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Merge pull request #1331 from akohlmey/collected-small-changes

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Collected small changes
This commit is contained in:
Axel Kohlmeyer
2019-02-13 16:47:27 +01:00
committed by GitHub
parent eaf2ca9c84 528e6632ed
commit 34d4209197
52 changed files with 191 additions and 136 deletions
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2
cmake/CMakeLists.txt
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@ -453,7 +453,7 @@ if(PKG_VORONOI)
set(VORO_BUILD_OPTIONS CXX=${CMAKE_CXX_COMPILER} CFLAGS=${VORO_BUILD_CFLAGS})
ExternalProject_Add(voro_build
URL http://math.lbl.gov/voro++/download/dir/voro++-0.4.6.tar.gz
URL https://download.lammps.org/thirdparty/voro++-0.4.6.tar.gz
URL_MD5 2338b824c3b7b25590e18e8df5d68af9
CONFIGURE_COMMAND "" BUILD_COMMAND make ${VORO_BUILD_OPTIONS} BUILD_IN_SOURCE 1 INSTALL_COMMAND ""
)

12
doc/src/Build_basics.txt
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@ -116,6 +116,18 @@ enables OpenMP. For GNU compilers it is -fopenmp. For (recent) Intel
compilers it is -qopenmp. If you are using a different compiler,
please refer to its documentation.
[OpenMP Compiler compatibility info]: :link(default-none-issues)
Some compilers do not fully support the 'default(none)' directive
and others (e.g. GCC version 9 and beyond) may implement OpenMP 4.0
semantics, which are incompatible with the OpenMP 3.1 directives used
in LAMMPS (for maximal compatibility with compiler versions in use).
In those case, all 'default(none)' directives (which aid in detecting
incorrect and unwanted sharing) can be replaced with 'default(shared)'
while dropping all 'shared()' directives. The script
'src/USER-OMP/hack_openmp_for_pgi_gcc9.sh' can be used to automate
this conversion.
:line
Choice of compiler and compile/link options :h4,link(compile)

4
doc/src/Build_extras.txt
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@ -932,7 +932,9 @@ LINKFLAGS: -fopenmp # for GNU Compilers
LINKFLAGS: -qopenmp # for Intel compilers on Linux :pre
For other platforms and compilers, please consult the documentation
about OpenMP support for your compiler.
about OpenMP support for your compiler. Please see the note about
how to address compatibility "issues with the 'default(none)'
directive"_Build_basics.html#default-none-issues of some compilers.
:line

13
doc/src/fix_wall_gran_region.txt
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@ -71,12 +71,13 @@ exterior surfaces of regions.
Regions can either be primitive shapes (block, sphere, cylinder, etc)
or combinations of primitive shapes specified via the {union} or
{intersect} region styles. These latter styles can be used to
construct particle containers with complex shapes. Regions can also
move dynamically via the "region"_region.html command keywords (move)
and {rotate}, or change their shape by use of variables as inputs to
the "region"_region.html command. If such a region is used with this
fix, then the region surface will move in time in the corresponding
manner.
construct particle containers with complex shapes.
Regions can also move dynamically via the "region"_region.html command
keywords (move) and {rotate}, or change their shape by use of variables
as inputs to the "region"_region.html command. If such a region is used
with this fix, then the region surface will move in time in the
corresponding manner.
NOTE: As discussed on the "region"_region.html command doc page,
regions in LAMMPS do not get wrapped across periodic boundaries. It

2
doc/utils/sphinx-config/false_positives.txt
View File

@ -1951,6 +1951,7 @@ ons
OO
openKIM
OpenMP
openmp
openmpi
opls
Oppelstrup
@ -2044,6 +2045,7 @@ peru
Peskin
Pettifor
pfactor
pgi
ph
Phillpot
phiphi

2
lib/voronoi/Install.py
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@ -18,7 +18,7 @@ parser = ArgumentParser(prog='Install.py',
# settings
version = "voro++-0.4.6"
url = "http://math.lbl.gov/voro++/download/dir/%s.tar.gz" % version
url = "https://download.lammps.org/thirdparty/%s.tar.gz" % version
# known checksums for different Voro++ versions. used to validate the download.
checksums = { \

4
src/GPU/fix_gpu.cpp
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@ -283,7 +283,7 @@ void FixGPU::min_setup(int vflag)
/* ---------------------------------------------------------------------- */
void FixGPU::post_force(int vflag)
void FixGPU::post_force(int /* vflag */)
{
if (!force->pair) return;
@ -315,7 +315,7 @@ void FixGPU::min_post_force(int vflag)
/* ---------------------------------------------------------------------- */
void FixGPU::post_force_respa(int vflag, int ilevel, int iloop)
void FixGPU::post_force_respa(int vflag, int /* ilevel */, int /* iloop */)
{
post_force(vflag);
}

