(5f3af951) · Commits · 郑智淋 / lammps

src/compute_property_atom.cpp

+1 −1

Original line number	Diff line number	Diff line
		@@ -249,7 +249,7 @@ void ComputePropertyAtom::compute_peratom()
		buf = vector;
		(this->*pack_choice[0])(0);
		} else {
		buf = array[0];
		if (array) buf = array[0];
		for (int n = 0; n < nvalues; n++)
		(this->*pack_choice[n])(n);
		}

src/compute_property_local.cpp

+15 −6

Original line number	Diff line number	Diff line
		@@ -14,15 +14,13 @@
		#include "string.h"
		#include "compute_property_local.h"
		#include "atom.h"
		#include "atom_vec.h"
		#include "update.h"
		#include "force.h"
		#include "domain.h"
		#include "memory.h"
		#include "error.h"


		#include "comm.h"

		using namespace LAMMPS_NS;

		// customize by adding keyword
		@@ -110,7 +108,7 @@ ComputePropertyLocal::ComputePropertyLocal(LAMMPS lmp, int narg, char *arg) :
		error->all("Compute property/local cannot use these inputs together");
		kindflag = DIHEDRAL;
		} else if (strcmp(arg[iarg],"datom4") == 0) {
		pack_choice[i] = &ComputePropertyLocal::pack_datom3;
		pack_choice[i] = &ComputePropertyLocal::pack_datom4;
		if (kindflag != NONE && kindflag != DIHEDRAL)
		error->all("Compute property/local cannot use these inputs together");
		kindflag = DIHEDRAL;
		@@ -136,7 +134,7 @@ ComputePropertyLocal::ComputePropertyLocal(LAMMPS lmp, int narg, char *arg) :
		error->all("Compute property/local cannot use these inputs together");
		kindflag = IMPROPER;
		} else if (strcmp(arg[iarg],"iatom4") == 0) {
		pack_choice[i] = &ComputePropertyLocal::pack_iatom3;
		pack_choice[i] = &ComputePropertyLocal::pack_iatom4;
		if (kindflag != NONE && kindflag != IMPROPER)
		error->all("Compute property/local cannot use these inputs together");
		kindflag = IMPROPER;
		@@ -149,6 +147,17 @@ ComputePropertyLocal::ComputePropertyLocal(LAMMPS lmp, int narg, char *arg) :
		} else error->all("Invalid keyword in compute property/local command");
		}

		// error check

		if (kindflag == BOND && atom->avec->bonds_allow == 0)
		error->all("Compute property/local for property that isn't allocated");
		if (kindflag == ANGLE && atom->avec->angles_allow == 0)
		error->all("Compute property/local for property that isn't allocated");
		if (kindflag == DIHEDRAL && atom->avec->dihedrals_allow == 0)
		error->all("Compute property/local for property that isn't allocated");
		if (kindflag == IMPROPER && atom->avec->impropers_allow == 0)
		error->all("Compute property/local for property that isn't allocated");

		nmax = 0;
		vector = NULL;
		array = NULL;
		@@ -207,7 +216,7 @@ void ComputePropertyLocal::compute_local()
		buf = vector;
		(this->*pack_choice[0])(0);
		} else {
		buf = array[0];
		if (array) buf = array[0];
		for (int n = 0; n < nvalues; n++)
		(this->*pack_choice[n])(n);
		}

src/dump.cpp

+1 −0

Original line number	Diff line number	Diff line
		@@ -52,6 +52,7 @@ Dump::Dump(LAMMPS lmp, int narg, char *arg) : Pointers(lmp)
		format = NULL;
		format_user = NULL;

		clearstep = 0;
		sort_flag = 0;
		append_flag = 0;

src/dump.h

+1 −0

Original line number	Diff line number	Diff line
		@@ -37,6 +37,7 @@ class Dump : protected Pointers {
		int sort_flag; // 1 if write in sorted order, 0 if not
		int append_flag; // 1 if open file in append mode, 0 if not
		int singlefile_opened; // 1 = one big file, already opened, else 0
		int clearstep; // 1 if dump invokes computes, 0 if not

		char *format_default; // default format string
		char *format_user; // format string set by user

src/dump_custom.cpp

+23 −21

Original line number	Diff line number	Diff line
		@@ -51,6 +51,8 @@ DumpCustom::DumpCustom(LAMMPS lmp, int narg, char *arg) :
		{
		if (narg == 5) error->all("No dump custom arguments specified");

		clearstep = 1;

		nevery = atoi(arg[3]);

		size_one = nfield = narg-5;
		@@ -81,7 +83,7 @@ DumpCustom::DumpCustom(LAMMPS lmp, int narg, char *arg) :
		variable = NULL;
		vbuf = NULL;

		// process keywords
		// process attributes

		parse_fields(narg,arg);

		@@ -974,7 +976,7 @@ void DumpCustom::parse_fields(int narg, char **arg)
		char *ptr = strchr(suffix,'[');
		if (ptr) {
		if (suffix[strlen(suffix)-1] != ']')
		error->all("Invalid keyword in dump custom command");
		error->all("Invalid attribute in dump custom command");
		argindex[i] = atoi(ptr+1);
		*ptr = '\0';
		} else argindex[i] = 0;
		@@ -1008,7 +1010,7 @@ void DumpCustom::parse_fields(int narg, char **arg)
		char *ptr = strchr(suffix,'[');
		if (ptr) {
		if (suffix[strlen(suffix)-1] != ']')
		error->all("Invalid keyword in dump custom command");
		error->all("Invalid attribute in dump custom command");
		argindex[i] = atoi(ptr+1);
		*ptr = '\0';
		} else argindex[i] = 0;
		@@ -1048,7 +1050,7 @@ void DumpCustom::parse_fields(int narg, char **arg)
		field2index[i] = add_variable(suffix);
		delete [] suffix;

