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Merge pull request #3117 from akohlmey/collected-small-changes

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Collected small changes
This commit is contained in:
Axel Kohlmeyer
2022-02-08 20:21:46 -05:00
committed by GitHub
parent b75c306543 861195130c
commit ce83ca1efd
13 changed files with 45 additions and 53 deletions
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6
.github/workflows/compile-msvc.yml vendored
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@ -17,9 +17,15 @@ jobs:
with:
fetch-depth: 2
- name: Select Python version
uses: actions/setup-python@v2
with:
python-version: '3.10'
- name: Building LAMMPS via CMake
shell: bash
run: |
python3 -m pip install numpy
cmake -C cmake/presets/windows.cmake \
-D PKG_PYTHON=on \
-S cmake -B build \

4
src/CG-DNA/pair_oxdna2_coaxstk.cpp
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@ -119,8 +119,8 @@ void PairOxdna2Coaxstk::compute(int eflag, int vflag)
double rb_cs[3],rb_cst[3];
// Cartesian unit vectors in lab frame
double ax[3],ay[3],az[3];
double bx[3],by[3],bz[3];
double ax[3],az[3];
double bx[3],bz[3];
double **x = atom->x;
double **f = atom->f;

2
src/CG-DNA/pair_oxdna_coaxstk.cpp
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@ -130,7 +130,7 @@ void PairOxdnaCoaxstk::compute(int eflag, int vflag)
double rb_cs[3],rb_cst[3];
// Cartesian unit vectors in lab frame
double ax[3],ay[3],az[3];
double bx[3],by[3],bz[3];
double bx[3],bz[3];
double **x = atom->x;
double **f = atom->f;

2
src/CG-DNA/pair_oxdna_excv.cpp
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@ -143,7 +143,7 @@ void PairOxdnaExcv::compute(int eflag, int vflag)
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
int *ellipsoid = atom->ellipsoid;
int n,a,b,in,ia,ib,anum,bnum,atype,btype;
int a,b,in,ia,ib,anum,bnum,atype,btype;
evdwl = 0.0;
ev_init(eflag,vflag);

4
src/CG-DNA/pair_oxdna_hbond.cpp
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@ -149,8 +149,8 @@ void PairOxdnaHbond::compute(int eflag, int vflag)
// vectors COM-h-bonding site in lab frame
double ra_chb[3],rb_chb[3];
// Cartesian unit vectors in lab frame
double ax[3],ay[3],az[3];
double bx[3],by[3],bz[3];
double ax[3],az[3];
double bx[3],bz[3];
double **x = atom->x;
double **f = atom->f;

4
src/CG-DNA/pair_oxdna_xstk.cpp
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@ -126,8 +126,8 @@ void PairOxdnaXstk::compute(int eflag, int vflag)
// vectors COM-h-bonding site in lab frame
double ra_chb[3],rb_chb[3];
// Cartesian unit vectors in lab frame
double ax[3],ay[3],az[3];
double bx[3],by[3],bz[3];
double ax[3],az[3];
double bx[3],bz[3];
double **x = atom->x;
double **f = atom->f;

4
src/CG-DNA/pair_oxrna2_xstk.cpp
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@ -121,8 +121,8 @@ void PairOxrna2Xstk::compute(int eflag, int vflag)
double ra_chb[3],rb_chb[3];
// Cartesian unit vectors in lab frame
double ax[3],ay[3],az[3];
double bx[3],by[3],bz[3];
double ax[3],az[3];
double bx[3],bz[3];
double **x = atom->x;
double **f = atom->f;

7
src/EXTRA-FIX/fix_numdiff.cpp
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@ -41,7 +41,7 @@ using namespace FixConst;
/* ---------------------------------------------------------------------- */
FixNumDiff::FixNumDiff(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), id_pe(nullptr), numdiff_forces(nullptr), temp_x(nullptr), temp_f(nullptr)
Fix(lmp, narg, arg), id_pe(nullptr), pe(nullptr), numdiff_forces(nullptr), temp_x(nullptr), temp_f(nullptr)
{
if (narg < 5) error->all(FLERR, "Illegal fix numdiff command");
@ -109,9 +109,8 @@ void FixNumDiff::init()
// check for PE compute
int icompute = modify->find_compute(id_pe);
if (icompute < 0) error->all(FLERR, "Compute ID for fix numdiff does not exist");
pe = modify->compute[icompute];
pe = modify->get_compute_by_id(id_pe);
if (!pe) error->all(FLERR, "PE compute ID for fix numdiff does not exist");
if (force->pair && force->pair->compute_flag)
pair_compute_flag = 1;