5
src/GPU/pair_beck_gpu.cpp
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@ -171,8 +171,9 @@ double PairBeckGPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairBeckGPU::cpu_compute(int start, int inum, int eflag, int vflag,
int *ilist, int *numneigh, int **firstneigh) {
void PairBeckGPU::cpu_compute(int start, int inum, int eflag,
int /* vflag */, int *ilist,
int *numneigh, int **firstneigh) {
int i,j,ii,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,r5,force_beck,factor_lj;

6
src/GPU/pair_born_coul_wolf_gpu.cpp
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@ -191,9 +191,9 @@ double PairBornCoulWolfGPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairBornCoulWolfGPU::cpu_compute(int start, int inum, int eflag, int vflag,
int *ilist, int *numneigh,
int **firstneigh) {
void PairBornCoulWolfGPU::cpu_compute(int start, int inum, int eflag,
int /* vflag */, int *ilist,
int *numneigh, int **firstneigh) {
int i,j,ii,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,qtmp,delx,dely,delz,evdwl,ecoul,fpair;
double rsq,r2inv,r6inv,forcecoul,forceborn,factor_coul,factor_lj;

5
src/GPU/pair_born_gpu.cpp
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@ -185,8 +185,9 @@ double PairBornGPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairBornGPU::cpu_compute(int start, int inum, int eflag, int vflag,
int *ilist, int *numneigh, int **firstneigh) {
void PairBornGPU::cpu_compute(int start, int inum, int eflag,
int /* vflag */, int *ilist,
int *numneigh, int **firstneigh) {
int i,j,ii,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,r2inv,r6inv,forceborn,factor_lj;

6
src/GPU/pair_buck_coul_cut_gpu.cpp
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@ -179,9 +179,9 @@ double PairBuckCoulCutGPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairBuckCoulCutGPU::cpu_compute(int start, int inum, int eflag, int vflag,
int *ilist, int *numneigh,
int **firstneigh) {
void PairBuckCoulCutGPU::cpu_compute(int start, int inum, int eflag,
int /* vflag */, int *ilist,
int *numneigh, int **firstneigh) {
int i,j,ii,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,qtmp,delx,dely,delz,evdwl,ecoul,fpair;
double rsq,r2inv,r6inv,forcecoul,forcebuck,factor_coul,factor_lj;

2
src/GPU/pair_buck_gpu.cpp
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@ -182,7 +182,7 @@ double PairBuckGPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairBuckGPU::cpu_compute(int start, int inum, int eflag, int vflag,
void PairBuckGPU::cpu_compute(int start, int inum, int eflag, int /* vflag */,
int *ilist, int *numneigh, int **firstneigh) {
int i,j,ii,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;

6
src/GPU/pair_coul_cut_gpu.cpp
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@ -186,9 +186,9 @@ double PairCoulCutGPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairCoulCutGPU::cpu_compute(int start, int inum, int eflag, int vflag,
int *ilist, int *numneigh,
int **firstneigh)
void PairCoulCutGPU::cpu_compute(int start, int inum, int eflag,
int /* vflag */, int *ilist,
int *numneigh, int **firstneigh)
{
int i,j,ii,jj,jnum,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,ecoul,fpair;

2
src/GPU/pair_coul_debye_gpu.cpp
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@ -189,7 +189,7 @@ double PairCoulDebyeGPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairCoulDebyeGPU::cpu_compute(int start, int inum, int eflag,
int vflag, int *ilist,
int /* vflag */, int *ilist,
int *numneigh, int **firstneigh)
{
int i,j,ii,jj,jnum,itype,jtype;

6
src/GPU/pair_coul_dsf_gpu.cpp
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@ -196,9 +196,9 @@ double PairCoulDSFGPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairCoulDSFGPU::cpu_compute(int start, int inum, int eflag, int vflag,
int *ilist, int *numneigh,
int **firstneigh)
void PairCoulDSFGPU::cpu_compute(int start, int inum, int eflag,
int /* vflag */, int *ilist,
int *numneigh, int **firstneigh)
{
int i,j,ii,jj,jnum;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,ecoul,fpair;

2
src/GPU/pair_dpd_gpu.cpp
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@ -319,7 +319,7 @@ double PairDPDGPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairDPDGPU::cpu_compute(int start, int inum, int eflag, int vflag,
void PairDPDGPU::cpu_compute(int start, int inum, int eflag, int /* vflag */,
int *ilist, int *numneigh, int **firstneigh) {
int i,j,ii,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;

5
src/GPU/pair_dpd_tstat_gpu.cpp
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@ -336,8 +336,9 @@ double PairDPDTstatGPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairDPDTstatGPU::cpu_compute(int start, int inum, int eflag, int vflag,
int *ilist, int *numneigh, int **firstneigh) {
void PairDPDTstatGPU::cpu_compute(int start, int inum, int /* eflag */,
int /* vflag */, int *ilist,
int *numneigh, int **firstneigh) {
int i,j,ii,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,fpair;
double vxtmp,vytmp,vztmp,delvx,delvy,delvz;

