5d0626e50e
20 changed files with 77 additions and 56 deletions
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3
doc/src/Section_packages.txt
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@ -705,7 +705,7 @@ dynamics can be run with LAMMPS using density-functional tight-binding
quantum forces calculated by LATTE.
More information on LATTE can be found at this web site:
"https://github.com/lanl/LATTE"_#latte_home. A brief technical
"https://github.com/lanl/LATTE"_latte_home. A brief technical
description is given with the "fix latte"_fix_latte.html command.
:link(latte_home,https://github.com/lanl/LATTE)
@ -728,6 +728,7 @@ make lib-latte args="-b" # download and build in lib/latte/LATTE-
make lib-latte args="-p $HOME/latte" # use existing LATTE installation in $HOME/latte
make lib-latte args="-b -m gfortran" # download and build in lib/latte and
# copy Makefile.lammps.gfortran to Makefile.lammps
:pre
Note that 3 symbolic (soft) links, "includelink" and "liblink" and
"filelink", are created in lib/latte to point into the LATTE home dir.

10
doc/src/fix_latte.txt
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@ -66,7 +66,7 @@ reference charge of overlapping atom-centered densities and bond
integrals are parameterized using a Slater-Koster tight-binding
approach. This procedure, which usually is referred to as the DFTB
method has been described in detail by ("Elstner"_#Elstner) and
("Finnis"_#Finnis) and coworkers.
("Finnis"_#Finnis2) and coworkers.
The work of the LATTE developers follows that of Elstner closely with
respect to the physical model. However, the development of LATTE is
@ -173,7 +173,7 @@ M. Haugk, T. Frauenheim, S. Suhai, and G. Seifert, Phys. Rev. B, 58,
M. Haugk, T. Frauenheim, S. Suhai, and G. Seifert, Phys. Rev. B, 58,
7260 (1998).
:link(Finnis)
:link(Finnis2)
[(Finnis)] M. W. Finnis, A. T. Paxton, M. Methfessel, and M. van
Schilfgarde, Phys. Rev. Lett., 81, 5149 (1998).
@ -197,11 +197,11 @@ J. Sci. Comput. 36 (2), 147-170, (2014).
[(Niklasson2014)] A. M. N. Niklasson and M. Cawkwell, J. Chem. Phys.,
141, 164123, (2014).
:link(Niklasson2014)
:link(Niklasson2017)
[(Niklasson2017)] A. M. N. Niklasson, J. Chem. Phys., 147, 054103 (2017).
:link(Niklasson2012)
[(Niklasson2017)] A. M. N. Niklasson, M. J. Cawkwell, Phys. Rev. B, 86
:link(Cawkwell2012)
[(Cawkwell2012)] A. M. N. Niklasson, M. J. Cawkwell, Phys. Rev. B, 86
(17), 174308 (2012).
:link(Negre2016)

4
doc/src/fix_neb.txt
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@ -93,7 +93,7 @@ intermediate replica with the previous and the next image:
Fnudge_parallel = {Kspring} * (|Ri+1 - Ri| - |Ri - Ri-1|) :pre
Note that in this case the specified {Kspring) is in force/distance
Note that in this case the specified {Kspring} is in force/distance
units.
With a value of {ideal}, the spring force is computed as suggested in
@ -105,7 +105,7 @@ where RD is the "reaction coordinate" see "neb"_neb.html section, and
RDideal is the ideal RD for which all the images are equally spaced.
I.e. RDideal = (I-1)*meanDist when the climbing replica is off, where
I is the replica number). The meanDist is the average distance
between replicas. Note that in this case the specified {Kspring) is
between replicas. Note that in this case the specified {Kspring} is
in force units.
Note that the {ideal} form of nudging can often be more effective at

1
doc/src/fixes.txt
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@ -59,6 +59,7 @@ Fixes :h1
fix_langevin
fix_langevin_drude
fix_langevin_eff
fix_latte
fix_lb_fluid
fix_lb_momentum
fix_lb_pc

1
doc/src/lammps.book
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@ -187,6 +187,7 @@ fix_ipi.html
fix_langevin.html
fix_langevin_drude.html
fix_langevin_eff.html
fix_latte.html
fix_lb_fluid.html
fix_lb_momentum.html
fix_lb_pc.html