8
src/EXTRA-FIX/fix_numdiff_virial.cpp
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@ -41,7 +41,7 @@ using namespace FixConst;
/* ---------------------------------------------------------------------- */
FixNumDiffVirial::FixNumDiffVirial(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), id_pe(nullptr), temp_x(nullptr), temp_f(nullptr)
Fix(lmp, narg, arg), id_pe(nullptr), pe(nullptr), temp_x(nullptr), temp_f(nullptr)
{
if (narg < 5) error->all(FLERR, "Illegal fix numdiff/virial command");
if (igroup) error->all(FLERR, "Compute numdiff/virial must use group all");
@ -121,9 +121,8 @@ void FixNumDiffVirial::init()
{
// check for PE compute
int icompute = modify->find_compute(id_pe);
if (icompute < 0) error->all(FLERR, "Compute ID for fix numdiff does not exist");
pe = modify->compute[icompute];
pe = modify->get_compute_by_id(id_pe);
if (!pe) error->all(FLERR, "PE compute ID for fix numdiff/virial does not exist");
if (force->pair && force->pair->compute_flag)
pair_compute_flag = 1;
@ -210,7 +209,6 @@ void FixNumDiffVirial::calculate_virial()
// loop over 6 strain directions
// compute a finite difference force in each dimension
int flag, allflag;
double nktv2p = force->nktv2p;
double inv_volume = 1.0 / (domain->xprd * domain->yprd * domain->zprd);

9
src/PHONON/dynamical_matrix.cpp
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@ -282,10 +282,11 @@ void DynamicalMatrix::calculateMatrix()
dynmat_clear(dynmat);
if (me == 0 && screen) {
fprintf(screen,"Calculating Dynamical Matrix ...\n");
fprintf(screen," Total # of atoms = " BIGINT_FORMAT "\n", natoms);
fprintf(screen," Atoms in group = " BIGINT_FORMAT "\n", gcount);
fprintf(screen," Total dynamical matrix elements = " BIGINT_FORMAT "\n", (dynlen*dynlen) );
fputs("Calculating Dynamical Matrix ...\n", screen);
fmt::print(screen," Total # of atoms = {}\n"
" Atoms in group = {}\n"
" Total dynamical matrix elements = {}\n",
natoms, gcount, dynlen*dynlen);
}
// emit dynlen rows of dimalpha*dynlen*dimbeta elements