2
src/GPU/pair_gauss_gpu.cpp
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@ -178,7 +178,7 @@ double PairGaussGPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairGaussGPU::cpu_compute(int start, int inum, int eflag, int vflag,
void PairGaussGPU::cpu_compute(int start, int inum, int eflag, int /* vflag */,
int *ilist, int *numneigh, int **firstneigh) {
int i,j,ii,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;

5
src/GPU/pair_lj96_cut_gpu.cpp
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@ -171,8 +171,9 @@ double PairLJ96CutGPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairLJ96CutGPU::cpu_compute(int start, int inum, int eflag, int vflag,
int *ilist, int *numneigh, int **firstneigh)
void PairLJ96CutGPU::cpu_compute(int start, int inum, int eflag,
int /* vflag */, int *ilist,
int *numneigh, int **firstneigh)
{
int i,j,ii,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;

5
src/GPU/pair_lj_class2_gpu.cpp
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@ -168,8 +168,9 @@ double PairLJClass2GPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairLJClass2GPU::cpu_compute(int start, int inum, int eflag, int vflag,
int *ilist, int *numneigh, int **firstneigh)
void PairLJClass2GPU::cpu_compute(int start, int inum, int eflag,
int /* vflag */, int *ilist,
int *numneigh, int **firstneigh)
{
int i,j,ii,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;

5
src/GPU/pair_lj_cubic_gpu.cpp
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@ -174,8 +174,9 @@ double PairLJCubicGPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairLJCubicGPU::cpu_compute(int start, int inum, int eflag, int vflag,
int *ilist, int *numneigh, int **firstneigh) {
void PairLJCubicGPU::cpu_compute(int start, int inum, int eflag,
int /* vflag */, int *ilist,
int *numneigh, int **firstneigh) {
int i,j,ii,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,r2inv,r6inv,forcelj,factor_lj;

6
src/GPU/pair_lj_cut_coul_cut_gpu.cpp
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@ -180,9 +180,9 @@ double PairLJCutCoulCutGPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairLJCutCoulCutGPU::cpu_compute(int start, int inum, int eflag, int vflag,
int *ilist, int *numneigh,
int **firstneigh)
void PairLJCutCoulCutGPU::cpu_compute(int start, int inum, int eflag,
int /* vflag */, int *ilist,
int *numneigh, int **firstneigh)
{
int i,j,ii,jj,jnum,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;

2
src/GPU/pair_lj_cut_coul_debye_gpu.cpp
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@ -184,7 +184,7 @@ double PairLJCutCoulDebyeGPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairLJCutCoulDebyeGPU::cpu_compute(int start, int inum, int eflag,
int vflag, int *ilist,
int /* vflag */, int *ilist,
int *numneigh, int **firstneigh)
{
int i,j,ii,jj,jnum,itype,jtype;

6
src/GPU/pair_lj_cut_coul_dsf_gpu.cpp
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@ -198,9 +198,9 @@ double PairLJCutCoulDSFGPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairLJCutCoulDSFGPU::cpu_compute(int start, int inum, int eflag, int vflag,
int *ilist, int *numneigh,
int **firstneigh)
void PairLJCutCoulDSFGPU::cpu_compute(int start, int inum, int eflag,
int /* vflag */, int *ilist,
int *numneigh, int **firstneigh)
{
int i,j,ii,jj,jnum,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;

2
src/GPU/pair_lj_cut_gpu.cpp
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@ -184,7 +184,7 @@ double PairLJCutGPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairLJCutGPU::cpu_compute(int start, int inum, int eflag, int vflag,
void PairLJCutGPU::cpu_compute(int start, int inum, int eflag, int /* vflag */,
int *ilist, int *numneigh, int **firstneigh) {
int i,j,ii,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;

5
src/GPU/pair_lj_expand_gpu.cpp
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@ -181,8 +181,9 @@ double PairLJExpandGPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairLJExpandGPU::cpu_compute(int start, int inum, int eflag, int vflag,
int *ilist, int *numneigh, int **firstneigh)
void PairLJExpandGPU::cpu_compute(int start, int inum, int eflag,
int /* vflag */, int *ilist,
int *numneigh, int **firstneigh)
{
int i,j,ii,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;

2
src/GPU/pair_lj_gromacs_gpu.cpp
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@ -177,7 +177,7 @@ double PairLJGromacsGPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairLJGromacsGPU::cpu_compute(int start, int inum, int eflag,
int vflag, int *ilist,
int /* vflag */, int *ilist,
int *numneigh, int **firstneigh)
{
int i,j,ii,jj,jnum,itype,jtype;

2
src/MANYBODY/pair_airebo.cpp
View File

@ -2117,7 +2117,7 @@ but of the vector r_ij.
*/
double PairAIREBO::bondorderLJ(int i, int j, double /*rij_mod*/[3], double rijmag_mod,
double PairAIREBO::bondorderLJ(int i, int j, double /* rij_mod */[3], double rijmag_mod,
double VA, double rij[3], double rijmag,
double **f, int vflag_atom)
{

