(2472cdc8) · Commits · 郑智淋 / lammps

src/compute_property_atom.cpp

0 → 100644

+1027 −0

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src/compute_property_atom.h

0 → 100644

+91 −0

Original line number	Diff line number	Diff line
		/* ----------------------------------------------------------------------
		LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
		http://lammps.sandia.gov, Sandia National Laboratories
		Steve Plimpton, sjplimp@sandia.gov

		Copyright (2003) Sandia Corporation. Under the terms of Contract
		DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
		certain rights in this software. This software is distributed under
		the GNU General Public License.

		See the README file in the top-level LAMMPS directory.
		------------------------------------------------------------------------- */

		#ifndef COMPUTE_PROPERTY_ATOM_H
		#define COMPUTE_PROPERTY_ATOM_H

		#include "compute.h"

		namespace LAMMPS_NS {

		class ComputePropertyAtom : public Compute {
		public:
		ComputePropertyAtom(class LAMMPS , int, char *);
		~ComputePropertyAtom();
		void init() {}
		void compute_peratom();
		double memory_usage();

		private:
		int nvalues;
		int nmax;
		double *vector;
		double **array;
		double *buf;

		typedef void (ComputePropertyAtom::*FnPtrPack)(int);
		FnPtrPack *pack_choice; // ptrs to pack functions

		void pack_id(int);
		void pack_molecule(int);
		void pack_type(int);
		void pack_mass(int);

		void pack_x(int);
		void pack_y(int);
		void pack_z(int);
		void pack_xs(int);
		void pack_ys(int);
		void pack_zs(int);
		void pack_xs_triclinic(int);
		void pack_ys_triclinic(int);
		void pack_zs_triclinic(int);
		void pack_xu(int);
		void pack_yu(int);
		void pack_zu(int);
		void pack_xu_triclinic(int);
		void pack_yu_triclinic(int);
		void pack_zu_triclinic(int);
		void pack_ix(int);
		void pack_iy(int);
		void pack_iz(int);

		void pack_vx(int);
		void pack_vy(int);
		void pack_vz(int);
		void pack_fx(int);
		void pack_fy(int);
		void pack_fz(int);
		void pack_q(int);
		void pack_mux(int);
		void pack_muy(int);
		void pack_muz(int);
		void pack_radius(int);
		void pack_omegax(int);
		void pack_omegay(int);
		void pack_omegaz(int);
		void pack_angmomx(int);
		void pack_angmomy(int);
		void pack_angmomz(int);
		void pack_quatw(int);
		void pack_quati(int);
		void pack_quatj(int);
		void pack_quatk(int);
		void pack_tqx(int);
		void pack_tqy(int);
		void pack_tqz(int);
		};

		}

		#endif

src/dump_custom.cpp

+41 −40

Original line number	Diff line number	Diff line
		@@ -30,7 +30,8 @@

		using namespace LAMMPS_NS;

		// customize by adding keyword to 1st enum
		// customize by adding keyword
		// same as in compute_property.cpp, also customize that command