42
src/PHONON/third_order.cpp
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@ -232,6 +232,7 @@ void ThirdOrder::options(int narg, char **arg)
if (iarg+2 > narg) error->all(FLERR, "Illegal third_order command");
filename = arg[iarg + 1];
file_flag = 1;
iarg += 2;
} else if (strcmp(arg[iarg],"fold") == 0) {
if (iarg+2 > narg) error->all(FLERR, "Illegal Third Order command");
if (strcmp(arg[iarg+1],"yes") == 0) {
@ -300,11 +301,11 @@ void ThirdOrder::calculateMatrix()
getNeighbortags();
if (comm->me == 0 && screen) {
fprintf(screen, "Calculating Third Order ...\n");
fprintf(screen, " Total # of atoms = " BIGINT_FORMAT "\n", natoms);
fprintf(screen, " Atoms in group = " BIGINT_FORMAT "\n", gcount);
fprintf(screen, " Total third order elements = "
BIGINT_FORMAT "\n", (dynlen * dynlen * dynlen));
fputs("Calculating Third Order ...\n", screen);
fmt::print(screen," Total # of atoms = {}\n"
" Atoms in group = {}\n"
" Total third order elements = {}\n",
natoms, gcount, dynlen*dynlen*dynlen);
}
update->nsteps = 0;
@ -436,31 +437,19 @@ void ThirdOrder::writeMatrix(double *dynmat, bigint i, int a, bigint j, int b)
clearerr(fp);
if (folded){
for (int k = 0; k < atom->natoms; k++){
norm = square(dynmat[k*3])+
square(dynmat[k*3+1])+
square(dynmat[k*3+2]);
norm = square(dynmat[k*3])+square(dynmat[k*3+1])+square(dynmat[k*3+2]);
if (norm > 1.0e-16)
fprintf(fp,
BIGINT_FORMAT " %d " BIGINT_FORMAT " %d " BIGINT_FORMAT
" %7.8f %7.8f %7.8f\n",
i+1, a + 1, j+1, b + 1, k+1,
dynmat[k*3] * conversion,
dynmat[k*3+1] * conversion,
dynmat[k*3+2] * conversion);
fmt::print(fp, "{} {} {} {} {} {:17.8f} {:17.8f} {:17.8f}\n",
i+1, a+1, j+1, b+1, k+1, dynmat[k*3] * conversion,
dynmat[k*3+1] * conversion, dynmat[k*3+2] * conversion);
}
} else {
for (int k = 0; k < gcount; k++){
norm = square(dynmat[k*3])+
square(dynmat[k*3+1])+
square(dynmat[k*3+2]);
norm = square(dynmat[k*3])+square(dynmat[k*3+1])+square(dynmat[k*3+2]);
if (norm > 1.0e-16)
fprintf(fp,
BIGINT_FORMAT " %d " BIGINT_FORMAT " %d " BIGINT_FORMAT
" %7.8f %7.8f %7.8f\n",
i+1, a + 1, j+1, b + 1, groupmap[k]+1,
dynmat[k*3] * conversion,
dynmat[k*3+1] * conversion,
dynmat[k*3+2] * conversion);
fmt::print(fp, "{} {} {} {} {} {:17.8f} {:17.8f} {:17.8f}\n",
i+1, a+1, j+1, b+1, groupmap[k]+1, dynmat[k*3] * conversion,
dynmat[k*3+1] * conversion, dynmat[k*3+2] * conversion);
}
}
} else if (binaryflag && fp) {
@ -672,8 +661,7 @@ void ThirdOrder::create_groupmap()
}
//combine subgroup maps into total temporary groupmap
MPI_Allgatherv(sub_groupmap,gid,MPI_LMP_BIGINT,
temp_groupmap,recv,displs,MPI_LMP_BIGINT,world);
MPI_Allgatherv(sub_groupmap,gid,MPI_LMP_BIGINT,temp_groupmap,recv,displs,MPI_LMP_BIGINT,world);
std::sort(temp_groupmap,temp_groupmap+gcount);
//populate member groupmap based on temp groupmap

4
unittest/CMakeLists.txt
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@ -5,8 +5,8 @@
########################################
# download and build googletest framework
message(STATUS "Downloading and building googletest framework")
set(GTEST_URL "https://github.com/google/googletest/archive/release-1.11.0.tar.gz" CACHE STRING "URL of googletest source")
set(GTEST_MD5 "e8a8df240b6938bb6384155d4c37d937" CACHE STRING "MD5 sum for googletest source")
set(GTEST_URL "https://github.com/google/googletest/archive/43efa0a4efd40c78b9210d15373112081899a97c.tar.gz" CACHE STRING "URL of googletest source")
set(GTEST_MD5 "0259ff833c03cdbbedda4e5d02fbc6bd" CACHE STRING "MD5 sum for googletest source")
mark_as_advanced(GTEST_URL)
mark_as_advanced(GTEST_MD5)
set(gtest_force_shared_crt ON CACHE BOOL "" FORCE)

2
unittest/force-styles/tests/mol-pair-lj_cut_tip4p_long.yaml
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@ -1,7 +1,7 @@
---
lammps_version: 10 Feb 2021
date_generated: Fri Feb 26 23:08:49 2021
epsilon: 1e-13
epsilon: 5e-12
prerequisites: ! |
atom full
pair lj/cut/tip4p/long