26
src/USER-MISC/fix_ave_correlate_long.cpp
View File

@ -307,7 +307,7 @@ FixAveCorrelateLong::FixAveCorrelateLong(LAMMPS * lmp, int narg, char **arg):
for (int i=0;i<npair;i++)
for (int j=0;j<numcorrelators;j++) {
for (int k=0;k<p;k++) {
for (unsigned int k=0;k<p;k++) {
shift[i][j][k]=-2E10;
shift2[i][j][k]=0.0;
correlation[i][j][k]=0.0;
@ -317,7 +317,7 @@ FixAveCorrelateLong::FixAveCorrelateLong(LAMMPS * lmp, int narg, char **arg):
}
for (int i=0;i<numcorrelators;i++) {
for (int j=0;j<p;j++) ncorrelation[i][j]=0;
for (unsigned int j=0;j<p;j++) ncorrelation[i][j]=0;
naccumulator[i]=0;
insertindex[i]=0;
}
@ -515,7 +515,7 @@ void FixAveCorrelateLong::evaluate() {
unsigned int jm=0;
// First correlator
for (int j=0;j<p;++j) {
for (unsigned int j=0;j<p;++j) {
if (ncorrelation[0][j] > 0) {
t[jm] = j;
for (int i=0;i<npair;++i)
@ -526,7 +526,7 @@ void FixAveCorrelateLong::evaluate() {
// Subsequent correlators
for (int k=1;k<kmax;++k) {
for (int j=dmin;j<p;++j) {
for (unsigned int j=dmin;j<p;++j) {
if (ncorrelation[k][j]>0) {
t[jm] = j * pow((double)m, k);
for (int i=0;i<npair;++i)
@ -610,7 +610,7 @@ void FixAveCorrelateLong::add(const int i, const double w, const int k){
unsigned int ind1=insertindex[k];
if (k==0) { // First correlator is different
int ind2=ind1;
for (int j=0;j<p;++j) {
for (unsigned int j=0;j<p;++j) {
if (shift[i][k][ind2] > -1e10) {
correlation[i][k][j]+= shift[i][k][ind1]*shift[i][k][ind2];
if (i==0) ++ncorrelation[k][j];
@ -620,7 +620,7 @@ void FixAveCorrelateLong::add(const int i, const double w, const int k){
}
} else {
int ind2=ind1-dmin;
for (int j=dmin;j<p;++j) {
for (unsigned int j=dmin;j<p;++j) {
if (ind2<0) ind2+=p;
if (shift[i][k][ind2] > -1e10) {
correlation[i][k][j]+= shift[i][k][ind1]*shift[i][k][ind2];
@ -661,7 +661,7 @@ void FixAveCorrelateLong::add(const int i, const double wA, const double wB,
unsigned int ind1=insertindex[k];
if (k==0) {
int ind2=ind1;
for (int j=0;j<p;++j) {
for (unsigned int j=0;j<p;++j) {
if (shift[i][k][ind2] > -1e10) {
correlation[i][k][j]+= shift[i][k][ind1]*shift2[i][k][ind2];
if (i==0) ++ncorrelation[k][j];
@ -672,7 +672,7 @@ void FixAveCorrelateLong::add(const int i, const double wA, const double wB,
}
else {
int ind2=ind1-dmin;
for (int j=dmin;j<p;++j) {
for (unsigned int j=dmin;j<p;++j) {
if (ind2<0) ind2+=p;
if (shift[i][k][ind2] > -1e10) {
correlation[i][k][j]+= shift[i][k][ind1]*shift2[i][k][ind2];
@ -743,7 +743,7 @@ void FixAveCorrelateLong::write_restart(FILE *fp) {
list[n++] = last_accumulated_step;
for (int i=0;i<npair;i++)
for (int j=0;j<numcorrelators;j++) {
for (int k=0;k<p;k++) {
for (unsigned int k=0;k<p;k++) {
list[n++]=shift[i][j][k];
list[n++]=shift2[i][j][k];
list[n++]=correlation[i][j][k];
@ -752,7 +752,7 @@ void FixAveCorrelateLong::write_restart(FILE *fp) {
list[n++]=accumulator2[i][j];
}
for (int i=0;i<numcorrelators;i++) {
for (int j=0;j<p;j++) list[n++]=ncorrelation[i][j];
for (unsigned int j=0;j<p;j++) list[n++]=ncorrelation[i][j];
list[n++]=naccumulator[i];
list[n++]=insertindex[i];
}
@ -779,12 +779,12 @@ void FixAveCorrelateLong::restart(char *buf)
last_accumulated_step = static_cast<int> (list[n++]);
if ((npairin!=npair) || (numcorrelatorsin!=numcorrelators)
|| (pin!=p) || (min!=m))
|| (pin!=(int)p) || (min!=(int)m))
error->all(FLERR,"Fix ave/correlate/long: restart and input data are different");
for (int i=0;i<npair;i++)
for (int j=0;j<numcorrelators;j++) {
for (int k=0;k<p;k++) {
for (unsigned int k=0;k<p;k++) {
shift[i][j][k] = list[n++];
shift2[i][j][k] = list[n++];
correlation[i][j][k] = list[n++];
@ -793,7 +793,7 @@ void FixAveCorrelateLong::restart(char *buf)
accumulator2[i][j] = list[n++];
}
for (int i=0;i<numcorrelators;i++) {
for (int j=0;j<p;j++)
for (unsigned int j=0;j<p;j++)
ncorrelation[i][j] = static_cast<unsigned long int>(list[n++]);
naccumulator[i] = static_cast<unsigned int> (list[n++]);
insertindex[i] = static_cast<unsigned int> (list[n++]);

