add convenience functions to modify to simplify creation of fixes and computes (1ea0eca2) · Commits · 郑智淋 / lammps

src/compute_chunk_atom.cpp

+3 −14

Original line number	Diff line number	Diff line
		@@ -36,6 +36,7 @@
		#include "math_const.h"
		#include "memory.h"
		#include "error.h"
		#include "fmt/format.h"

		using namespace LAMMPS_NS;
		using namespace MathConst;
		@@ -581,21 +582,9 @@ void ComputeChunkAtom::init()
		// fixstore initializes all values to 0.0

		if ((idsflag == ONCE \|\| lockcount) && !fixstore) {
		int n = strlen(id) + strlen("_COMPUTE_STORE") + 1;
		id_fix = new char[n];
		strcpy(id_fix,id);
		strcat(id_fix,"_COMPUTE_STORE");

		char *newarg = new char[6];
		newarg[0] = id_fix;
		newarg[1] = group->names[igroup];
		newarg[2] = (char *) "STORE";
		newarg[3] = (char *) "peratom";
		newarg[4] = (char *) "1";
		newarg[5] = (char *) "1";
		modify->add_fix(6,newarg);
		modify->add_fix(fmt::format("{}_COMPUTE_STORE {} STORE peratom 1 1",
		id,group->names[igroup]));
		fixstore = (FixStore *) modify->fix[modify->nfix-1];
		delete [] newarg;
		}

		if ((idsflag != ONCE && !lockcount) && fixstore) {

src/compute_displace_atom.cpp

+3 −14

Original line number	Diff line number	Diff line
		@@ -24,6 +24,7 @@
		#include "variable.h"
		#include "memory.h"
		#include "error.h"
		#include "fmt/format.h"

		using namespace LAMMPS_NS;

		@@ -72,21 +73,9 @@ ComputeDisplaceAtom::ComputeDisplaceAtom(LAMMPS lmp, int narg, char *arg) :
		// create a new fix STORE style
		// id = compute-ID + COMPUTE_STORE, fix group = compute group

		int n = strlen(id) + strlen("_COMPUTE_STORE") + 1;
		id_fix = new char[n];
		strcpy(id_fix,id);
		strcat(id_fix,"_COMPUTE_STORE");

		char *newarg = new char[6];
		newarg[0] = id_fix;
		newarg[1] = group->names[igroup];
		newarg[2] = (char *) "STORE";
		newarg[3] = (char *) "peratom";
		newarg[4] = (char *) "1";
		newarg[5] = (char *) "3";
		modify->add_fix(6,newarg);
		modify->add_fix(fmt::format("{}_COMPUTE_STORE {} STORE peratom 1 3",
		id,group->names[igroup]));
		fix = (FixStore *) modify->fix[modify->nfix-1];
		delete [] newarg;

		// calculate xu,yu,zu for fix store array
		// skip if reset from restart file

src/modify.cpp

+34 −0

Original line number	Diff line number	Diff line
		@@ -941,6 +941,23 @@ void Modify::add_fix(int narg, char **arg, int trysuffix)
		fix[ifix]->post_constructor();
		}

		/* ----------------------------------------------------------------------
		convenience function to allow adding a fix from a single string
		------------------------------------------------------------------------- */

		void Modify::add_fix(const std::string &fixcmd, int trysuffix)
		{
		std::vector<std::string> args = utils::split_words(fixcmd);
		char *newarg = new char[args.size()];
		int i=0;
		for (const auto &arg : args) {
		newarg[i++] = (char *)arg.c_str();
		}
		add_fix(args.size(),newarg,trysuffix);
		delete[] newarg;
		}


		/* ----------------------------------------------------------------------
		replace replaceID fix with a new fix
		this is used by callers to preserve ordering of fixes
		@@ -1228,6 +1245,23 @@ void Modify::add_compute(int narg, char **arg, int trysuffix)
		ncompute++;
		}

		/* ----------------------------------------------------------------------
		convenience function to allow adding a compute from a single string
		------------------------------------------------------------------------- */

		void Modify::add_compute(const std::string &computecmd, int trysuffix)
		{
		std::vector<std::string> args = utils::split_words(computecmd);
		char *newarg = new char[args.size()];
		int i=0;
		for (const auto &arg : args) {
		newarg[i++] = (char *)arg.c_str();
		}
		add_compute(args.size(),newarg,trysuffix);
		delete[] newarg;
		}


		/* ----------------------------------------------------------------------
		one instance per compute in style_compute.h
		------------------------------------------------------------------------- */

src/modify.h

+2 −0

Original line number	Diff line number	Diff line
		@@ -96,6 +96,7 @@ class Modify : protected Pointers {
		virtual int min_reset_ref();

		void add_fix(int, char **, int trysuffix=1);
		void add_fix(const std::string &, int trysuffix=1);
		void replace_fix(const char , int, char *, int trysuffix=1);
		void modify_fix(int, char **);
		void delete_fix(const char *);
		@@ -108,6 +109,7 @@ class Modify : protected Pointers {
		int check_rigid_list_overlap(int *);

		void add_compute(int, char **, int trysuffix=1);
		void add_compute(const std::string &, int trysuffix=1);
		void modify_compute(int, char **);
		void delete_compute(const char *);
		int find_compute(const char *);

src/output.cpp

+4 −19

Original line number	Diff line number	Diff line
		@@ -46,28 +46,13 @@ Output::Output(LAMMPS *lmp) : Pointers(lmp)
		{
		// create default computes for temp,pressure,pe

		char *newarg = new char[4];
		newarg[0] = (char *) "thermo_temp";
		newarg[1] = (char *) "all";
		newarg[2] = (char *) "temp";
		modify->add_compute(3,newarg);

		newarg[0] = (char *) "thermo_press";
		newarg[1] = (char *) "all";
		newarg[2] = (char *) "pressure";
		newarg[3] = (char *) "thermo_temp";
		modify->add_compute(4,newarg);

		newarg[0] = (char *) "thermo_pe";
		newarg[1] = (char *) "all";
		newarg[2] = (char *) "pe";
		modify->add_compute(3,newarg);

		delete [] newarg;
		modify->add_compute("thermo_temp all temp");
		modify->add_compute("thermo_press all pressure thermo_temp");
		modify->add_compute("thermo_pe all pe");

		// create default Thermo class

		newarg = new char*[1];
		char *newarg = new char[1];
		newarg[0] = (char *) "one";
		thermo = new Thermo(lmp,1,newarg);
		delete [] newarg;

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