git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8226 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -5,7 +5,7 @@
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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@ -86,7 +86,7 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) :
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gfactor1 = new double[atom->ntypes+1];
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gfactor2 = new double[atom->ntypes+1];
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ratio = new double[atom->ntypes+1];
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// optional args
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for (int i = 1; i <= atom->ntypes; i++) ratio[i] = 1.0;
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@ -113,7 +113,7 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) :
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int itype = atoi(arg[iarg+1]);
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double scale = atof(arg[iarg+2]);
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if (itype <= 0 || itype > atom->ntypes)
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error->all(FLERR,"Illegal fix langevin command");
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error->all(FLERR,"Illegal fix langevin command");
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ratio[itype] = scale;
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iarg += 3;
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} else if (strcmp(arg[iarg],"tally") == 0) {
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@ -135,7 +135,7 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) :
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if (aflag) {
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avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
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if (!avec)
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if (!avec)
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error->all(FLERR,"Fix langevin angmom requires atom style ellipsoid");
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}
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@ -192,7 +192,7 @@ void FixLangevin::init()
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if (tstr) {
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tvar = input->variable->find(tstr);
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if (tvar < 0)
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if (tvar < 0)
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error->all(FLERR,"Variable name for fix langevin does not exist");
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if (input->variable->equalstyle(tvar)) tstyle = EQUAL;
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else if (input->variable->atomstyle(tvar)) tstyle = ATOM;
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@ -208,8 +208,8 @@ void FixLangevin::init()
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit)
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if (radius[i] == 0.0)
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error->one(FLERR,"Fix langevin omega requires extended particles");
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if (radius[i] == 0.0)
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error->one(FLERR,"Fix langevin omega requires extended particles");
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}
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if (aflag) {
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@ -219,8 +219,8 @@ void FixLangevin::init()
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit)
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if (ellipsoid[i] < 0)
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error->one(FLERR,"Fix langevin angmom requires extended particles");
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if (ellipsoid[i] < 0)
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error->one(FLERR,"Fix langevin angmom requires extended particles");
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}
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// set force prefactors
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@ -228,9 +228,9 @@ void FixLangevin::init()
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if (!atom->rmass) {
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for (int i = 1; i <= atom->ntypes; i++) {
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gfactor1[i] = -atom->mass[i] / t_period / force->ftm2v;
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gfactor2[i] = sqrt(atom->mass[i]) *
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sqrt(24.0*force->boltz/t_period/update->dt/force->mvv2e) /
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force->ftm2v;
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gfactor2[i] = sqrt(atom->mass[i]) *
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sqrt(24.0*force->boltz/t_period/update->dt/force->mvv2e) /
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force->ftm2v;
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gfactor1[i] *= 1.0/ratio[i];
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gfactor2[i] *= 1.0/sqrt(ratio[i]);
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}
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@ -299,20 +299,20 @@ void FixLangevin::post_force_no_tally()
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if (tstyle == EQUAL) {
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t_target = input->variable->compute_equal(tvar);
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if (t_target < 0.0)