2
src/USER-MISC/fix_ave_correlate_long.h
View File

@ -52,7 +52,7 @@ class FixAveCorrelateLong : public Fix {
unsigned int *insertindex;
int numcorrelators; // Recommended 20
int p; // Points per correlator (recommended 16)
unsigned int p; // Points per correlator (recommended 16)
unsigned int m; // Num points for average (recommended 2; p mod m = 0)
unsigned int dmin; // Min distance between ponts for correlators k>0; dmin=p/m

12
src/USER-MISC/pair_extep.cpp
View File

@ -1075,10 +1075,10 @@ void PairExTeP::costheta_d(double *rij_hat, double rij,
// initialize spline for F_corr (based on PairLCBOP::F_conj)
void PairExTeP::spline_init() {
for ( size_t iel=0; iel<atom->ntypes; iel++) {
for ( size_t jel=0; jel<atom->ntypes; jel++) {
for ( size_t N_ij=0; N_ij<4; N_ij++ ) {
for ( size_t N_ji=0; N_ji<4; N_ji++ ) {
for ( int iel=0; iel<atom->ntypes; iel++) {
for ( int jel=0; jel<atom->ntypes; jel++) {
for ( int N_ij=0; N_ij<4; N_ij++ ) {
for ( int N_ji=0; N_ji<4; N_ji++ ) {
TF_corr_param &f = F_corr_param[iel][jel][N_ij][N_ji];
// corner points for each spline function
@ -1150,8 +1150,8 @@ double PairExTeP::F_corr(int iel, int jel, double Ndij, double Ndji, double *dFN
// compute F_XY
size_t Ndij_int = static_cast<size_t>( floor( Ndij ) );
size_t Ndji_int = static_cast<size_t>( floor( Ndji ) );
int Ndij_int = static_cast<int>( floor( Ndij ) );
int Ndji_int = static_cast<int>( floor( Ndji ) );
double x = Ndij - Ndij_int;
double y = Ndji - Ndji_int;
TF_corr_param &f = F_corr_param[iel][jel][Ndij_int][Ndji_int];

5
src/USER-MISC/pair_lebedeva_z.cpp
View File

@ -82,8 +82,8 @@ void PairLebedevaZ::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair,der;
double rsq,r,rhosq,rho,exp1,exp2,exp3,r6,r8;
double frho,sumD,Ulm,fxy,fz,rdsq;
double rsq,r,rhosq,exp1,exp2,exp3,r6,r8;
double sumD,Ulm,fxy,fz;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = 0.0;
@ -120,7 +120,6 @@ void PairLebedevaZ::compute(int eflag, int vflag)
delz = ztmp - x[j][2];
// rho^2 = r^2 - z^2
rhosq = delx*delx + dely*dely;
rho = sqrt(rhosq);
rsq = rhosq + delz*delz;
if (rsq < cutsq[itype][jtype]) {

2
src/USER-MOLFILE/reader_molfile.cpp
View File

@ -197,7 +197,7 @@ void ReaderMolfile::skip()
bigint ReaderMolfile::read_header(double box[3][3], int &triclinic,
int fieldinfo, int nfield,
int *fieldtype, char **fieldlabel,
int *fieldtype, char ** /* fieldlabel */,
int scaleflag, int wrapflag, int &fieldflag,
int &xflag, int &yflag, int &zflag)
{

4
src/USER-OMP/fix_gravity_omp.cpp
View File

@ -42,7 +42,7 @@ FixGravityOMP::FixGravityOMP(LAMMPS *lmp, int narg, char **arg) :
/* ---------------------------------------------------------------------- */
void FixGravityOMP::post_force(int vflag)
void FixGravityOMP::post_force(int /* vflag */)
{
// update gravity due to variables
@ -106,7 +106,7 @@ void FixGravityOMP::post_force(int vflag)
/* ---------------------------------------------------------------------- */
void FixGravityOMP::post_force_respa(int vflag, int ilevel, int iloop)
void FixGravityOMP::post_force_respa(int vflag, int ilevel, int /* iloop */)
{
if (ilevel == ilevel_respa) post_force(vflag);
}

