up-to-date (36bac809) · Commits · 郑智淋 / lammps

doc/utils/sphinx-config/false_positives.txt

+2 −0

Original line number	Diff line number	Diff line
		@@ -1667,6 +1667,7 @@ Maras
		Marchetti
		Marchi
		Mariella
		Marinica
		Marrink
		Marroquin
		Marsaglia
		@@ -2837,6 +2838,7 @@ sw
		Swegat
		swiggle
		Swiler
		Swinburne
		Swol
		Swope
		Sx

src/USER-MISC/fix_pafi.cpp

+4 −48

Original line number	Diff line number	Diff line
		@@ -29,7 +29,6 @@
		#include "update.h"
		#include "modify.h"
		#include "domain.h"
		#include "region.h"
		#include "respa.h"
		#include "comm.h"
		#include "compute.h"
		@@ -61,7 +60,7 @@ using namespace FixConst;
		/* ---------------------------------------------------------------------- */

		FixPAFI::FixPAFI(LAMMPS lmp, int narg, char *arg) :
		Fix(lmp, narg, arg), idregion(NULL), random(NULL), computename(NULL),
		Fix(lmp, narg, arg), random(NULL), computename(NULL),
		h(NULL), step_respa(NULL)
		{
		if (lmp->citeme) lmp->citeme->add(cite_fix_pafi_package);
		@@ -81,7 +80,6 @@ FixPAFI::FixPAFI(LAMMPS lmp, int narg, char *arg) :
		computename = new char[n];
		strcpy(computename,&arg[3][0]);


		icompute = modify->find_compute(computename);
		if (icompute == -1)
		error->all(FLERR,"Compute ID for fix pafi does not exist");
		@@ -110,8 +108,6 @@ FixPAFI::FixPAFI(LAMMPS lmp, int narg, char *arg) :
		sqrtD = sqrt(1.) * sqrt(24.0force->boltz/t_period/update->dt/force->mvv2etemperature) / force->ftm2v;

		// optional args
		iregion = -1;
		idregion = NULL; // not used
		int iarg = 7;
		while (iarg < narg) {
		if (strcmp(arg[iarg],"overdamped") == 0) {
		@@ -156,7 +152,6 @@ FixPAFI::~FixPAFI()
		{
		if (copymode) return;
		delete random;
		delete [] idregion;
		delete [] computename;
		memory->destroy(h);
		}
		@@ -181,18 +176,9 @@ int FixPAFI::setmask()

		void FixPAFI::init()
		{
		// set index and check validity of region
		// nve
		dtv = update->dt;
		dtf = 0.5 * update->dt * force->ftm2v;

		if (iregion >= 0) {
		iregion = domain->find_region(idregion);
		if (iregion == -1)
		error->all(FLERR,"Region ID for fix pafi does not exist");
		}


		icompute = modify->find_compute(computename);
		if (icompute == -1)
		error->all(FLERR,"Compute ID for fix pafi does not exist");
		@@ -203,7 +189,6 @@ void FixPAFI::init()
		error->all(FLERR,"Compute for fix pafi must have 9 fields per atom");



		if (strstr(update->integrate_style,"respa")) {
		step_respa = ((Respa *) update->integrate)->step; // nve
		nlevels_respa = ((Respa *) update->integrate)->nlevels;
		@@ -244,13 +229,7 @@ void FixPAFI::post_force(int vflag)
		int *type = atom->type;
		int *mask = atom->mask;
		int nlocal = atom->nlocal;
		// update region if necessary

		Region *region = NULL;
		if (iregion >= 0) {
		region = domain->regions[iregion];
		region->prematch();
		}
		// reallocate norm array if necessary
		if (atom->nmax > maxatom) {
		maxatom = atom->nmax;
		@@ -282,8 +261,6 @@ void FixPAFI::post_force(int vflag)
		force_flag=0;
		for (int i = 0; i < nlocal; i++) {
		if (mask[i] & groupbit) {
		if (region && !region->match(x[i][0],x[i][1],x[i][2])) continue;

		h[i][0] = random->uniform() - 0.5;
		h[i][1] = random->uniform() - 0.5;
		h[i][2] = random->uniform() - 0.5;
		@@ -321,7 +298,6 @@ void FixPAFI::post_force(int vflag)
		} else {
		for (int i = 0; i < nlocal; i++)
		if (mask[i] & groupbit) {
		if (region && !region->match(x[i][0],x[i][1],x[i][2])) continue;

		c_v[0] += f[i][0];
		c_v[1] += f[i][1];
		@@ -341,7 +317,6 @@ void FixPAFI::post_force(int vflag)
		MPI_Allreduce(proj,proj_all,5,MPI_DOUBLE,MPI_SUM,world);
		MPI_Allreduce(c_v,c_v_all,10,MPI_DOUBLE,MPI_SUM,world);

