import updated fix msst file with some additional cleanup and simplification (60c67b07) · Commits · 郑智淋 / lammps

src/SHOCK/fix_msst.cpp

+51 −40

Original line number	Diff line number	Diff line
		@@ -446,7 +446,7 @@ void FixMSST::initial_integrate(int vflag)
		{
		int i,k;
		double p_msst; // MSST driving pressure
		double vol,TS,TS_term,escale_term;
		double vol;

		int nlocal = atom->nlocal;
		int *mask = atom->mask;
		@@ -469,12 +469,16 @@ void FixMSST::initial_integrate(int vflag)
		// must convert energy to mv^2 units

		if (dftb) {
		double TS_dftb = fix_external->compute_vector(0);
		TS = force->ftm2v*TS_dftb;
		const double TS_dftb = fix_external->compute_vector(0);
		const double TS = force->ftm2v*TS_dftb;
		// update S_elec terms and compute TS_dot via finite differences
		S_elec_2 = S_elec_1;
		S_elec_1 = S_elec;
		const double Temp = temperature->compute_scalar();
		S_elec = TS/Temp;
		TS_dot = Temp(3.0S_elec-4.0S_elec_1+S_elec_2)/(2.0update->dt);
		TS_int += (update->dt*TS_dot);
		if (update->ntimestep == 1) T0S0 = TS;
		} else {
		TS = 0.0;
		T0S0 = 0.0;
		}

		// compute new pressure and volume
		@@ -484,16 +488,6 @@ void FixMSST::initial_integrate(int vflag)
		couple();
		vol = compute_vol();

		// update S_elec terms and compute TS_dot via finite differences

		S_elec_2 = S_elec_1;
		S_elec_1 = S_elec;
		double Temp = temperature->compute_scalar();
		S_elec = TS/Temp;
		TS_dot = Temp(3.0S_elec-4.0S_elec_1+S_elec_2)/(2.0update->dt);
		TS_int += (update->dt*TS_dot);
		//TS_int += (update->dt*TS_dot)/total_mass;

		// compute etot + extra terms for conserved quantity

		double e_scale = compute_etotal() + compute_scalar();
		@@ -530,9 +524,9 @@ void FixMSST::initial_integrate(int vflag)
		for (i = 0; i < nlocal; i++) {
		if (mask[i] & groupbit) {
		for ( k = 0; k < 3; k++ ) {
		double C = f[i][k] * force->ftm2v / mass[type[i]];
		TS_term = TS_dot/(mass[type[i]]*velocity_sum);
		escale_term = force->ftm2vbeta(e0-e_scale) /
		const double C = f[i][k] * force->ftm2v / mass[type[i]];
		const double TS_term = TS_dot/(mass[type[i]]*velocity_sum);
		const double escale_term = force->ftm2vbeta(e0-e_scale) /
		(mass[type[i]]*velocity_sum);
		double D = mu * omega[sd] * omega[sd] /
		(velocity_sum * mass[type[i]] * vol );
		@@ -540,7 +534,7 @@ void FixMSST::initial_integrate(int vflag)
		old_velocity[i][k] = v[i][k];
		if ( k == direction ) D -= 2.0 * omega[sd] / vol;
		if ( fabs(dthalf * D) > 1.0e-06 ) {
		double expd = exp(D * dthalf);
		const double expd = exp(D * dthalf);
		v[i][k] = expd * ( C + D * v[i][k] - C / expd ) / D;
		} else {
		v[i][k] = v[i][k] + ( C + D * v[i][k] ) * dthalf +
		@@ -553,15 +547,15 @@ void FixMSST::initial_integrate(int vflag)
		for (i = 0; i < nlocal; i++) {
		if (mask[i] & groupbit) {
		for ( k = 0; k < 3; k++ ) {
		double C = f[i][k] * force->ftm2v / mass[type[i]];
		const double C = f[i][k] * force->ftm2v / mass[type[i]];
		double D = mu * omega[sd] * omega[sd] /
		(velocity_sum * mass[type[i]] * vol );
		old_velocity[i][k] = v[i][k];
		if ( k == direction ) {
		D = D - 2.0 * omega[sd] / vol;
		D -= 2.0 * omega[sd] / vol;
		}
		if ( fabs(dthalf * D) > 1.0e-06 ) {
		double expd = exp(D * dthalf);
		const double expd = exp(D * dthalf);
		v[i][k] = expd * ( C + D * v[i][k] - C / expd ) / D;
		} else {
		v[i][k] = v[i][k] + ( C + D * v[i][k] ) * dthalf +
		@@ -590,16 +584,16 @@ void FixMSST::initial_integrate(int vflag)
		for (i = 0; i < nlocal; i++) {
		if (mask[i] & groupbit) {
		for ( k = 0; k < 3; k++ ) {
		double C = f[i][k] * force->ftm2v / mass[type[i]];
		TS_term = TS_dot/(mass[type[i]]*velocity_sum);
		escale_term = force->ftm2vbeta(e0-e_scale) /
		const double C = f[i][k] * force->ftm2v / mass[type[i]];
		const double TS_term = TS_dot/(mass[type[i]]*velocity_sum);
		const double escale_term = force->ftm2vbeta(e0-e_scale) /
		(mass[type[i]]*velocity_sum);
		double D = mu * omega[sd] * omega[sd] /
		(velocity_sum * mass[type[i]] * vol );
		D += escale_term - TS_term;
		if ( k == direction ) D -= 2.0 * omega[sd] / vol;
		if ( fabs(dthalf * D) > 1.0e-06 ) {
		double expd = exp(D * dthalf);
		const double expd = exp(D * dthalf);
		v[i][k] = expd * ( C + D * v[i][k] - C / expd ) / D;
		} else {
		v[i][k] = v[i][k] + ( C + D * v[i][k] ) * dthalf +
		@@ -612,14 +606,14 @@ void FixMSST::initial_integrate(int vflag)
		for (i = 0; i < nlocal; i++) {
		if (mask[i] & groupbit) {
		for ( k = 0; k < 3; k++ ) {
		double C = f[i][k] * force->ftm2v / mass[type[i]];
		const double C = f[i][k] * force->ftm2v / mass[type[i]];
		double D = mu * omega[sd] * omega[sd] /
		(velocity_sum * mass[type[i]] * vol );
		if ( k == direction ) {
		D = D - 2.0 * omega[sd] / vol;
		D -= 2.0 * omega[sd] / vol;
		}
		if ( fabs(dthalf * D) > 1.0e-06 ) {
		double expd = exp(D * dthalf);
		const double expd = exp(D * dthalf);
		v[i][k] = expd * ( C + D * v[i][k] - C / expd ) / D;
		} else {
		v[i][k] = v[i][k] + ( C + D * v[i][k] ) * dthalf +
		@@ -669,7 +663,6 @@ void FixMSST::final_integrate()
		{
		int i;
		double p_msst; // MSST driving pressure
		double TS_term,escale_term;