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error->one(FLERR,"Fix langevin variable returned negative temperature");
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error->one(FLERR,"Fix langevin variable returned negative temperature");
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tsqrt = sqrt(t_target);
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} else {
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if (nlocal > maxatom2) {
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maxatom2 = atom->nmax;
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memory->destroy(tforce);
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memory->create(tforce,maxatom2,"langevin:tforce");
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maxatom2 = atom->nmax;
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memory->destroy(tforce);
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memory->create(tforce,maxatom2,"langevin:tforce");
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}
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input->variable->compute_atom(tvar,igroup,tforce,1,0);
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit)
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if (tforce[i] < 0.0)
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error->one(FLERR,
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"Fix langevin variable returned negative temperature");
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if (mask[i] & groupbit)
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if (tforce[i] < 0.0)
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error->one(FLERR,
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"Fix langevin variable returned negative temperature");
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}
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modify->addstep_compute(update->ntimestep + 1);
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}
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@ -325,7 +325,7 @@ void FixLangevin::post_force_no_tally()
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// and added force has extra term not multiplied by v = 0
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// for ZEROFLAG:
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// sum random force over all atoms in group
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// subtract sum/count from each atom in group
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// subtract sum/count from each atom in group
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double fran[3],fsum[3],fsumall[3];
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fsum[0] = fsum[1] = fsum[2] = 0.0;
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@ -335,103 +335,103 @@ void FixLangevin::post_force_no_tally()
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double dt = update->dt;
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double mvv2e = force->mvv2e;
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double ftm2v = force->ftm2v;
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if (zeroflag) {
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count = group->count(igroup);
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if (count == 0)
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error->all(FLERR,"Cannot zero Langevin force of 0 atoms");
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}
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if (rmass) {
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if (which == NOBIAS) {
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
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gamma1 = -rmass[i] / t_period / ftm2v;
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gamma2 = sqrt(rmass[i]) * sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v;
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gamma1 *= 1.0/ratio[type[i]];
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gamma2 *= 1.0/sqrt(ratio[type[i]]) * tsqrt;
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fran[0] = gamma2*(random->uniform()-0.5);
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fran[1] = gamma2*(random->uniform()-0.5);
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fran[2] = gamma2*(random->uniform()-0.5);
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f[i][0] += gamma1*v[i][0] + fran[0];
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f[i][1] += gamma1*v[i][1] + fran[1];
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f[i][2] += gamma1*v[i][2] + fran[2];
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fsum[0] += fran[0];
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fsum[1] += fran[1];
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fsum[2] += fran[2];
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}
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if (mask[i] & groupbit) {
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if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
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gamma1 = -rmass[i] / t_period / ftm2v;
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gamma2 = sqrt(rmass[i]) * sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v;
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gamma1 *= 1.0/ratio[type[i]];
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gamma2 *= 1.0/sqrt(ratio[type[i]]) * tsqrt;
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fran[0] = gamma2*(random->uniform()-0.5);
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fran[1] = gamma2*(random->uniform()-0.5);
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fran[2] = gamma2*(random->uniform()-0.5);