		// results - f.n(1-psi), (f.n)^2(1-psi)^2, 1-psi, dX.n
		results_all[0] = proj_all[0] * (1.-proj_all[3]);
		results_all[1] = results_all[0] * results_all[0];
		results_all[2] = 1.-proj_all[3];
		@@ -350,7 +325,6 @@ void FixPAFI::post_force(int vflag)

		for (int i = 0; i < nlocal; i++){
		if (mask[i] & groupbit) {
		if (region && !region->match(x[i][0],x[i][1],x[i][2])) continue;

		f[i][0] -= proj_all[0] * path[i][3] + c_v_all[0]/c_v_all[9];
		f[i][1] -= proj_all[0] * path[i][4] + c_v_all[1]/c_v_all[9];
		@@ -369,7 +343,6 @@ void FixPAFI::post_force(int vflag)
		if (od_flag == 0) {
		for (int i = 0; i < nlocal; i++){
		if (mask[i] & groupbit) {
		if (region && !region->match(x[i][0],x[i][1],x[i][2])) continue;
		if(rmass) mass_f = sqrt(rmass[i]);
		else mass_f = sqrt(mass[type[i]]);

		@@ -385,7 +358,6 @@ void FixPAFI::post_force(int vflag)
		} else {
		for (int i = 0; i < nlocal; i++){
		if (mask[i] & groupbit) {
		if (region && !region->match(x[i][0],x[i][1],x[i][2])) continue;

		if(rmass) mass_f = sqrt(rmass[i]);
		else mass_f = sqrt(mass[type[i]]);
		@@ -410,11 +382,6 @@ void FixPAFI::post_force_respa(int vflag, int ilevel, int iloop)

		if (ilevel == ilevel_respa) post_force(vflag);
		else {
		Region *region = NULL;
		if (iregion >= 0) {
		region = domain->regions[iregion];
		region->prematch();
		}
		double **x = atom->x;
		double **f = atom->f;
		int *mask = atom->mask;
		@@ -422,7 +389,6 @@ void FixPAFI::post_force_respa(int vflag, int ilevel, int iloop)

		for (int i = 0; i < nlocal; i++)
		if (mask[i] & groupbit) {
		if (region && !region->match(x[i][0],x[i][1],x[i][2])) continue;
		for (int k = 0; k < 3; k++) f[i][k] = 0.0;
		}
		}
		@@ -438,13 +404,6 @@ void FixPAFI::min_post_force(int vflag)
		int *type = atom->type;
		int *mask = atom->mask;
		int nlocal = atom->nlocal;
		// update region if necessary

		Region *region = NULL;
		if (iregion >= 0) {
		region = domain->regions[iregion];
		region->prematch();
		}

		PathCompute->compute_peratom();
		double **path = PathCompute->array_atom;
		@@ -470,7 +429,6 @@ void FixPAFI::min_post_force(int vflag)
		force_flag=0;
		for (int i = 0; i < nlocal; i++) {
		if (mask[i] & groupbit) {
		if (region && !region->match(x[i][0],x[i][1],x[i][2])) continue;

		proj[0] += f[i][0] * path[i][3]; // f.n
		proj[0] += f[i][1] * path[i][4]; // f.n
		@@ -505,7 +463,6 @@ void FixPAFI::min_post_force(int vflag)
		} else {
		for (int i = 0; i < nlocal; i++)
		if (mask[i] & groupbit) {
		if (region && !region->match(x[i][0],x[i][1],x[i][2])) continue;

		c_v[0] += f[i][0];
		c_v[1] += f[i][1];
		@@ -528,14 +485,13 @@ void FixPAFI::min_post_force(int vflag)
		results_all[0] = proj_all[0] * (1.-proj_all[3]); // f.n * psi
		results_all[1] = results_all[0] * results_all[0]; // (f.n * psi)^2
		results_all[2] = 1.-proj_all[3]; // psi
		results_all[3] = fabs(proj_all[4]); // dX.n
		results_all[3] = proj_all[4]; // dX.n

		MPI_Bcast(results_all,4,MPI_DOUBLE,0,world);
		force_flag = 1;

		for (int i = 0; i < nlocal; i++){
		if (mask[i] & groupbit) {
		if (region && !region->match(x[i][0],x[i][1],x[i][2])) continue;

		f[i][0] -= proj_all[0] * path[i][3] + c_v_all[0]/c_v_all[9];
		f[i][1] -= proj_all[0] * path[i][4] + c_v_all[1]/c_v_all[9];

src/USER-MISC/fix_pafi.h

+2 −2

Original line number	Diff line number	Diff line
		@@ -48,8 +48,8 @@ class FixPAFI : public Fix {
		double memory_usage();

		protected:
		int varflag,iregion,icompute;
		char idregion, computename;
		int varflag,icompute;
		char *computename;
		class Compute *PathCompute;
		double proj[5], proj_all[5]; // f,v,h, psi
		double results[4], results_all[4]; // f.n, (f.n)**2, psi, dx.n

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