Merge branch 'master' into fix_gjf_bugs (3ab4be85) · Commits · 郑智淋 / lammps

cmake/presets/most.cmake

+1 −1

Original line number	Diff line number	Diff line
		@@ -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})

+17 −8

Original line number	Diff line number	Diff line
		@@ -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 {

+1 −2

Original line number	Diff line number	Diff line
		@@ -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 */

+1 −1

Original line number	Diff line number	Diff line
		@@ -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;
		}

+16 −8

Original line number	Diff line number	Diff line
		@@ -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;

		for (int ii = 0; ii < 3; ++ii) {
		xo[ii] = x[i][ii];
		xh1[ii] = x[iH1][ii];
		xh2[ii] = x[iH2][ii];
		}

		domain->lamda2x(x[i],xo);
		domain->lamda2x(x[iH1],xh1);
		domain->lamda2x(x[iH2],xh2);
		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 {