		enum{ID,MOL,TYPE,MASS,
		X,Y,Z,XS,YS,ZS,XSTRI,YSTRI,ZSTRI,XU,YU,ZU,XUTRI,YUTRI,ZUTRI,IX,IY,IZ,
		@@ -392,7 +393,7 @@ int DumpCustom::count()
		nstride = 1;
		} else if (thresh_array[ithresh] == MOL) {
		if (!atom->molecule_flag)
		error->all("Threshhold for an atom quantity that isn't allocated");
		error->all("Threshhold for an atom property that isn't allocated");
		int *molecule = atom->molecule;
		for (i = 0; i < nlocal; i++) dchoose[i] = molecule[i];
		ptr = dchoose;
		@@ -577,92 +578,92 @@ int DumpCustom::count()
		nstride = 3;
		} else if (thresh_array[ithresh] == Q) {
		if (!atom->q_flag)
		error->all("Threshhold for an atom quantity that isn't allocated");
		error->all("Threshhold for an atom property that isn't allocated");
		ptr = atom->q;
		nstride = 1;
		} else if (thresh_array[ithresh] == MUX) {
		if (!atom->mu_flag)
		error->all("Threshhold for an atom quantity that isn't allocated");
		error->all("Threshhold for an atom property that isn't allocated");
		ptr = &atom->mu[0][0];
		nstride = 3;
		} else if (thresh_array[ithresh] == MUY) {
		if (!atom->mu_flag)
		error->all("Threshhold for an atom quantity that isn't allocated");
		error->all("Threshhold for an atom property that isn't allocated");
		ptr = &atom->mu[0][1];
		nstride = 3;
		} else if (thresh_array[ithresh] == MUZ) {
		if (!atom->mu_flag)
		error->all("Threshhold for an atom quantity that isn't allocated");
		error->all("Threshhold for an atom property that isn't allocated");
		ptr = &atom->mu[0][2];
		nstride = 3;
		} else if (thresh_array[ithresh] == RADIUS) {
		if (!atom->radius_flag)
		error->all("Threshhold for an atom quantity that isn't allocated");
		error->all("Threshhold for an atom property that isn't allocated");
		ptr = atom->radius;
		nstride = 1;
		} else if (thresh_array[ithresh] == OMEGAX) {
		if (!atom->omega_flag)
		error->all("Threshhold for an atom quantity that isn't allocated");
		error->all("Threshhold for an atom property that isn't allocated");
		ptr = &atom->omega[0][0];
		nstride = 3;
		} else if (thresh_array[ithresh] == OMEGAY) {
		if (!atom->omega_flag)
		error->all("Threshhold for an atom quantity that isn't allocated");
		error->all("Threshhold for an atom property that isn't allocated");
		ptr = &atom->omega[0][1];
		nstride = 3;
		} else if (thresh_array[ithresh] == OMEGAZ) {
		if (!atom->omega_flag)
		error->all("Threshhold for an atom quantity that isn't allocated");
		error->all("Threshhold for an atom property that isn't allocated");
		ptr = &atom->omega[0][2];
		nstride = 3;
		} else if (thresh_array[ithresh] == ANGMOMX) {
		if (!atom->angmom_flag)
		error->all("Threshhold for an atom quantity that isn't allocated");
		error->all("Threshhold for an atom property that isn't allocated");
		ptr = &atom->angmom[0][0];
		nstride = 3;
		} else if (thresh_array[ithresh] == ANGMOMY) {
		if (!atom->angmom_flag)
		error->all("Threshhold for an atom quantity that isn't allocated");
		error->all("Threshhold for an atom property that isn't allocated");
		ptr = &atom->angmom[0][1];
		nstride = 3;
		} else if (thresh_array[ithresh] == ANGMOMZ) {
		if (!atom->angmom_flag)
		error->all("Threshhold for an atom quantity that isn't allocated");
		error->all("Threshhold for an atom property that isn't allocated");
		ptr = &atom->angmom[0][2];
		nstride = 3;
		} else if (thresh_array[ithresh] == QUATW) {
		if (!atom->quat_flag)
		error->all("Threshhold for an atom quantity that isn't allocated");
		error->all("Threshhold for an atom property that isn't allocated");
		ptr = &atom->quat[0][0];
		nstride = 4;
		} else if (thresh_array[ithresh] == QUATI) {
		if (!atom->quat_flag)
		error->all("Threshhold for an atom quantity that isn't allocated");
		error->all("Threshhold for an atom property that isn't allocated");
		ptr = &atom->quat[0][1];
		nstride = 4;
		} else if (thresh_array[ithresh] == QUATJ) {
		if (!atom->quat_flag)
		error->all("Threshhold for an atom quantity that isn't allocated");
		error->all("Threshhold for an atom property that isn't allocated");
		ptr = &atom->quat[0][2];
		nstride = 4;
		} else if (thresh_array[ithresh] == QUATK) {
		if (!atom->quat_flag)
		error->all("Threshhold for an atom quantity that isn't allocated");
		error->all("Threshhold for an atom property that isn't allocated");
		ptr = &atom->quat[0][3];
		nstride = 4;
		} else if (thresh_array[ithresh] == TQX) {
		if (!atom->torque_flag)
		error->all("Threshhold for an atom quantity that isn't allocated");
		error->all("Threshhold for an atom property that isn't allocated");
		ptr = &atom->torque[0][0];
		nstride = 3;
		} else if (thresh_array[ithresh] == TQY) {
		if (!atom->torque_flag)
		error->all("Threshhold for an atom quantity that isn't allocated");
		error->all("Threshhold for an atom property that isn't allocated");
		ptr = &atom->torque[0][1];
		nstride = 3;
		} else if (thresh_array[ithresh] == TQZ) {
		if (!atom->torque_flag)
		error->all("Threshhold for an atom quantity that isn't allocated");
		error->all("Threshhold for an atom property that isn't allocated");
		ptr = &atom->torque[0][2];
		nstride = 3;