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f[i][0] += gamma1*v[i][0] + fran[0];
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f[i][1] += gamma1*v[i][1] + fran[1];
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f[i][2] += gamma1*v[i][2] + fran[2];
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fsum[0] += fran[0];
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fsum[1] += fran[1];
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fsum[2] += fran[2];
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}
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}
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} else if (which == BIAS) {
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temperature->compute_scalar();
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
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gamma1 = -rmass[i] / t_period / ftm2v;
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gamma2 = sqrt(rmass[i]) * sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v;
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gamma1 *= 1.0/ratio[type[i]];
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gamma2 *= 1.0/sqrt(ratio[type[i]]) * tsqrt;
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temperature->remove_bias(i,v[i]);
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fran[0] = gamma2*(random->uniform()-0.5);
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fran[1] = gamma2*(random->uniform()-0.5);
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fran[2] = gamma2*(random->uniform()-0.5);
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if (v[i][0] != 0.0)
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f[i][0] += gamma1*v[i][0] + fran[0];
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if (v[i][1] != 0.0)
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f[i][1] += gamma1*v[i][1] + fran[1];
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if (v[i][2] != 0.0)
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f[i][2] += gamma1*v[i][2] + fran[2];
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fsum[0] += fran[0];
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fsum[1] += fran[1];
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fsum[2] += fran[2];
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temperature->restore_bias(i,v[i]);
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}
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if (mask[i] & groupbit) {
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if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
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gamma1 = -rmass[i] / t_period / ftm2v;
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gamma2 = sqrt(rmass[i]) * sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v;
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gamma1 *= 1.0/ratio[type[i]];
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gamma2 *= 1.0/sqrt(ratio[type[i]]) * tsqrt;
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temperature->remove_bias(i,v[i]);
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fran[0] = gamma2*(random->uniform()-0.5);
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fran[1] = gamma2*(random->uniform()-0.5);
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fran[2] = gamma2*(random->uniform()-0.5);
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if (v[i][0] != 0.0)
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f[i][0] += gamma1*v[i][0] + fran[0];
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if (v[i][1] != 0.0)
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f[i][1] += gamma1*v[i][1] + fran[1];
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if (v[i][2] != 0.0)
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f[i][2] += gamma1*v[i][2] + fran[2];
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fsum[0] += fran[0];
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fsum[1] += fran[1];
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fsum[2] += fran[2];
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temperature->restore_bias(i,v[i]);
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}
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}
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}
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} else {
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if (which == NOBIAS) {
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
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gamma1 = gfactor1[type[i]];
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gamma2 = gfactor2[type[i]] * tsqrt;
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fran[0] = gamma2*(random->uniform()-0.5);
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fran[1] = gamma2*(random->uniform()-0.5);
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fran[2] = gamma2*(random->uniform()-0.5);
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f[i][0] += gamma1*v[i][0] + fran[0];
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f[i][1] += gamma1*v[i][1] + fran[1];
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f[i][2] += gamma1*v[i][2] + fran[2];
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fsum[0] += fran[0];
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fsum[1] += fran[1];
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fsum[2] += fran[2];
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}
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if (mask[i] & groupbit) {
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if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
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gamma1 = gfactor1[type[i]];
