(cb994067) · Commits · 郑智淋 / lammps

src/fix.cpp

+1 −0

Original line number	Diff line number	Diff line
		@@ -53,6 +53,7 @@ Fix::Fix(LAMMPS lmp, int narg, char *arg) : Pointers(lmp)
		virial_flag = 0;
		no_change_box = 0;
		time_integrate = 0;
		restart_pbc = 0;

		scalar_flag = vector_flag = peratom_flag = 0;

src/fix.h

+2 −0

Original line number	Diff line number	Diff line
		@@ -34,6 +34,8 @@ class Fix : protected Pointers {
		int virial_flag; // 1 if Fix contributes to virial, 0 if not
		int no_change_box; // 1 if cannot swap ortho <-> triclinic
		int time_integrate; // 1 if fix performs time integration, 0 if no
		int restart_pbc; // 1 if fix moves atoms (except integrate)
		// so that write_restart must remap to PBC

		int scalar_flag; // 0/1 if compute_scalar() function exists
		int vector_flag; // 0/1 if compute_vector() function exists

src/modify.cpp

+6 −0

Original line number	Diff line number	Diff line
		@@ -166,6 +166,12 @@ void Modify::init()
		for (i = 0; i < ncompute; i++) compute[i]->init();
		modify->addstep_compute_all(update->ntimestep);

		// set global flag if any fix has its restart_pbc flag set

		restart_pbc_any = 0;
		for (i = 0; i < nfix; i++)
		if (fix[i]->restart_pbc) restart_pbc_any = 1;

		// warn if any particle is time integrated more than once

		int nlocal = atom->nlocal;

src/modify.h

+2 −0

Original line number	Diff line number	Diff line
		@@ -28,6 +28,8 @@ class Modify : protected Pointers {
		int n_min_post_force,n_min_energy;
		int nfix_restart_peratom;

		int restart_pbc_any; // 1 if any fix sets restart_pbc

		class Fix **fix; // list of fixes
		int *fmask; // bit mask for when each fix is applied

src/write_restart.cpp

+53 −1

Original line number	Diff line number	Diff line
		@@ -36,6 +36,9 @@

		using namespace LAMMPS_NS;

		#define MIN(A,B) ((A) < (B)) ? (A) : (B)
		#define MAX(A,B) ((A) > (B)) ? (A) : (B)

		// same as read_restart.cpp and tools/restart2data.cpp

		enum{VERSION,UNITS,NTIMESTEP,DIMENSION,NPROCS,PROCGRID_0,PROCGRID_1,PROCGRID_2,
		@@ -106,7 +109,7 @@ void WriteRestart::command(int narg, char **arg)
		}

		/* ----------------------------------------------------------------------
		called from output within run/minimize loop
		called from command() and directly from output within run/minimize loop
		file = final file name to write, except may contain a "%"
		------------------------------------------------------------------------- */

		@@ -179,6 +182,55 @@ void WriteRestart::write(char *file)
		int n = 0;
		for (int i = 0; i < atom->nlocal; i++) n += avec->pack_restart(i,&buf[n]);

		// if any fix requires it, remap each atom's coords via PBC
		// is because fix changes atom coords (excepting an integrate fix)
		// just remap in buffer, not actual atoms

		if (modify->restart_pbc_any) {
		int triclinic = domain->triclinic;
		double lo,hi,*period;

		if (triclinic == 0) {
		lo = domain->boxlo;
		hi = domain->boxhi;
		period = domain->prd;
		} else {
		lo = domain->boxlo_lamda;
		hi = domain->boxhi_lamda;
		period = domain->prd_lamda;
		}

		int xperiodic = domain->xperiodic;
		int yperiodic = domain->yperiodic;
		int zperiodic = domain->zperiodic;

		double *x;
		int m = 0;
		for (int i = 0; i < atom->nlocal; i++) {
		x = &buf[m+1];
		if (triclinic) domain->x2lamda(x,x);

		if (xperiodic) {
		if (x[0] < lo[0]) x[0] += period[0];
		if (x[0] >= hi[0]) x[0] -= period[0];
		x[0] = MAX(x[0],lo[0]);
		}
		if (yperiodic) {
		if (x[1] < lo[1]) x[1] += period[1];
		if (x[1] >= hi[1]) x[1] -= period[1];
		x[1] = MAX(x[1],lo[1]);
		}
		if (zperiodic) {
		if (x[2] < lo[2]) x[2] += period[2];
		if (x[2] >= hi[2]) x[2] -= period[2];
		x[2] = MAX(x[2],lo[2]);
		}

		if (triclinic) domain->x2lamda(x,x);
		m += static_cast<int> (buf[m]);
		}
		}

		// if single file:
		// write one chunk of atoms per proc to file
		// proc 0 pings each proc, receives its chunk, writes to file

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