4
doc/src/pair_eam.txt
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@ -294,7 +294,7 @@ distribution have a ".cdeam" suffix.
Style {eam/fs} computes pairwise interactions for metals and metal
alloys using a generalized form of EAM potentials due to Finnis and
Sinclair "(Finnis)"_#Finnis. The total energy Ei of an atom I is
Sinclair "(Finnis)"_#Finnis1. The total energy Ei of an atom I is
given by
:c,image(Eqs/pair_eam_fs.jpg)
@ -442,7 +442,7 @@ of Physics: Condensed Matter, 16, S2629 (2004).
[(Daw)] Daw, Baskes, Phys Rev Lett, 50, 1285 (1983).
Daw, Baskes, Phys Rev B, 29, 6443 (1984).
:link(Finnis)
:link(Finnis1)
[(Finnis)] Finnis, Sinclair, Philosophical Magazine A, 50, 45 (1984).
:link(Stukowski)

6
lib/latte/Install.py
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@ -159,13 +159,13 @@ if buildflag or pathflag:
os.remove("includelink")
if os.path.isfile("liblink") or os.path.islink("liblink"):
os.remove("liblink")
if os.path.isfile("filelink") or os.path.islink("filelink"):
os.remove("filelink")
if os.path.isfile("filelink.o") or os.path.islink("filelink.o"):
os.remove("filelink.o")
cmd = 'ln -s "%s/src" includelink' % lattedir
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
cmd = 'ln -s "%s" liblink' % lattedir
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
cmd = 'ln -s "%s/src/latte_c_bind.o" filelink' % lattedir
cmd = 'ln -s "%s/src/latte_c_bind.o" filelink.o' % lattedir
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
# copy Makefile.lammps.suffix to Makefile.lammps

2
lib/latte/Makefile.lammps.gfortran
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@ -3,5 +3,5 @@
# GNU Fortran settings
latte_SYSINC =
latte_SYSLIB = ../../lib/latte/filelink -llatte -lgfortran -llapack -lblas
latte_SYSLIB = ../../lib/latte/filelink.o -llatte -lgfortran -llapack -lblas
latte_SYSPATH = -fopenmp

2
lib/latte/Makefile.lammps.ifort
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@ -3,7 +3,7 @@
# Intel ifort settings
latte_SYSINC =
latte_SYSLIB = ../../lib/latte/filelink \
latte_SYSLIB = ../../lib/latte/filelink.o \
-llatte -lifcore -lsvml -lompstub -limf -lmkl_intel_lp64 \
-lmkl_intel_thread -lmkl_core -lmkl_intel_thread -lpthread \
-openmp -O0

2
src/.gitignore vendored
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@ -405,6 +405,8 @@
/fix_lambdah_calc.h
/fix_langevin_eff.cpp
/fix_langevin_eff.h
/fix_latte.cpp
/fix_latte.h
/fix_lb_fluid.cpp
/fix_lb_fluid.h
/fix_lb_momentum.cpp

4
src/Depend.sh
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@ -119,6 +119,10 @@ if (test $1 = "USER-DPD") then
depend KOKKOS
fi
if (test $1 = "USER-DRUDE") then
depend USER-OMP
fi
if (test $1 = "USER-FEP") then
depend USER-OMP
fi

2
src/MAKE/OPTIONS/Makefile.intel_cpu_mpich
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@ -15,7 +15,7 @@ DEPFLAGS = -M
LINK = mpicxx -cxx=icc
LINKFLAGS = -g -qopenmp $(OPTFLAGS)
LIB =
LIB = -ltbbmalloc
SIZE = size
ARCHIVE = ar

1
src/REPLICA/prd.cpp
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@ -310,6 +310,7 @@ void PRD::command(int narg, char **arg)
time_dephase = time_dynamics = time_quench = time_comm = time_output = 0.0;
bigint clock = 0;
timer->init();
timer->barrier_start();
time_start = timer->get_wall(Timer::TOTAL);

1
src/REPLICA/tad.cpp
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@ -274,6 +274,7 @@ void TAD::command(int narg, char **arg)
nbuild = ndanger = 0;
time_neb = time_dynamics = time_quench = time_comm = time_output = 0.0;
timer->init();
timer->barrier_start();
time_start = timer->get_wall(Timer::TOTAL);

