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Merge branch 'master' into fix_gjf_bugs

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This commit is contained in:
Axel Kohlmeyer
2019-10-15 17:16:33 +02:00
parent d53b882a5a e7d1d547a1
commit 3ab4be859c
6 changed files with 37 additions and 20 deletions
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2
cmake/presets/most.cmake
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@ -7,7 +7,7 @@ set(ALL_PACKAGES ASPHERE CLASS2 COLLOID CORESHELL DIPOLE
PYTHON QEQ REPLICA RIGID SHOCK SRD VORONOI
USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD
USER-DRUDE USER-FEP USER-MEAMC USER-MESO
USER-MISC USER-MOFFF USER-OMP USER-PLUMED USER-PHONON USER-REAXC
USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REAXC
USER-SPH USER-SMD USER-UEF USER-YAFF)
foreach(PKG ${ALL_PACKAGES})

25
src/KSPACE/pppm_tip4p.cpp
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@ -500,11 +500,18 @@ void PPPMTIP4P::find_M(int i, int &iH1, int &iH2, double *xM)
// since local atoms are in lambda coordinates, but ghosts are not.
int *sametag = atom->sametag;
double xo[3],xh1[3],xh2[3];
double xo[3],xh1[3],xh2[3],xm[3];
const int nlocal = atom->nlocal;
domain->lamda2x(x[i],xo);
domain->lamda2x(x[iH1],xh1);
domain->lamda2x(x[iH2],xh2);
for (int ii = 0; ii < 3; ++ii) {
xo[ii] = x[i][ii];
xh1[ii] = x[iH1][ii];
xh2[ii] = x[iH2][ii];
}
if (i < nlocal) domain->lamda2x(x[i],xo);
if (iH1 < nlocal) domain->lamda2x(x[iH1],xh1);
if (iH2 < nlocal) domain->lamda2x(x[iH2],xh2);
double delx = xo[0] - xh1[0];
double dely = xo[1] - xh1[1];
@ -513,6 +520,8 @@ void PPPMTIP4P::find_M(int i, int &iH1, int &iH2, double *xM)
double rsq;
int closest = iH1;
// no need to run lamda2x() here -> ghost atoms
while (sametag[iH1] >= 0) {
iH1 = sametag[iH1];
delx = xo[0] - x[iH1][0];
@ -561,13 +570,13 @@ void PPPMTIP4P::find_M(int i, int &iH1, int &iH2, double *xM)
double dely2 = xh2[1] - xo[1];
double delz2 = xh2[2] - xo[2];
xM[0] = xo[0] + alpha * 0.5 * (delx1 + delx2);
xM[1] = xo[1] + alpha * 0.5 * (dely1 + dely2);
xM[2] = xo[2] + alpha * 0.5 * (delz1 + delz2);
xm[0] = xo[0] + alpha * 0.5 * (delx1 + delx2);
xm[1] = xo[1] + alpha * 0.5 * (dely1 + dely2);
xm[2] = xo[2] + alpha * 0.5 * (delz1 + delz2);
// ... and convert M to lamda space for PPPM
domain->x2lamda(xM,xM);
domain->x2lamda(xm,xM);
} else {

3
src/STUBS/mpi.c
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@ -12,14 +12,13 @@
------------------------------------------------------------------------ */
/* Single-processor "stub" versions of MPI routines */
/* -I. in Makefile insures dummy mpi.h in this dir is included */
#include <stdlib.h>
#include <string.h>
#include <stdio.h>
#include <stdint.h>
#include <sys/time.h>
#include <mpi.h>
#include "mpi.h"
#include "../version.h"
/* data structure for double/int */

2
src/USER-OMP/pppm_omp.cpp
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@ -48,7 +48,7 @@ using namespace MathSpecial;
PPPMOMP::PPPMOMP(LAMMPS *lmp) : PPPM(lmp), ThrOMP(lmp, THR_KSPACE)
{
triclinic_support = 0;
triclinic_support = 1;
suffix_flag |= Suffix::OMP;
}

24
src/USER-OMP/pppm_tip4p_omp.cpp
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@ -750,11 +750,18 @@ void PPPMTIP4POMP::find_M_thr(int i, int &iH1, int &iH2, dbl3_t &xM)
// since local atoms are in lambda coordinates, but ghosts are not.
int *sametag = atom->sametag;
double xo[3],xh1[3],xh2[3];
double xo[3],xh1[3],xh2[3],xm[3];
const int nlocal = atom->nlocal;
domain->lamda2x(x[i],xo);
domain->lamda2x(x[iH1],xh1);
domain->lamda2x(x[iH2],xh2);
for (int ii = 0; ii < 3; ++ii) {
xo[ii] = x[i][ii];
xh1[ii] = x[iH1][ii];
xh2[ii] = x[iH2][ii];
}
if (i < nlocal) domain->lamda2x(x[i],xo);
if (iH1 < nlocal) domain->lamda2x(x[iH1],xh1);
if (iH2 < nlocal) domain->lamda2x(x[iH2],xh2);
double delx = xo[0] - xh1[0];
double dely = xo[1] - xh1[1];
@ -763,6 +770,7 @@ void PPPMTIP4POMP::find_M_thr(int i, int &iH1, int &iH2, dbl3_t &xM)
double rsq;
int closest = iH1;
// no need to run lamda2x here -> ghost atoms
while (sametag[iH1] >= 0) {
iH1 = sametag[iH1];
delx = xo[0] - x[iH1][0];
@ -811,13 +819,13 @@ void PPPMTIP4POMP::find_M_thr(int i, int &iH1, int &iH2, dbl3_t &xM)
double dely2 = xh2[1] - xo[1];
double delz2 = xh2[2] - xo[2];
xM.x = xo[0] + alpha * 0.5 * (delx1 + delx2);
xM.y = xo[1] + alpha * 0.5 * (dely1 + dely2);
xM.z = xo[2] + alpha * 0.5 * (delz1 + delz2);
xm[0] = xo[0] + alpha * 0.5 * (delx1 + delx2);
xm[1] = xo[1] + alpha * 0.5 * (dely1 + dely2);
xm[2] = xo[2] + alpha * 0.5 * (delz1 + delz2);
// ... and convert M to lamda space for PPPM
domain->x2lamda((double *)&xM,(double *)&xM);
domain->x2lamda(xm,(double *)&xM);
} else {

1
src/force.cpp
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@ -21,6 +21,7 @@
#include "style_improper.h"
#include "style_pair.h"
#include "style_kspace.h"
#include "atom.h"
#include "comm.h"
#include "pair.h"
#include "pair_hybrid.h"