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gamma2 = gfactor2[type[i]] * tsqrt;
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fran[0] = gamma2*(random->uniform()-0.5);
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fran[1] = gamma2*(random->uniform()-0.5);
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fran[2] = gamma2*(random->uniform()-0.5);
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f[i][0] += gamma1*v[i][0] + fran[0];
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f[i][1] += gamma1*v[i][1] + fran[1];
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f[i][2] += gamma1*v[i][2] + fran[2];
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fsum[0] += fran[0];
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fsum[1] += fran[1];
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fsum[2] += fran[2];
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}
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}
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} else if (which == BIAS) {
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temperature->compute_scalar();
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
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gamma1 = gfactor1[type[i]];
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gamma2 = gfactor2[type[i]] * tsqrt;
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temperature->remove_bias(i,v[i]);
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fran[0] = gamma2*(random->uniform()-0.5);
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fran[1] = gamma2*(random->uniform()-0.5);
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fran[2] = gamma2*(random->uniform()-0.5);
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if (v[i][0] != 0.0)
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f[i][0] += gamma1*v[i][0] + fran[0];
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if (v[i][1] != 0.0)
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f[i][1] += gamma1*v[i][1] + fran[1];
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if (v[i][2] != 0.0)
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f[i][2] += gamma1*v[i][2] + fran[2];
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fsum[0] += fran[0];
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fsum[1] += fran[1];
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fsum[2] += fran[2];
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temperature->restore_bias(i,v[i]);
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}
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if (mask[i] & groupbit) {
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if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
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gamma1 = gfactor1[type[i]];
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gamma2 = gfactor2[type[i]] * tsqrt;
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temperature->remove_bias(i,v[i]);
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fran[0] = gamma2*(random->uniform()-0.5);
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fran[1] = gamma2*(random->uniform()-0.5);
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fran[2] = gamma2*(random->uniform()-0.5);
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if (v[i][0] != 0.0)
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f[i][0] += gamma1*v[i][0] + fran[0];
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if (v[i][1] != 0.0)
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f[i][1] += gamma1*v[i][1] + fran[1];
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if (v[i][2] != 0.0)
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f[i][2] += gamma1*v[i][2] + fran[2];
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fsum[0] += fran[0];
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fsum[1] += fran[1];
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fsum[2] += fran[2];
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temperature->restore_bias(i,v[i]);
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}
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}
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}
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}
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@ -445,9 +445,9 @@ void FixLangevin::post_force_no_tally()
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fsumall[2] /= count;
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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f[i][0] -= fsumall[0];
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f[i][1] -= fsumall[1];
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f[i][2] -= fsumall[2];
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f[i][0] -= fsumall[0];
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f[i][1] -= fsumall[1];
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f[i][2] -= fsumall[2];
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}
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}
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}
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@ -494,20 +494,20 @@ void FixLangevin::post_force_tally()
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if (tstyle == EQUAL) {
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t_target = input->variable->compute_equal(tvar);
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if (t_target < 0.0)
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error->one(FLERR,"Fix langevin variable returned negative temperature");
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error->one(FLERR,"Fix langevin variable returned negative temperature");