		@@ -795,7 +796,7 @@ void DumpCustom::parse_fields(int narg, char **arg)
		vtype[i] = INT;
		} else if (strcmp(arg[iarg],"mol") == 0) {
		if (!atom->molecule_flag)
		error->all("Dumping an atom quantity that isn't allocated");
		error->all("Dumping an atom property that isn't allocated");
		pack_choice[i] = &DumpCustom::pack_molecule;
		vtype[i] = INT;
		} else if (strcmp(arg[iarg],"type") == 0) {
		@@ -869,94 +870,94 @@ void DumpCustom::parse_fields(int narg, char **arg)

		} else if (strcmp(arg[iarg],"q") == 0) {
		if (!atom->q_flag)
		error->all("Dumping an atom quantity that isn't allocated");
		error->all("Dumping an atom property that isn't allocated");
		pack_choice[i] = &DumpCustom::pack_q;
		vtype[i] = DOUBLE;
		} else if (strcmp(arg[iarg],"mux") == 0) {
		if (!atom->mu_flag)
		error->all("Dumping an atom quantity that isn't allocated");
		error->all("Dumping an atom property that isn't allocated");
		pack_choice[i] = &DumpCustom::pack_mux;
		vtype[i] = DOUBLE;
		} else if (strcmp(arg[iarg],"muy") == 0) {
		if (!atom->mu_flag)
		error->all("Dumping an atom quantity that isn't allocated");
		error->all("Dumping an atom property that isn't allocated");
		pack_choice[i] = &DumpCustom::pack_muy;
		vtype[i] = DOUBLE;
		} else if (strcmp(arg[iarg],"muz") == 0) {
		if (!atom->mu_flag)
		error->all("Dumping an atom quantity that isn't allocated");
		error->all("Dumping an atom property that isn't allocated");
		pack_choice[i] = &DumpCustom::pack_muz;
		vtype[i] = DOUBLE;

		} else if (strcmp(arg[iarg],"radius") == 0) {
		if (!atom->radius_flag)
		error->all("Dumping an atom quantity that isn't allocated");
		error->all("Dumping an atom property that isn't allocated");
		pack_choice[i] = &DumpCustom::pack_radius;
		vtype[i] = DOUBLE;
		} else if (strcmp(arg[iarg],"omegax") == 0) {
		if (!atom->omega_flag)
		error->all("Dumping an atom quantity that isn't allocated");
		error->all("Dumping an atom property that isn't allocated");
		pack_choice[i] = &DumpCustom::pack_omegax;
		vtype[i] = DOUBLE;
		} else if (strcmp(arg[iarg],"omegay") == 0) {
		if (!atom->omega_flag)
		error->all("Dumping an atom quantity that isn't allocated");
		error->all("Dumping an atom property that isn't allocated");
		pack_choice[i] = &DumpCustom::pack_omegay;
		vtype[i] = DOUBLE;
		} else if (strcmp(arg[iarg],"omegaz") == 0) {
		if (!atom->omega_flag)
		error->all("Dumping an atom quantity that isn't allocated");
		error->all("Dumping an atom property that isn't allocated");
		pack_choice[i] = &DumpCustom::pack_omegaz;
		vtype[i] = DOUBLE;
		} else if (strcmp(arg[iarg],"angmomx") == 0) {
		if (!atom->angmom_flag)
		error->all("Dumping an atom quantity that isn't allocated");
		error->all("Dumping an atom property that isn't allocated");
		pack_choice[i] = &DumpCustom::pack_angmomx;
		vtype[i] = DOUBLE;
		} else if (strcmp(arg[iarg],"angmomy") == 0) {
		if (!atom->angmom_flag)
		error->all("Dumping an atom quantity that isn't allocated");
		error->all("Dumping an atom property that isn't allocated");
		pack_choice[i] = &DumpCustom::pack_angmomy;
		vtype[i] = DOUBLE;
		} else if (strcmp(arg[iarg],"angmomz") == 0) {
		if (!atom->angmom_flag)
		error->all("Dumping an atom quantity that isn't allocated");
		error->all("Dumping an atom property that isn't allocated");
		pack_choice[i] = &DumpCustom::pack_angmomz;
		vtype[i] = DOUBLE;