2
src/USER-OMP/fix_nve_omp.cpp
View File

@ -29,7 +29,7 @@ FixNVEOMP::FixNVEOMP(LAMMPS *lmp, int narg, char **arg) :
allow for both per-type and per-atom mass
------------------------------------------------------------------------- */
void FixNVEOMP::initial_integrate(int vflag)
void FixNVEOMP::initial_integrate(int /* vflag */)
{
// update v and x of atoms in group

2
src/USER-OMP/fix_nve_sphere_omp.cpp
View File

@ -37,7 +37,7 @@ enum{NODLM,DLM};
/* ---------------------------------------------------------------------- */
void FixNVESphereOMP::initial_integrate(int vflag)
void FixNVESphereOMP::initial_integrate(int /* vflag */)
{
double * const * const x = atom->x;
double * const * const v = atom->v;

2
src/USER-OMP/fix_qeq_comb_omp.cpp
View File

@ -73,7 +73,7 @@ void FixQEQCombOMP::init()
/* ---------------------------------------------------------------------- */
void FixQEQCombOMP::post_force(int vflag)
void FixQEQCombOMP::post_force(int /* vflag */)
{
int i,ii,iloop,loopmax,inum,*ilist;
double heatpq,qmass,dtq,dtq2;

2
src/USER-OMP/fix_qeq_reax_omp.cpp
View File

@ -275,7 +275,7 @@ void FixQEqReaxOMP::init_storage()
/* ---------------------------------------------------------------------- */
void FixQEqReaxOMP::pre_force(int vflag)
void FixQEqReaxOMP::pre_force(int /* vflag */)
{
#ifdef OMP_TIMING

6
src/USER-OMP/fix_wall_gran_omp.cpp
View File

@ -37,7 +37,7 @@ FixWallGranOMP::FixWallGranOMP(LAMMPS *lmp, int narg, char **arg) :
/* ---------------------------------------------------------------------- */
void FixWallGranOMP::post_force(int vflag)
void FixWallGranOMP::post_force(int /* vflag */)
{
double vwall[3];
@ -48,7 +48,7 @@ void FixWallGranOMP::post_force(int vflag)
if (neighbor->ago == 0 && fix_rigid) {
int tmp;
const int * const body = (const int * const) fix_rigid->extract("body",tmp);
const int * const body = (const int *) fix_rigid->extract("body",tmp);
double *mass_body = (double *) fix_rigid->extract("masstotal",tmp);
if (atom->nmax > nmax) {
memory->destroy(mass_rigid);
@ -180,7 +180,7 @@ void FixWallGranOMP::post_force(int vflag)
/* ---------------------------------------------------------------------- */
void FixWallGranOMP::post_force_respa(int vflag, int ilevel, int iloop)
void FixWallGranOMP::post_force_respa(int vflag, int ilevel, int /* iloop */)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}

8
src/USER-OMP/hack_openmp_for_pgi.sh
View File

@ -1,8 +0,0 @@
#!/bin/sh
for f in *.h *.cpp
do \
sed -e '/#pragma omp/s/^\(.*default\)(none)\(.*\)$/\1(shared)\2/' \
-e '/#pragma omp/s/shared([a-z0-9,_]\+)//' \
-i.bak $f
done

12
src/USER-OMP/hack_openmp_for_pgi_gcc9.sh Executable file
View File

@ -0,0 +1,12 @@
#!/bin/sh
# convert default(none) directives for OpenMP pragmas to default(shared) and remove shared() directive
# this allows compiling OpenMP pragmas in LAMMPS with compilers that don't support default(none) properly
# or require backward incompatible OpenMP 4 and OpenMP 5 semantics
for f in *.h *.cpp
do \
sed -e '/#pragma omp/s/^\(.*default\)(none)\(.*\)$/\1(shared)\2/' \
-e '/#pragma omp/s/shared([a-z0-9,_]\+)//' \
-i.bak $f
done

2
src/USER-OMP/pair_airebo_omp.cpp
View File

@ -1869,7 +1869,7 @@ there probably also need to be performed here.
*/
double PairAIREBOOMP::bondorderLJ_thr(int i, int j, double rij_mod[3], double rijmag_mod,
double PairAIREBOOMP::bondorderLJ_thr(int i, int j, double /* rij_mod */[3], double rijmag_mod,
double VA, double rij[3], double rijmag,
int vflag_atom, ThrData * const thr)
{

2
src/USER-OMP/pair_rebo_omp.cpp
View File

@ -24,7 +24,7 @@ PairREBOOMP::PairREBOOMP(LAMMPS *lmp) : PairAIREBOOMP(lmp) {}
global settings
------------------------------------------------------------------------- */
void PairREBOOMP::settings(int narg, char **arg)
void PairREBOOMP::settings(int narg, char ** /* arg */)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");