10
src/USER-MANIFOLD/manifold_gaussian_bump.cpp
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@ -134,7 +134,7 @@ public:
// Manifold itself:
manifold_gaussian_bump::manifold_gaussian_bump(class LAMMPS* lmp,
int narg, char **arg)
: manifold(lmp), lut_z(NULL), lut_zp(NULL) {}
: manifold(lmp), lut_z(NULL), lut_zp(NULL) {}
manifold_gaussian_bump::~manifold_gaussian_bump()
@ -361,13 +361,13 @@ void manifold_gaussian_bump::test_lut()
n( x, nn );
double taper_z;
if( xx <= rc1 ){
taper_z = gaussian_bump(xx);
taper_z = gaussian_bump(xx);
}else if( xx < rc2 ){
taper_z = lut_get_z( xx );
taper_z = lut_get_z( xx );
}else{
taper_z = 0.0;
taper_z = 0.0;
}
fprintf( fp, "%g %g %g %g %g\n", xx, gaussian_bump(xx), taper_z,
fprintf( fp, "%g %g %g %g %g %g %g\n", xx, gaussian_bump(xx), taper_z,
gg, nn[0], nn[1], nn[2] );
}
fclose(fp);

6
src/dump.cpp
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@ -238,7 +238,7 @@ void Dump::init()
int gcmcflag = 0;
for (int i = 0; i < modify->nfix; i++)
if ((strcmp(modify->fix[i]->style,"gcmc") == 0))
gcmcflag = 1;
gcmcflag = 1;
if (sortcol == 0 && atom->tag_consecutive() && !gcmcflag) {
tagint *tag = atom->tag;
@ -898,7 +898,7 @@ void Dump::modify_params(int narg, char **arg)
} else if (strcmp(arg[iarg],"fileper") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
if (!multiproc)
error->all(FLERR,"Cannot use dump_modify fileper "
error->all(FLERR,"Cannot use dump_modify fileper "
"without % in dump file name");
int nper = force->inumeric(FLERR,arg[iarg+1]);
if (nper <= 0) error->all(FLERR,"Illegal dump_modify command");
@ -973,7 +973,7 @@ void Dump::modify_params(int narg, char **arg)
} else if (strcmp(arg[iarg],"nfile") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
if (!multiproc)
error->all(FLERR,"Cannot use dump_modify nfile "
error->all(FLERR,"Cannot use dump_modify nfile "
"without % in dump file name");
int nfile = force->inumeric(FLERR,arg[iarg+1]);
if (nfile <= 0) error->all(FLERR,"Illegal dump_modify command");

6
src/finish.cpp
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@ -130,7 +130,7 @@ void Finish::end(int flag)
atom->natoms);
if (logfile) fprintf(logfile,fmt1,time_loop,ntasks,update->nsteps,
atom->natoms);
// Gromacs/NAMD-style performance metric for suitable unit settings
if ( timeflag && !minflag && !prdflag && !tadflag &&
@ -144,7 +144,7 @@ void Finish::end(int flag)
double one_fs = force->femtosecond;
double t_step = ((double) time_loop) / ((double) update->nsteps);
double step_t = 1.0/t_step;
if (strcmp(update->unit_style,"lj") == 0) {
double tau_day = 24.0*3600.0 / t_step * update->dt / one_fs;
const char perf[] = "Performance: %.3f tau/day, %.3f timesteps/s\n";
@ -161,7 +161,7 @@ void Finish::end(int flag)
}
// CPU use on MPI tasks and OpenMP threads
if (timeflag) {
if (lmp->kokkos) {
const char fmt2[] =

2
src/input.cpp
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@ -18,7 +18,7 @@
#include <errno.h>
#include <ctype.h>
#include <unistd.h>
#include "sys/stat.h"
#include <sys/stat.h>
#include "input.h"
#include "style_command.h"
#include "universe.h"

10
src/main.cpp
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@ -22,6 +22,10 @@
#include <fenv.h>
#endif
#ifdef FFT_FFTW3
#include <fftw3.h>
#endif
using namespace LAMMPS_NS;
/* ----------------------------------------------------------------------
@ -62,4 +66,10 @@ int main(int argc, char **argv)
#endif
MPI_Barrier(MPI_COMM_WORLD);
MPI_Finalize();
#ifdef FFT_FFTW3
// tell fftw3 to delete its global memory pool
// and thus avoid bogus valgrind memory leak reports
fftw_cleanup();
#endif
}