		} else if (strcmp(arg[iarg],"quatw") == 0) {
		if (!atom->quat_flag)
		error->all("Dumping an atom quantity that isn't allocated");
		error->all("Dumping an atom property that isn't allocated");
		pack_choice[i] = &DumpCustom::pack_quatw;
		vtype[i] = DOUBLE;
		} else if (strcmp(arg[iarg],"quati") == 0) {
		if (!atom->quat_flag)
		error->all("Dumping an atom quantity that isn't allocated");
		error->all("Dumping an atom property that isn't allocated");
		pack_choice[i] = &DumpCustom::pack_quati;
		vtype[i] = DOUBLE;
		} else if (strcmp(arg[iarg],"quatj") == 0) {
		if (!atom->quat_flag)
		error->all("Dumping an atom quantity that isn't allocated");
		error->all("Dumping an atom property that isn't allocated");
		pack_choice[i] = &DumpCustom::pack_quatj;
		vtype[i] = DOUBLE;
		} else if (strcmp(arg[iarg],"quatk") == 0) {
		if (!atom->quat_flag)
		error->all("Dumping an atom quantity that isn't allocated");
		error->all("Dumping an atom property that isn't allocated");
		pack_choice[i] = &DumpCustom::pack_quatk;
		vtype[i] = DOUBLE;
		} else if (strcmp(arg[iarg],"tqx") == 0) {
		if (!atom->torque_flag)
		error->all("Dumping an atom quantity that isn't allocated");
		error->all("Dumping an atom property that isn't allocated");
		pack_choice[i] = &DumpCustom::pack_tqx;
		vtype[i] = DOUBLE;
		} else if (strcmp(arg[iarg],"tqy") == 0) {
		if (!atom->torque_flag)
		error->all("Dumping an atom quantity that isn't allocated");
		error->all("Dumping an atom property that isn't allocated");
		pack_choice[i] = &DumpCustom::pack_tqy;
		vtype[i] = DOUBLE;
		} else if (strcmp(arg[iarg],"tqz") == 0) {
		if (!atom->torque_flag)
		error->all("Dumping an atom quantity that isn't allocated");
		error->all("Dumping an atom property that isn't allocated");
		pack_choice[i] = &DumpCustom::pack_tqz;
		vtype[i] = DOUBLE;

		@@ -1458,7 +1459,7 @@ void DumpCustom::pack_variable(int n)

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

src/style.h

+2 −0

Original line number	Diff line number	Diff line
		@@ -93,6 +93,7 @@ CommandStyle(write_restart,WriteRestart)
		#include "compute_reduce.h"
		#include "compute_reduce_region.h"
		#include "compute_erotate_sphere.h"
		#include "compute_property_atom.h"
		#include "compute_stress_atom.h"
		#include "compute_temp.h"
		#include "compute_temp_com.h"
		@@ -122,6 +123,7 @@ ComputeStyle(pressure,ComputePressure)
		ComputeStyle(reduce,ComputeReduce)
		ComputeStyle(reduce/region,ComputeReduceRegion)
		ComputeStyle(erotate/sphere,ComputeERotateSphere)
		ComputeStyle(property/atom,ComputePropertyAtom)
		ComputeStyle(stress/atom,ComputeStressAtom)
		ComputeStyle(temp,ComputeTemp)
		ComputeStyle(temp/com,ComputeTempCOM)

src/variable.cpp

+3 −3

Original line number	Diff line number	Diff line
		@@ -1024,7 +1024,7 @@ double Variable::evaluate(char str, Tree *tree)
		i = ptr-str+1;
		}

		// v_name = non atom-style variable = global value
		// v_name = scalar from non atom-style global scalar

		if (nbracket == 0 && style[ivar] != ATOM) {

		@@ -1039,7 +1039,7 @@ double Variable::evaluate(char str, Tree *tree)
		treestack[ntreestack++] = newtree;
		} else argstack[nargstack++] = atof(var);

		// v_name = atom-style variable
		// v_name = vector from atom-style per-atom vector

		} else if (nbracket == 0 && style[ivar] == ATOM) {

		@@ -1049,7 +1049,7 @@ double Variable::evaluate(char str, Tree *tree)
		double tmp = evaluate(data[ivar][0],&newtree);
		treestack[ntreestack++] = newtree;

		// v_name[N] = global value from atom-style variable
		// v_name[N] = scalar from atom-style per-atom vector
		// compute the per-atom variable in result
		// use peratom2global to extract single value from result

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