(1dbad849) · Commits · 郑智淋 / lammps

src/atom.cpp

+18 −17

Original line number	Diff line number	Diff line
		@@ -52,6 +52,10 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
		extra_bond_per_atom = 0;

		firstgroupname = NULL;
		sortfreq = 0;
		maxbin = maxnext = 0;
		binhead = NULL;
		next = permute = NULL;

		// initialize atom arrays
		// customize by adding new array
		@@ -110,13 +114,6 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
		nextra_store = 0;
		extra = NULL;

		// sorting

		sortflag = 0;
		maxbin = maxnext = 0;
		binhead = NULL;
		next = permute = NULL;

		// default mapping values and hash table primes

		tag_enable = 1;
		@@ -146,7 +143,11 @@ Atom::~Atom()
		{
		delete [] atom_style;
		delete avec;

		delete [] firstgroupname;
		memory->sfree(binhead);
		memory->sfree(next);
		memory->sfree(permute);

		// delete atom arrays
		// customize by adding new array
		@@ -211,12 +212,6 @@ Atom::~Atom()
		delete [] dipole;
		delete [] dipole_setflag;

		// delete sorting arrays

		memory->sfree(binhead);
		memory->sfree(next);
		memory->sfree(permute);

		// delete extra arrays

		memory->sfree(extra_grow);
		@@ -315,7 +310,7 @@ void Atom::setup()
		// setup for sorting
		// binsize = user setting or 1/2 of neighbor cutoff

		if (sortflag) {
		if (sortfreq > 0) {
		double binsize;
		if (userbinsize > 0.0) binsize = userbinsize;
		else binsize = 0.5 * neighbor->cutneighmax;
		@@ -341,6 +336,8 @@ int Atom::style_match(const char *style)

		/* ----------------------------------------------------------------------
		modify parameters of the atom style
		some options can only be invoked before simulation box is defined
		first and sort options cannot be used together
		------------------------------------------------------------------------- */

		void Atom::modify_params(int narg, char **arg)
		@@ -354,6 +351,8 @@ void Atom::modify_params(int narg, char **arg)
		if (strcmp(arg[iarg+1],"array") == 0) map_style = 1;
		else if (strcmp(arg[iarg+1],"hash") == 0) map_style = 2;
		else error->all("Illegal atom_modify command");
		if (domain->box_exist)
		error->all("Atom_modify map command after simulation box is defined");
		iarg += 2;
		} else if (strcmp(arg[iarg],"first") == 0) {
		if (iarg+2 > narg) error->all("Illegal atom_modify command");
		@@ -363,6 +362,7 @@ void Atom::modify_params(int narg, char **arg)
		firstgroupname = new char[n];
		strcpy(firstgroupname,arg[iarg+1]);
		}
		sortfreq = 0;
		iarg += 2;
		} else if (strcmp(arg[iarg],"sort") == 0) {
		if (iarg+3 > narg) error->all("Illegal atom_modify command");
		@@ -370,8 +370,9 @@ void Atom::modify_params(int narg, char **arg)
		userbinsize = atof(arg[iarg+2]);
		if (sortfreq < 0 \|\| userbinsize < 0.0)
		error->all("Illegal atom_modify command");
		if (sortfreq == 0) sortflag = 0;
		else sortflag = 1;
		if (sortfreq >= 0 && firstgroupname)
		error->all("Atom_modify sort and first options "
		"cannot be used together");
		iarg += 3;
		} else error->all("Illegal atom_modify command");
		}
		@@ -1370,7 +1371,7 @@ void Atom::sort()
		permute = (int ) memory->smalloc(maxnextsizeof(int),"atom:permute");
		}

		// insure one extra location at end of atom arrays
		// insure there is one extra atom location at end of arrays for swaps

		if (nlocal == nmax) avec->grow(0);

src/atom.h

+1 −2

Original line number	Diff line number	Diff line
		@@ -102,7 +102,7 @@ class Atom : protected Pointers {

		// spatial sorting of atoms

		int sortflag; // 0 = off, 1 = on
		int sortfreq; // sort atoms every this many steps, 0 = off
		int nextsort; // next timestep to sort on

		// functions
		@@ -203,7 +203,6 @@ class Atom : protected Pointers {
		int *permute; // permutation vector
		double userbinsize; // sorting bin size
		double bininv;
		int sortfreq;

		int memlength; // allocated size of memstr
		char *memstr; // string of array names already counted

src/compute_pressure.cpp

+2 −2

Original line number	Diff line number	Diff line
		@@ -172,7 +172,7 @@ double ComputePressure::compute_scalar()

		double t;
		if (keflag) {
		if (temperature->invoked_scalar == update->ntimestep)
		if (temperature->invoked_scalar != update->ntimestep)
		t = temperature->compute_scalar();
		else t = temperature->scalar;
		}
		@@ -209,7 +209,7 @@ void ComputePressure::compute_vector()
		if (update->vflag_global != invoked_vector)
		error->all("Virial was not tallied on needed timestep");

		// invoke temperature it it hasn't been already
		// invoke temperature if it hasn't been already

		double *ke_tensor;
		if (keflag) {

src/input.cpp

+0 −2

Original line number	Diff line number	Diff line
		@@ -691,8 +691,6 @@ void Input::angle_style()

		void Input::atom_modify()
		{
		if (domain->box_exist)
		error->all("Atom_modify command after simulation box is defined");
		atom->modify_params(narg,arg);
		}

src/modify.cpp

+9 −1

Original line number	Diff line number	Diff line
		@@ -192,12 +192,20 @@ void Modify::init()
		list_init_compute();

		// init each compute
		// set invoked_scalar,vector,etc to -1 to force new run to re-compute them
		// add initial timestep to all computes that store invocation times
		// since any of them may be invoked by initial thermo
		// do not clear out invocation times stored within a compute,
		// b/c some may be holdovers from previous run, like for ave fixes

		for (i = 0; i < ncompute; i++) compute[i]->init();
		for (i = 0; i < ncompute; i++) {
		compute[i]->init();
		compute[i]->invoked_scalar = -1;
		compute[i]->invoked_vector = -1;
		compute[i]->invoked_array = -1;
		compute[i]->invoked_peratom = -1;
		compute[i]->invoked_local = -1;
		}
		addstep_compute_all(update->ntimestep);

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

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