(31790144) · Commits · 郑智淋 / lammps

src/atom.cpp

+6 −1

Original line number	Diff line number	Diff line
		@@ -83,6 +83,10 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
		eradius = ervel = erforce = NULL;
		cs = csforce = vforce = ervelforce = NULL;
		etag = NULL;
		rho = drho = NULL;
		e = de = NULL;
		cv = NULL;
		vest = NULL;

		maxspecial = 1;
		nspecial = NULL;
		@@ -106,12 +110,13 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
		// customize by adding new flag

		sphere_flag = ellipsoid_flag = peri_flag = electron_flag = 0;
		wavepacket_flag = 0;
		wavepacket_flag = sph_flag = 0;

		molecule_flag = q_flag = mu_flag = 0;
		rmass_flag = radius_flag = omega_flag = torque_flag = angmom_flag = 0;
		vfrac_flag = spin_flag = eradius_flag = ervel_flag = erforce_flag = 0;
		cs_flag = csforce_flag = vforce_flag = ervelforce_flag= etag_flag = 0;
		rho_flag = e_flag = cv_flag = vest_flag = 0;

		// ntype-length arrays

src/atom.h

+6 −1

Original line number	Diff line number	Diff line
		@@ -56,6 +56,10 @@ class Atom : protected Pointers {
		double eradius,ervel,erforce,ervelforce;
		double cs,csforce,*vforce;
		int *etag;
		double rho, drho;
		double e, de;
		double **vest;
		double *cv;

		int **nspecial; // 0,1,2 = cummulative # of 1-2,1-3,1-4 neighs
		int **special; // IDs of 1-2,1-3,1-4 neighs of each atom
		@@ -81,12 +85,13 @@ class Atom : protected Pointers {
		// customize by adding new flag

		int sphere_flag,ellipsoid_flag,peri_flag,electron_flag;
		int wavepacket_flag;
		int wavepacket_flag,sph_flag;

		int molecule_flag,q_flag,mu_flag;
		int rmass_flag,radius_flag,omega_flag,torque_flag,angmom_flag;
		int vfrac_flag,spin_flag,eradius_flag,ervel_flag,erforce_flag;
		int cs_flag,csforce_flag,vforce_flag,ervelforce_flag,etag_flag;
		int rho_flag,e_flag,cv_flag,vest_flag;

		// extra peratom info in restart file destined for fix & diag

src/fix_gravity.cpp

+28 −0

Original line number	Diff line number	Diff line
		@@ -34,6 +34,9 @@ FixGravity::FixGravity(LAMMPS lmp, int narg, char *arg) :
		if (narg < 5) error->all("Illegal fix gravity command");

		time_depend = 1;
		scalar_flag = 1;
		global_freq = 1;
		extscalar = 1;

		magnitude = atof(arg[3]);

		@@ -90,6 +93,9 @@ FixGravity::FixGravity(LAMMPS lmp, int narg, char *arg) :
		}

		time_origin = update->ntimestep;

		eflag = 0;
		egrav = 0.0;
		}

		/* ---------------------------------------------------------------------- */
		@@ -98,6 +104,7 @@ int FixGravity::setmask()
		{
		int mask = 0;
		mask \|= POST_FORCE;
		mask \|= THERMO_ENERGY;
		mask \|= POST_FORCE_RESPA;
		return mask;
		}
		@@ -155,6 +162,7 @@ void FixGravity::post_force(int vflag)
		zacc = magnitude*zgrav;
		}

		double **x = atom->x;
		double **f = atom->f;
		double *rmass = atom->rmass;
		double *mass = atom->mass;
		@@ -163,6 +171,9 @@ void FixGravity::post_force(int vflag)
		int nlocal = atom->nlocal;
		double massone;

		eflag = 0;
		egrav = 0.0;

		if (rmass) {
		for (int i = 0; i < nlocal; i++)
		if (mask[i] & groupbit) {
		@@ -170,6 +181,7 @@ void FixGravity::post_force(int vflag)
		f[i][0] += massone*xacc;
		f[i][1] += massone*yacc;
		f[i][2] += massone*zacc;
		egrav -= massone * (xaccx[i][0] + yaccx[i][1] + zacc*x[i][2]);
		}
		} else {
		for (int i = 0; i < nlocal; i++)
		@@ -178,6 +190,7 @@ void FixGravity::post_force(int vflag)
		f[i][0] += massone*xacc;
		f[i][1] += massone*yacc;
		f[i][2] += massone*zacc;
		egrav -= massone * (xaccx[i][0] + yaccx[i][1] + zacc*x[i][2]);
		}
		}
		}
		@@ -188,3 +201,18 @@ void FixGravity::post_force_respa(int vflag, int ilevel, int iloop)
		{
		if (ilevel == nlevels_respa-1) post_force(vflag);
		}

		/* ----------------------------------------------------------------------
		potential energy in gravity field
		------------------------------------------------------------------------- */

		double FixGravity::compute_scalar()
		{
		// only sum across procs one time

		if (eflag == 0) {
		MPI_Allreduce(&egrav,&egrav_all,1,MPI_DOUBLE,MPI_SUM,world);
		eflag = 1;
		}
		return egrav_all;
		}

src/fix_gravity.h

+3 −0

Original line number	Diff line number	Diff line
		@@ -34,6 +34,7 @@ class FixGravity : public Fix {
		void setup(int);
		void post_force(int);
		void post_force_respa(int, int, int);
		double compute_scalar();

		private:
		int style;
		@@ -44,6 +45,8 @@ class FixGravity : public Fix {
		double degree2rad;
		int nlevels_respa;
		int time_origin;
		int eflag;
		double egrav,egrav_all;
		};

		}

src/min.cpp

+15 −1

Original line number	Diff line number	Diff line
		@@ -137,12 +137,16 @@ void Min::init()
		ev_setup();

		// set flags for what arrays to clear in force_clear()
		// need to clear torques,erforce if arrays exists
		// need to clear additionals arrays if they exist

		torqueflag = 0;
		if (atom->torque_flag) torqueflag = 1;
		erforceflag = 0;
		if (atom->erforce_flag) erforceflag = 1;
		e_flag = 0;
		if (atom->e_flag) e_flag = 1;
		rho_flag = 0;
		if (atom->rho_flag) rho_flag = 1;

		// orthogonal vs triclinic simulation box

		@@ -537,6 +541,16 @@ void Min::force_clear()
		double *erforce = atom->erforce;
		for (i = 0; i < nall; i++) erforce[i] = 0.0;
		}

		if (e_flag) {
		double *de = atom->de;
		for (i = 0; i < nall; i++) de[i] = 0.0;
		}

		if (rho_flag) {
		double *drho = atom->drho;
		for (i = 0; i < nall; i++) drho[i] = 0.0;
		}
		}

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

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