		// v update only for atoms in MSST group

		@@ -687,22 +680,38 @@ void FixMSST::final_integrate()

		double e_scale = compute_etotal() + compute_scalar();

		// for DFTB, extract TS_dftb from fix external
		// must convert energy to mv^2 units

		if (dftb) {
		const double TS_dftb = fix_external->compute_vector(0);
		const double TS = force->ftm2v*TS_dftb;
		S_elec_2 = S_elec_1;
		S_elec_1 = S_elec;
		const double Temp = temperature->compute_scalar();
		// update S_elec terms and compute TS_dot via finite differences
		S_elec = TS/Temp;
		TS_dot = Temp(3.0S_elec-4.0S_elec_1+S_elec_2)/(2.0update->dt);
		TS_int += (update->dt*TS_dot);
		if (update->ntimestep == 1) T0S0 = TS;
		}

		// propagate particle velocities 1/2 step

		if (dftb) {
		for (i = 0; i < nlocal; i++) {
		if (mask[i] & groupbit) {
		for ( int k = 0; k < 3; k++ ) {
		double C = f[i][k] * force->ftm2v / mass[type[i]];
		TS_term = TS_dot/(mass[type[i]]*velocity_sum);
		escale_term = force->ftm2vbeta(e0-e_scale) /
		const double C = f[i][k] * force->ftm2v / mass[type[i]];
		const double TS_term = TS_dot/(mass[type[i]]*velocity_sum);
		const double escale_term = force->ftm2vbeta(e0-e_scale) /
		(mass[type[i]]*velocity_sum);
		double D = mu * omega[sd] * omega[sd] /
		(velocity_sum * mass[type[i]] * vol );
		D += escale_term - TS_term;
		if ( k == direction ) D -= 2.0 * omega[sd] / vol;
		if ( fabs(dthalf * D) > 1.0e-06 ) {
		double expd = exp(D * dthalf);
		const double expd = exp(D * dthalf);
		v[i][k] = expd * ( C + D * v[i][k] - C / expd ) / D;
		} else {
		v[i][k] = v[i][k] + ( C + D * v[i][k] ) * dthalf +
		@@ -715,14 +724,14 @@ void FixMSST::final_integrate()
		for (i = 0; i < nlocal; i++) {
		if (mask[i] & groupbit) {
		for ( int k = 0; k < 3; k++ ) {
		double C = f[i][k] * force->ftm2v / mass[type[i]];
		const double C = f[i][k] * force->ftm2v / mass[type[i]];
		double D = mu * omega[sd] * omega[sd] /
		(velocity_sum * mass[type[i]] * vol );
		if ( k == direction ) {
		D = D - 2.0 * omega[sd] / vol;
		D -= 2.0 * omega[sd] / vol;
		}
		if ( fabs(dthalf * D) > 1.0e-06 ) {
		double expd = exp(D * dthalf);
		const double expd = exp(D * dthalf);
		v[i][k] = expd * ( C + D * v[i][k] - C / expd ) / D;
		} else {
		v[i][k] = v[i][k] + ( C + D * v[i][k] ) * dthalf +
		@@ -748,7 +757,7 @@ void FixMSST::final_integrate()
		( v0 - vol )/( v0 * v0 );
		double A = total_mass * ( p_current[sd] - p0 - p_msst ) /
		( qmass * nktv2p * mvv2e );
		double B = total_mass * mu / ( qmass * vol );
		const double B = total_mass * mu / ( qmass * vol );

		// prevent blow-up of the volume

		@@ -950,7 +959,9 @@ double FixMSST::compute_scalar()

		// subtract off precomputed TS_int integral value

		if (dftb) { // TS_int == 0 for non DFTB calculations
		energy -= TS_int;
		}

		return energy;
		}

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