1
src/USER-UEF/uef_utils.h
View File

@ -103,7 +103,6 @@ bool mat_same(T x1[3][3], T x2[3][3])
template<typename T>
void transpose(T m[3][3])
{
T t[3][3];
for (int k=0;k<3;k++)
for (int j=k+1;j<3;j++) {
T x = m[k][j];

6
src/USER-YAFF/angle_cross.cpp
View File

@ -61,9 +61,9 @@ void AngleCross::compute(int eflag, int vflag)
int i1,i2,i3,n,type;
double delx1,dely1,delz1,delx2,dely2,delz2;
double eangle,f1[3],f3[3];
double dtheta,dtheta2,dtheta3,dtheta4,de_angle;
double dtheta;
double dr1,dr2,tk1,tk2,aa1,aa2,aa11,aa12,aa21,aa22;
double rsq1,rsq2,r1,r2,c,s,a,a11,a12,a22,b1,b2;
double rsq1,rsq2,r1,r2,c,s,b1,b2;
double vx11,vx12,vy11,vy12,vz11,vz12,vx21,vx22,vy21,vy22,vz21,vz22;
eangle = 0.0;
@ -305,7 +305,7 @@ void AngleCross::read_restart(FILE *fp)
void AngleCross::write_data(FILE *fp)
{
for (int i = 1; i <= atom->nangletypes; i++)
fprintf(fp,"%d %g %g %g %g\n",
fprintf(fp,"%d %g %g %g %g %g %g\n",
i,kss[i],kbs0[i],kbs1[i],r00[i],r01[i],theta0[i]/MY_PI*180.0);
}

4
src/USER-YAFF/angle_mm3.cpp
View File

@ -58,9 +58,7 @@ void AngleMM3::compute(int eflag, int vflag)
double delx1,dely1,delz1,delx2,dely2,delz2;
double eangle,f1[3],f3[3];
double dtheta,dtheta2,dtheta3,dtheta4,de_angle;
double dr1,dr2,tk1,tk2,aa1,aa2,aa11,aa12,aa21,aa22;
double rsq1,rsq2,r1,r2,c,s,a,a11,a12,a22,b1,b2;
double vx11,vx12,vy11,vy12,vz11,vz12,vx21,vx22,vy21,vy22,vz21,vz22;
double rsq1,rsq2,r1,r2,c,s,a,a11,a12,a22;
eangle = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);

3
src/USER-YAFF/bond_mm3.cpp
View File

@ -201,7 +201,8 @@ void BondMM3::write_data(FILE *fp)
/* ---------------------------------------------------------------------- */
double BondMM3::single(int type, double rsq, int i, int j, double &fforce)
double BondMM3::single(int type, double rsq,
int /* i */, int /* j */, double &fforce)
{
/*
E = K(r-r0)^2 [1-2.55*(r-r0)+(7/12)*2.55^(2)*(r-r0)^2]

19
src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp
View File

@ -82,13 +82,13 @@ PairLJSwitch3CoulGaussLong::~PairLJSwitch3CoulGaussLong()
void PairLJSwitch3CoulGaussLong::compute(int eflag, int vflag)
{
int i,ii,j,jj,inum,jnum,itype,jtype,itable,jtable,ktable;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,ecoul2,fpair;
double fraction,fraction2,table;
int i,ii,j,jj,inum,jnum,itype,jtype,itable;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
double fraction,table;
double r,r2inv,r6inv,forcecoul,forcecoul2,forcelj,factor_coul,factor_lj,tr,ftr,trx;
double grij,expm2,prefactor,prefactor2,t,erfc1,erfc2,rrij,expn2,expb,g_ewald2i,g_ewaldi;
double grij,expm2,prefactor,prefactor2,t,erfc1,erfc2,rrij,expn2;
int *ilist,*jlist,*numneigh,**firstneigh;
double rsq, lookup_corr;
double rsq;
evdwl = ecoul = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
@ -109,9 +109,6 @@ void PairLJSwitch3CoulGaussLong::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
g_ewaldi = 1.0/g_ewald;
g_ewald2i = g_ewaldi*g_ewaldi;
lookup_corr = 0.0;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@ -614,9 +611,9 @@ double PairLJSwitch3CoulGaussLong::single(int i, int j, int itype, int jtype,
double factor_coul, double factor_lj,
double &fforce)
{
double r2inv,r6inv,r,grij,expm2,t,erfc1,prefactor,prefactor2,rrij,expn2,erfc2;
double fraction,table,forcecoul,forcecoul2,forcelj,phicoul,phicoul2,philj;
double expb, ecoul, evdwl, trx, tr, ftr;
double r2inv,r6inv,r,grij,expm2,t,erfc1,prefactor,prefactor2;
double fraction,table,forcecoul,forcecoul2,forcelj,phicoul;
double rrij,expn2,erfc2,expb,ecoul,evdwl,trx,tr,ftr;
int itable;