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tsqrt = sqrt(t_target);
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} else {
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if (nlocal > maxatom2) {
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maxatom2 = atom->nmax;
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memory->destroy(tforce);
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memory->create(tforce,maxatom2,"langevin:tforce");
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maxatom2 = atom->nmax;
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memory->destroy(tforce);
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memory->create(tforce,maxatom2,"langevin:tforce");
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}
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input->variable->compute_atom(tvar,igroup,tforce,1,0);
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit)
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if (tforce[i] < 0.0)
|
||||
error->one(FLERR,
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"Fix langevin variable returned negative temperature");
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if (mask[i] & groupbit)
|
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if (tforce[i] < 0.0)
|
||||
error->one(FLERR,
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"Fix langevin variable returned negative temperature");
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}
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modify->addstep_compute(update->ntimestep + 1);
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}
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@ -527,80 +527,80 @@ void FixLangevin::post_force_tally()
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if (rmass) {
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if (which == NOBIAS) {
|
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for (int i = 0; i < nlocal; i++) {
|
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if (mask[i] & groupbit) {
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if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
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||||
gamma1 = -rmass[i] / t_period / ftm2v;
|
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gamma2 = sqrt(rmass[i]) * sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v;
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gamma1 *= 1.0/ratio[type[i]];
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gamma2 *= 1.0/sqrt(ratio[type[i]]) * tsqrt;
|
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flangevin[i][0] = gamma1*v[i][0] + gamma2*(random->uniform()-0.5);
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flangevin[i][1] = gamma1*v[i][1] + gamma2*(random->uniform()-0.5);
|
||||
flangevin[i][2] = gamma1*v[i][2] + gamma2*(random->uniform()-0.5);
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f[i][0] += flangevin[i][0];
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f[i][1] += flangevin[i][1];
|
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f[i][2] += flangevin[i][2];
|
||||
}
|
||||
if (mask[i] & groupbit) {
|
||||
if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
|
||||
gamma1 = -rmass[i] / t_period / ftm2v;
|
||||
gamma2 = sqrt(rmass[i]) * sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v;
|
||||
gamma1 *= 1.0/ratio[type[i]];
|
||||
gamma2 *= 1.0/sqrt(ratio[type[i]]) * tsqrt;
|
||||
flangevin[i][0] = gamma1*v[i][0] + gamma2*(random->uniform()-0.5);
|
||||
flangevin[i][1] = gamma1*v[i][1] + gamma2*(random->uniform()-0.5);
|
||||
flangevin[i][2] = gamma1*v[i][2] + gamma2*(random->uniform()-0.5);
|
||||
f[i][0] += flangevin[i][0];
|
||||
f[i][1] += flangevin[i][1];
|
||||
f[i][2] += flangevin[i][2];
|
||||
}
|
||||
}
|
||||
|
||||
} else if (which == BIAS) {
|
||||
temperature->compute_scalar();
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
|
||||
gamma1 = -rmass[i] / t_period / ftm2v;
|
||||
gamma2 = sqrt(rmass[i]) * sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v;
|
||||
gamma1 *= 1.0/ratio[type[i]];
|
||||
gamma2 *= 1.0/sqrt(ratio[type[i]]) * tsqrt;
|
||||
temperature->remove_bias(i,v[i]);
|
||||
flangevin[i][0] = gamma1*v[i][0] + gamma2*(random->uniform()-0.5);
|
||||
flangevin[i][1] = gamma1*v[i][1] + gamma2*(random->uniform()-0.5);
|
||||
flangevin[i][2] = gamma1*v[i][2] + gamma2*(random->uniform()-0.5);
|
||||
if (v[i][0] != 0.0) f[i][0] += flangevin[i][0];
|
||||
else flangevin[i][0] = 0;
|
||||
if (v[i][1] != 0.0) f[i][1] += flangevin[i][1];
|
||||
else flangevin[i][1] = 0;
|
||||
if (v[i][2] != 0.0) f[i][2] += flangevin[i][2];
|
||||
else flangevin[i][2] = 0;
|
||||
temperature->restore_bias(i,v[i]);
|
||||
}
|
||||
if (mask[i] & groupbit) {
|
||||
if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
|
||||
gamma1 = -rmass[i] / t_period / ftm2v;
|
||||
gamma2 = sqrt(rmass[i]) * sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v;
|
||||
gamma1 *= 1.0/ratio[type[i]];
|
||||
gamma2 *= 1.0/sqrt(ratio[type[i]]) * tsqrt;
|
||||
temperature->remove_bias(i,v[i]);
|
||||
flangevin[i][0] = gamma1*v[i][0] + gamma2*(random->uniform()-0.5);
|
||||
flangevin[i][1] = gamma1*v[i][1] + gamma2*(random->uniform()-0.5);
|
||||
flangevin[i][2] = gamma1*v[i][2] + gamma2*(random->uniform()-0.5);
|
||||
if (v[i][0] != 0.0) f[i][0] += flangevin[i][0];
|
||||
else flangevin[i][0] = 0;
|
||||
if (v[i][1] != 0.0) f[i][1] += flangevin[i][1];
|
||||
else flangevin[i][1] = 0;
|
||||
if (v[i][2] != 0.0) f[i][2] += flangevin[i][2];
|
||||
else flangevin[i][2] = 0;
|
||||
temperature->restore_bias(i,v[i]);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
} else {
|
||||
if (which == NOBIAS) {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
|
||||