		} else error->all("Invalid keyword in dump custom command");
		} else error->all("Invalid attribute in dump custom command");
		}
		}

		@@ -1173,7 +1175,7 @@ int DumpCustom::modify_param(int narg, char **arg)
		memory->srealloc(thresh_value,(nthresh+1)*sizeof(double),
		"dump:thresh_value");

		// set keyword type of threshhold
		// set attribute type of threshhold
		// customize by adding to if statement

		if (strcmp(arg[1],"id") == 0) thresh_array[nthresh] = ID;
		@@ -1258,25 +1260,25 @@ int DumpCustom::modify_param(int narg, char **arg)
		char *ptr = strchr(suffix,'[');
		if (ptr) {
		if (suffix[strlen(suffix)-1] != ']')
		error->all("Invalid keyword in dump custom command");
		error->all("Invalid attribute in dump modify command");
		argindex[nfield+nthresh] = atoi(ptr+1);
		*ptr = '\0';
		} else argindex[nfield+nthresh] = 0;

		n = modify->find_compute(suffix);
		if (n < 0) error->all("Could not find dump custom compute ID");
		if (n < 0) error->all("Could not find dump modify compute ID");

		if (modify->compute[n]->peratom_flag == 0)
		error->all("Dump custom compute ID does not compute per-atom info");
		error->all("Dump modify compute ID does not compute per-atom info");
		if (argindex[nfield+nthresh] == 0 &&
		modify->compute[n]->size_peratom_cols > 0)
		error->all("Dump custom compute ID does not compute per-atom vector");
		error->all("Dump modify compute ID does not compute per-atom vector");
		if (argindex[nfield+nthresh] > 0 &&
		modify->compute[n]->size_peratom_cols == 0)
		error->all("Dump custom compute ID does not compute per-atom array");
		error->all("Dump modify compute ID does not compute per-atom array");
		if (argindex[nfield+nthresh] > 0 &&
		argindex[nfield+nthresh] > modify->compute[n]->size_peratom_cols)
		error->all("Dump custom compute ID vector is not large enough");
		error->all("Dump modify compute ID vector is not large enough");

		field2index[nfield+nthresh] = add_compute(suffix);
		delete [] suffix;
		@@ -1300,25 +1302,25 @@ int DumpCustom::modify_param(int narg, char **arg)
		char *ptr = strchr(suffix,'[');
		if (ptr) {
		if (suffix[strlen(suffix)-1] != ']')
		error->all("Invalid keyword in dump custom command");
		error->all("Invalid attribute in dump modify command");
		argindex[nfield+nthresh] = atoi(ptr+1);
		*ptr = '\0';
		} else argindex[nfield+nthresh] = 0;

		n = modify->find_fix(suffix);
		if (n < 0) error->all("Could not find dump custom fix ID");
		if (n < 0) error->all("Could not find dump modify fix ID");

		if (modify->fix[n]->peratom_flag == 0)
		error->all("Dump custom fix ID does not compute per-atom info");
		error->all("Dump modify fix ID does not compute per-atom info");
		if (argindex[nfield+nthresh] == 0 &&
		modify->fix[n]->size_peratom_cols > 0)
		error->all("Dump custom fix ID does not compute per-atom vector");
		error->all("Dump modify fix ID does not compute per-atom vector");
		if (argindex[nfield+nthresh] > 0 &&
		modify->fix[n]->size_peratom_cols == 0)
		error->all("Dump custom fix ID does not compute per-atom array");
		error->all("Dump modify fix ID does not compute per-atom array");
		if (argindex[nfield+nthresh] > 0 &&
		argindex[nfield+nthresh] > modify->fix[n]->size_peratom_cols)
		error->all("Dump custom fix ID vector is not large enough");
		error->all("Dump modify fix ID vector is not large enough");

		field2index[nfield+nthresh] = add_fix(suffix);
		delete [] suffix;
		@@ -1341,9 +1343,9 @@ int DumpCustom::modify_param(int narg, char **arg)
		argindex[nfield+nthresh] = 0;

		n = input->variable->find(suffix);
		if (n < 0) error->all("Could not find dump custom variable name");
		if (n < 0) error->all("Could not find dump modify variable name");
		if (input->variable->atomstyle(n) == 0)
		error->all("Dump custom variable is not atom-style variable");
		error->all("Dump modify variable is not atom-style variable");

		field2index[nfield+nthresh] = add_variable(suffix);
		delete [] suffix;
		@@ -1457,9 +1459,9 @@ void DumpCustom::pack_variable(int n)
		}

		/* ----------------------------------------------------------------------
		one method for every keyword dump custom can output
		one method for every attribute dump custom can output
		the atom property is packed into buf starting at n with stride size_one
		customize a new keyword by adding a method
		customize a new attribute by adding a method
		------------------------------------------------------------------------- */

		/* ---------------------------------------------------------------------- */

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