19
src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp
View File

@ -82,13 +82,13 @@ PairMM3Switch3CoulGaussLong::~PairMM3Switch3CoulGaussLong()
void PairMM3Switch3CoulGaussLong::compute(int eflag, int vflag)
{
int i,ii,j,jj,inum,jnum,itype,jtype,itable,jtable,ktable;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,ecoul2,fpair;
double fraction,fraction2,table;
int i,ii,j,jj,inum,jnum,itype,jtype,itable;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
double fraction,table;
double r,r2inv,r6inv,forcecoul,forcecoul2,forcelj,factor_coul,factor_lj,tr,ftr,trx;
double grij,expm2,prefactor,prefactor2,t,erfc1,erfc2,rrij,expn2,expb,g_ewald2i,g_ewaldi;
double grij,expm2,prefactor,prefactor2,t,erfc1,erfc2,rrij,expn2,expb;
int *ilist,*jlist,*numneigh,**firstneigh;
double rsq, lookup_corr;
double rsq;
evdwl = ecoul = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
@ -109,9 +109,6 @@ void PairMM3Switch3CoulGaussLong::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
g_ewaldi = 1.0/g_ewald;
g_ewald2i = g_ewaldi*g_ewaldi;
lookup_corr = 0.0;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@ -615,9 +612,9 @@ double PairMM3Switch3CoulGaussLong::single(int i, int j, int itype, int jtype,
double factor_coul, double factor_lj,
double &fforce)
{
double r2inv,r6inv,r,grij,expm2,t,erfc1,prefactor,prefactor2,rrij,expn2,erfc2;
double fraction,table,forcecoul,forcecoul2,forcelj,phicoul,phicoul2,philj;
double expb, ecoul, evdwl, trx, tr, ftr;
double r2inv,r6inv,r,grij,expm2,t,erfc1,prefactor,prefactor2;
double fraction,table,forcecoul,forcecoul2,forcelj,phicoul;
double expb,rrij,expn2,erfc2,ecoul,evdwl,trx,tr,ftr;
int itable;

39
src/info.cpp
View File

@ -263,7 +263,7 @@ void Info::command(int narg, char **arg)
fprintf(out,"\nLAMMPS version: %s / %s\n\n",
universe->version, universe->num_ver);
char *infobuf = get_os_info();
const char *infobuf = get_os_info();
fprintf(out,"OS information: %s\n\n",infobuf);
delete[] infobuf;
@ -273,7 +273,7 @@ void Info::command(int narg, char **arg)
fprintf(out,"sizeof(bigint): %3d-bit\n",(int)sizeof(bigint)*8);
infobuf = get_compiler_info();
fprintf(out,"\nCompiler: %s\n",infobuf);
fprintf(out,"\nCompiler: %s with %s\n",infobuf,get_openmp_info());
delete[] infobuf;
fputs("\nActive compile time flags:\n\n",out);
@ -1150,6 +1150,41 @@ char *Info::get_compiler_info()
return buf;
}
const char *Info::get_openmp_info()
{
#if !defined(_OPENMP)
return (const char *)"OpenMP not enabled";
#else
// Supported OpenMP version corresponds to the release date of the
// specifications as posted at https://www.openmp.org/specifications/
#if _OPENMP > 201811
return (const char *)"OpenMP newer than version 5.0";
#elif _OPENMP == 201811
return (const char *)"OpenMP 5.0";
#elif _OPENMP == 201611
return (const char *)"OpenMP 5.0 preview 1";
#elif _OPENMP == 201511
return (const char *)"OpenMP 4.5";
#elif _OPENMP == 201307
return (const char *)"OpenMP 4.0";
#elif _OPENMP == 201107
return (const char *)"OpenMP 3.1";
#elif _OPENMP == 200805
return (const char *)"OpenMP 3.0";
#elif _OPENMP == 200505
return (const char *)"OpenMP 2.5";
#elif _OPENMP == 200203
return (const char *)"OpenMP 2.0";
#else
return (const char *)"unknown OpenMP version";
#endif
#endif
}
/* ---------------------------------------------------------------------- */
char **Info::get_variable_names(int &num) {

1
src/info.h
View File

@ -42,6 +42,7 @@ class Info : protected Pointers {
static char *get_os_info();
static char *get_compiler_info();
static const char *get_openmp_info();
char **get_variable_names(int &num);

2
src/lammps.cpp
View File

@ -1087,7 +1087,7 @@ void LAMMPS::print_config(FILE *fp)
delete[] infobuf;
infobuf = Info::get_compiler_info();
fprintf(fp,"Compiler: %s\n\n",infobuf);
fprintf(fp,"Compiler: %s with %s\n\n",infobuf,Info::get_openmp_info());
delete[] infobuf;
fputs("Active compile time flags:\n\n",fp);