56
src/modify.cpp
View File

@ -863,9 +863,9 @@ void Modify::add_fix(int narg, char **arg, int trysuffix)
fix[ifix]->restart(state_restart_global[i]);
used_restart_global[i] = 1;
if (comm->me == 0) {
if (screen)
if (screen)
fprintf(screen,"Resetting global fix info from restart file:\n");
if (logfile)
if (logfile)
fprintf(logfile,"Resetting global fix info from restart file:\n");
if (screen) fprintf(screen," fix style: %s, fix ID: %s\n",
fix[ifix]->style,fix[ifix]->id);
@ -885,9 +885,9 @@ void Modify::add_fix(int narg, char **arg, int trysuffix)
fix[ifix]->unpack_restart(j,index_restart_peratom[i]);
fix[ifix]->restart_reset = 1;
if (comm->me == 0) {
if (screen)
if (screen)
fprintf(screen,"Resetting peratom fix info from restart file:\n");
if (logfile)
if (logfile)
fprintf(logfile,"Resetting peratom fix info from restart file:\n");
if (screen) fprintf(screen," fix style: %s, fix ID: %s\n",
fix[ifix]->style,fix[ifix]->id);
@ -1409,24 +1409,24 @@ void Modify::restart_deallocate(int flag)
if (flag && comm->me == 0) {
int i;
for (i = 0; i < nfix_restart_global; i++)
if (used_restart_global[i] == 0) break;
if (used_restart_global[i] == 0) break;
if (i == nfix_restart_global) {
if (screen)
if (screen)
fprintf(screen,"All restart file global fix info "
"was re-assigned\n");
if (logfile)
if (logfile)
fprintf(logfile,"All restart file global fix info "
"was re-assigned\n");
} else {
if (screen) fprintf(screen,"Unused restart file global fix info:\n");
if (logfile) fprintf(logfile,"Unused restart file global fix info:\n");
for (i = 0; i < nfix_restart_global; i++) {
if (used_restart_global[i]) continue;
if (screen) fprintf(screen," fix style: %s, fix ID: %s\n",
style_restart_global[i],id_restart_global[i]);
if (logfile) fprintf(logfile," fix style: %s, fix ID: %s\n",
style_restart_global[i],id_restart_global[i]);
}
if (screen) fprintf(screen,"Unused restart file global fix info:\n");
if (logfile) fprintf(logfile,"Unused restart file global fix info:\n");
for (i = 0; i < nfix_restart_global; i++) {
if (used_restart_global[i]) continue;
if (screen) fprintf(screen," fix style: %s, fix ID: %s\n",
style_restart_global[i],id_restart_global[i]);
if (logfile) fprintf(logfile," fix style: %s, fix ID: %s\n",
style_restart_global[i],id_restart_global[i]);
}
}
}
@ -1445,24 +1445,24 @@ void Modify::restart_deallocate(int flag)
if (flag && comm->me == 0) {
int i;
for (i = 0; i < nfix_restart_peratom; i++)
if (used_restart_peratom[i] == 0) break;
if (used_restart_peratom[i] == 0) break;
if (i == nfix_restart_peratom) {
if (screen)
if (screen)
fprintf(screen,"All restart file peratom fix info "
"was re-assigned\n");
if (logfile)
if (logfile)
fprintf(logfile,"All restart file peratom fix info "
"was re-assigned\n");
} else {
if (screen) fprintf(screen,"Unused restart file peratom fix info:\n");
if (logfile) fprintf(logfile,"Unused restart file peratom fix info:\n");
for (i = 0; i < nfix_restart_peratom; i++) {
if (used_restart_peratom[i]) continue;
if (screen) fprintf(screen," fix style: %s, fix ID: %s\n",
style_restart_peratom[i],id_restart_peratom[i]);
if (logfile) fprintf(logfile," fix style: %s, fix ID: %s\n",
style_restart_peratom[i],id_restart_peratom[i]);
}
if (screen) fprintf(screen,"Unused restart file peratom fix info:\n");
if (logfile) fprintf(logfile,"Unused restart file peratom fix info:\n");
for (i = 0; i < nfix_restart_peratom; i++) {
if (used_restart_peratom[i]) continue;
if (screen) fprintf(screen," fix style: %s, fix ID: %s\n",
style_restart_peratom[i],id_restart_peratom[i]);
if (logfile) fprintf(logfile," fix style: %s, fix ID: %s\n",
style_restart_peratom[i],id_restart_peratom[i]);
}
}
}