Added changes to FixNH restart (26685383) · Commits · 郑智淋 / lammps

src/fix_nh.cpp

+38 −20

Original line number	Diff line number	Diff line
		@@ -642,14 +642,14 @@ void FixNH::setup(int vflag)
		tdof = temperature->dof;

		// t_target is needed by NPH and NPT in compute_scalar()
		// If no thermostat,
		// If no thermostat or using fix nphug,
		// t_target must be defined by other means.

		if (tstat_flag) {
		if (tstat_flag && strcmp(style,"nphug") != 0) {
		compute_temp_target();
		} else if (pstat_flag) {

		// t0 = initial value for piston mass and energy conservation
		// t0 = reference temperature for masses
		// cannot be done in init() b/c temperature cannot be called there
		// is b/c Modify::init() inits computes after fixes due to dof dependence
		// guesstimate a unit-dependent t0 if actual T = 0.0
		@@ -675,7 +675,7 @@ void FixNH::setup(int vflag)
		pressure->addstep(update->ntimestep+1);
		}

		// initial forces on thermostat variables
		// masses and initial forces on thermostat variables

		if (tstat_flag) {
		eta_mass[0] = tdof * boltz * t_target / (t_freq*t_freq);
		@@ -687,6 +687,8 @@ void FixNH::setup(int vflag)
		}
		}

		// masses and initial forces on barostat variables

		if (pstat_flag) {
		double kt = boltz * t_target;
		double nkt = atom->natoms * kt;
		@@ -700,7 +702,7 @@ void FixNH::setup(int vflag)
		if (p_flag[i]) omega_mass[i] = nkt/(p_freq[i]*p_freq[i]);
		}

		// initial forces on barostat thermostat variables
		// masses and initial forces on barostat thermostat variables

		if (mpchain) {
		etap_mass[0] = boltz * t_target / (p_freq_max*p_freq_max);
		@@ -729,9 +731,6 @@ void FixNH::initial_integrate(int vflag)

		if (tstat_flag) {
		compute_temp_target();
		eta_mass[0] = tdof * boltz * t_target / (t_freq*t_freq);
		for (int ich = 1; ich < mtchain; ich++)
		eta_mass[ich] = boltz * t_target / (t_freq*t_freq);
		nhc_temp_integrate();
		}

		@@ -828,9 +827,6 @@ void FixNH::initial_integrate_respa(int vflag, int ilevel, int iloop)

		if (tstat_flag) {
		compute_temp_target();
		eta_mass[0] = tdof * boltz * t_target / (t_freq*t_freq);
		for (int ich = 1; ich < mtchain; ich++)
		eta_mass[ich] = boltz * t_target / (t_freq*t_freq);
		nhc_temp_integrate();
		}

		@@ -1118,6 +1114,28 @@ void FixNH::remap()
		------------------------------------------------------------------------- */

		void FixNH::write_restart(FILE *fp)
		{
		int nsize = size_restart();

		double *list;
		memory->create(list,nsize,"nh:list");

		int n = pack_restart_data(list);

		if (comm->me == 0) {
		int size = nsize * sizeof(double);
		fwrite(&size,sizeof(int),1,fp);
		fwrite(list,sizeof(double),nsize,fp);
		}

		memory->destroy(list);
		}

		/* ----------------------------------------------------------------------
		calculate the number of data to be packed
		------------------------------------------------------------------------- */

		int FixNH::size_restart()
		{
		int nsize = 2;
		if (tstat_flag) nsize += 1 + 2*mtchain;
		@@ -1126,9 +1144,15 @@ void FixNH::write_restart(FILE *fp)
		if (deviatoric_flag) nsize += 6;
		}

		double *list;
		memory->create(list,nsize,"nh:list");
		return nsize;
		}

		/* ----------------------------------------------------------------------
		pack restart data
		------------------------------------------------------------------------- */

		int FixNH::pack_restart_data(double *list)
		{
		int n = 0;

		list[n++] = tstat_flag;
		@@ -1175,13 +1199,7 @@ void FixNH::write_restart(FILE *fp)
		}
		}

		if (comm->me == 0) {
		int size = nsize * sizeof(double);
		fwrite(&size,sizeof(int),1,fp);
		fwrite(list,sizeof(double),nsize,fp);
		}

		memory->destroy(list);
		return n;
		}

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

src/fix_nh.h

+7 −3

Original line number	Diff line number	Diff line
		@@ -31,9 +31,11 @@ class FixNH : public Fix {
		void final_integrate_respa(int, int);
		void pre_exchange();
		double compute_scalar();
		double compute_vector(int);
		virtual double compute_vector(int);
		void write_restart(FILE *);
		void restart(char *);
		virtual int pack_restart_data(double *); // pack restart data
		virtual int size_restart(); // return size
		virtual void restart(char *);
		int modify_param(int, char **);
		void reset_target(double);
		void reset_dt();
		@@ -42,7 +44,9 @@ class FixNH : public Fix {
		int dimension,which;
		double dtv,dtf,dthalf,dt4,dt8,dto;
		double boltz,nktv2p,tdof;
		double vol0,t0;
		double vol0; // reference volume
		double t0; // reference temperature
		// used for barostat mass

		double t_start,t_stop;
		double t_current,t_target,ke_target;

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