gamma1 = gfactor1[type[i]];
|
||||
gamma2 = gfactor2[type[i]] * tsqrt;
|
||||
flangevin[i][0] = gamma1*v[i][0] + gamma2*(random->uniform()-0.5);
|
||||
flangevin[i][1] = gamma1*v[i][1] + gamma2*(random->uniform()-0.5);
|
||||
flangevin[i][2] = gamma1*v[i][2] + gamma2*(random->uniform()-0.5);
|
||||
f[i][0] += flangevin[i][0];
|
||||
f[i][1] += flangevin[i][1];
|
||||
f[i][2] += flangevin[i][2];
|
||||
}
|
||||
if (mask[i] & groupbit) {
|
||||
if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
|
||||
gamma1 = gfactor1[type[i]];
|
||||
gamma2 = gfactor2[type[i]] * tsqrt;
|
||||
flangevin[i][0] = gamma1*v[i][0] + gamma2*(random->uniform()-0.5);
|
||||
flangevin[i][1] = gamma1*v[i][1] + gamma2*(random->uniform()-0.5);
|
||||
flangevin[i][2] = gamma1*v[i][2] + gamma2*(random->uniform()-0.5);
|
||||
f[i][0] += flangevin[i][0];
|
||||
f[i][1] += flangevin[i][1];
|
||||
f[i][2] += flangevin[i][2];
|
||||
}
|
||||
}
|
||||
|
||||
} else if (which == BIAS) {
|
||||
temperature->compute_scalar();
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
|
||||
gamma1 = gfactor1[type[i]];
|
||||
gamma2 = gfactor2[type[i]] * tsqrt;
|
||||
temperature->remove_bias(i,v[i]);
|
||||
flangevin[i][0] = gamma1*v[i][0] + gamma2*(random->uniform()-0.5);
|
||||
flangevin[i][1] = gamma1*v[i][1] + gamma2*(random->uniform()-0.5);
|
||||
flangevin[i][2] = gamma1*v[i][2] + gamma2*(random->uniform()-0.5);
|
||||
if (v[i][0] != 0.0) f[i][0] += flangevin[i][0];
|
||||
else flangevin[i][0] = 0.0;
|
||||
if (v[i][1] != 0.0) f[i][1] += flangevin[i][1];
|
||||
else flangevin[i][1] = 0.0;
|
||||
if (v[i][2] != 0.0) f[i][2] += flangevin[i][2];
|
||||
else flangevin[i][2] = 0.0;
|
||||
temperature->restore_bias(i,v[i]);
|
||||
}
|
||||
if (mask[i] & groupbit) {
|
||||
if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
|
||||
gamma1 = gfactor1[type[i]];
|
||||
gamma2 = gfactor2[type[i]] * tsqrt;
|
||||
temperature->remove_bias(i,v[i]);
|
||||
flangevin[i][0] = gamma1*v[i][0] + gamma2*(random->uniform()-0.5);
|
||||
flangevin[i][1] = gamma1*v[i][1] + gamma2*(random->uniform()-0.5);
|
||||
flangevin[i][2] = gamma1*v[i][2] + gamma2*(random->uniform()-0.5);
|
||||
if (v[i][0] != 0.0) f[i][0] += flangevin[i][0];
|
||||
else flangevin[i][0] = 0.0;
|
||||
if (v[i][1] != 0.0) f[i][1] += flangevin[i][1];
|
||||
else flangevin[i][1] = 0.0;
|
||||
if (v[i][2] != 0.0) f[i][2] += flangevin[i][2];
|
||||
else flangevin[i][2] = 0.0;
|
||||
temperature->restore_bias(i,v[i]);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
@ -686,7 +686,7 @@ void FixLangevin::angmom_thermostat()
|
||||
inertia[2] = EINERTIA*rmass[i] * (shape[0]*shape[0]+shape[1]*shape[1]);
|
||||
quat = bonus[ellipsoid[i]].quat;
|
||||
MathExtra::mq_to_omega(angmom[i],quat,inertia,omega);
|
||||
|
||||
|
||||
if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
|
||||
gamma1 = -1.0 / t_period / ftm2v;
|
||||
gamma2 = sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v;
|
||||
@ -712,14 +712,14 @@ void FixLangevin::end_of_step()
|
||||
|
||||
double **v = atom->v;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
energy_onestep = 0.0;
|
||||
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit)
|
||||
energy_onestep += flangevin[i][0]*v[i][0] + flangevin[i][1]*v[i][1] +
|
||||
flangevin[i][2]*v[i][2];
|
||||
energy_onestep += flangevin[i][0]*v[i][0] + flangevin[i][1]*v[i][1] +
|
||||
flangevin[i][2]*v[i][2];
|
||||
|
||||
energy += energy_onestep*update->dt;
|
||||
}
|
||||
@ -737,9 +737,9 @@ void FixLangevin::reset_dt()
|
||||
{
|
||||
if (atom->mass) {
|
||||
for (int i = 1; i <= atom->ntypes; i++) {
|
||||
gfactor2[i] = sqrt(atom->mass[i]) *
|
||||
sqrt(24.0*force->boltz/t_period/update->dt/force->mvv2e) /
|
||||
force->ftm2v;
|
||||
gfactor2[i] = sqrt(atom->mass[i]) *
|
||||
sqrt(24.0*force->boltz/t_period/update->dt/force->mvv2e) /
|
||||
force->ftm2v;
|
||||
gfactor2[i] *= 1.0/sqrt(ratio[i]);
|
||||
}
|
||||
}
|
||||
@ -757,13 +757,13 @@ int FixLangevin::modify_param(int narg, char **arg)
|
||||
strcpy(id_temp,arg[1]);
|
||||
|
||||
int icompute = modify->find_compute(id_temp);
|
||||
if (icompute < 0)
|
||||
if (icompute < 0)
|
||||
error->all(FLERR,"Could not find fix_modify temperature ID");
|
||||
temperature = modify->compute[icompute];
|
||||
|
||||
if (temperature->tempflag == 0)
|
||||
error->all(FLERR,
|
||||
"Fix_modify temperature ID does not compute temperature");
|
||||
"Fix_modify temperature ID does not compute temperature");
|
||||
if (temperature->igroup != igroup && comm->me == 0)
|
||||
error->warning(FLERR,"Group for fix_modify temp != fix group");
|
||||
return 2;
|
||||
@ -781,21 +781,21 @@ double FixLangevin::compute_scalar()
|
||||
|
||||
double **v = atom->v;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
if (update->ntimestep == update->beginstep) {
|
||||
energy_onestep = 0.0;
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit)
|
||||
energy_onestep += flangevin[i][0]*v[i][0] + flangevin[i][1]*v[i][1] +
|
||||
flangevin[i][2]*v[i][2];
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit)
|
||||
energy_onestep += flangevin[i][0]*v[i][0] + flangevin[i][1]*v[i][1] +
|
||||
flangevin[i][2]*v[i][2];
|
||||
energy = 0.5*energy_onestep*update->dt;
|
||||
}
|
||||
|
||||
double energy_me = energy - 0.5*energy_onestep*update->dt;
|
||||
|
||||
double energy_all;
|
||||
MPI_Allreduce(&energy_me,&energy_all,1,MPI_DOUBLE,MPI_SUM,world);
|
||||
double energy_all;
|
||||
MPI_Allreduce(&energy_me,&energy_all,1,MPI_DOUBLE,MPI_SUM,world);
|
||||
return -energy_all;
|
||||
}
|
||||
|
||||
@ -808,7 +808,7 @@ void *FixLangevin::extract(const char *str, int &dim)
|
||||
dim=0;
|
||||
if (strcmp(str,"t_target") == 0) {
|
||||
return &t_target;
|
||||
}
|
||||
}
|
||||
return NULL;
|
||||
}
|
||||
|
||||
|
||||
Reference in New Issue
Block a user