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Updated integrator, streamlined variables

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This commit is contained in:
talinke
2025-04-08 17:35:09 -07:00
parent 641d496d4b
commit bd6bb3ce10
2 changed files with 155 additions and 293 deletions
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423
src/EXTRA-FIX/fix_langevin_gjf.cpp
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@ -44,8 +44,8 @@ enum { CONSTANT, EQUAL, ATOM };
/* ---------------------------------------------------------------------- */
FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), gjfflag(0), gfactor1(nullptr), gfactor2(nullptr), ratio(nullptr),
FixLangevinGJF::FixLangevinGJF(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), gjfflag(0),
tstr(nullptr), flangevin(nullptr), tforce(nullptr), lv(nullptr), id_temp(nullptr), random(nullptr)
{
if (narg < 8) error->all(FLERR, "Illegal fix langevin/gjf command");
@ -78,16 +78,10 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) :
random = new RanMars(lmp, seed + comm->me);
// allocate per-type arrays for force prefactors
// gfactor1 = new double[atom->ntypes + 1];
// gfactor2 = new double[atom->ntypes + 1];
// ratio = new double[atom->ntypes + 1];
int GJmethods = 8 // number of currently implemented GJ methods
// optional args
for (int i = 1; i <= atom->ntypes; i++) ratio[i] = 1.0;
osflag = 0;
GJmethod = 0;
@ -105,39 +99,28 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg], "method") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal fix langevin/gjf command");
GJmethod = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
if (GJmethod <= 0 || GJmethod > GJmethods) error->all(FLERR, "Invalid GJ method choice in langevin/gjf command");
if (GJmethod < 0 || GJmethod > GJmethods) error->all(FLERR, "Invalid GJ method choice in langevin/gjf command");
iarg += 2;
} else
error->all(FLERR, "Illegal fix langevin/gjf command");
}
// set temperature = nullptr, user can override via fix_modify if wants bias
id_temp = nullptr;
temperature = nullptr;
energy = 0.0;
// flangevin is unallocated until first call to setup()
// compute_scalar checks for this and returns 0.0
// if flangevin_allocated is not set
flangevin = nullptr;
flangevin_allocated = 0;
lv = nullptr;
tforce = nullptr;
maxatom1 = maxatom2 = 0;
// setup atom-based array for lv
// register with Atom class
// no need to set peratom_flag, b/c data is for internal use only
FixLangevin::grow_arrays(atom->nmax);
FixLangevinGJF::grow_arrays(atom->nmax);
atom->add_callback(Atom::GROW);
// initialize lv to zero
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
lv[i][0] = 0.0;
@ -148,17 +131,13 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) :
/* ---------------------------------------------------------------------- */
FixLangevin::~FixLangevin()
FixLangevinGJF::~FixLangevinGJF()
{
if (copymode) return;
delete random;
delete[] tstr;
delete[] gfactor1;
delete[] gfactor2;
delete[] ratio;
delete[] id_temp;
memory->destroy(flangevin);
memory->destroy(tforce);
memory->destroy(lv);
@ -167,18 +146,18 @@ FixLangevin::~FixLangevin()
/* ---------------------------------------------------------------------- */
int FixLangevin::setmask()
int FixLangevinGJF::setmask()
{
int mask = 0;
mask |= INITIAL_INTEGRATE;
mask |= FINAL_INTEGRATE;
mask |= END_OF_STEP;
if (!osflag) mask |= END_OF_STEP;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixLangevin::init()
void FixLangevinGJF::init()
{
if (id_temp) {
temperature = modify->get_compute_by_id(id_temp);
@ -193,23 +172,13 @@ void FixLangevin::init()
if (tstr) {
tvar = input->variable->find(tstr);
if (tvar < 0) error->all(FLERR, "Variable name {} for fix langevin does not exist", tstr);
if (tvar < 0) error->all(FLERR, "Variable name {} for fix langevin/gjf does not exist", tstr);
if (input->variable->equalstyle(tvar))
tstyle = EQUAL;
else if (input->variable->atomstyle(tvar))
tstyle = ATOM;
else
error->all(FLERR, "Variable {} for fix langevin is invalid style", tstr);
}
// set force prefactors
if (!atom->rmass) {
for (int i = 1; i <= atom->ntypes; i++) {
gfactor1[i] = -atom->mass[i] / t_period / force->ftm2v;
gfactor2[i] = sqrt(atom->mass[i]) / force->ftm2v;
gfactor2[i] *= sqrt(2.0 * update->dt * force->boltz / t_period / force->mvv2e); // gjfflag
}
error->all(FLERR, "Variable {} for fix langevin/gjf is invalid style", tstr);
}
if (temperature && temperature->tempbias)
@ -219,44 +188,44 @@ void FixLangevin::init()
if (utils::strmatch(update->integrate_style, "^respa")) {
nlevels_respa = (static_cast<Respa *>(update->integrate))->nlevels;
if (gjfflag) error->all(FLERR, "Fix langevin gjf and run style respa are not compatible");
}
if (gjfflag) {
gjfc2 = (1.0 - update->dt / 2.0 / t_period) / (1.0 + update->dt / 2.0 / t_period);
gjfc1 = 1.0 / (1.0 + update->dt / 2.0 / t_period);
error->all(FLERR, "Fix langevin gjf and run style respa are not compatible");
}
// Complete set of thermostats is given in Gronbech-Jensen, Molecular Physics, 118 (2020)
switch (GJmethod) {
case 1:
gjfc2 = (1.0 - update->dt / 2.0 / t_period) / (1.0 + update->dt / 2.0 / t_period);
gjfc1 = 1.0 / (1.0 + update->dt / 2.0 / t_period);
break;
case 2:
// Insert logic for method 2
gjfc2 = exp(-update->dt / t_period);
break;
case 3:
// Insert logic for method 3
gjfc2 = 1.0 - update->dt / t_period;
break;
case 4:
// Insert logic for method 4
gjfc2 = ( sqrt(1.0 + 4.0 * (update->dt / t_period) ) - 1.0 ) / ( 2.0 * update->dt / t_period );
break;
case 5:
// Insert logic for method 5
gjfc2 = 1.0 / (1.0 + update->dt / t_period);
break;
case 6:
// Insert logic for method 6
gjfc2 = (1.0 / (1.0 + update->dt / 2.0 / t_period)) * (1.0 / (1.0 + update->dt / 2.0 / t_period));
break;
case 7:
// Insert logic for method 7
case 7: // provided in Finkelstein (2021)
gjfc2 = 1; // TODO: correct this
break;
case 8:
// Insert logic for method 8
case 8: // provided in Gronbech-Jensen (2024)
gjfc2 = sqrt( (update->dt / t_period)*(update->dt / t_period) + 1.0 ) - update->dt / t_period;
break;
case 0:
gjfc2 = 0.0;
break;
default:
error->all(FLERR, "Fix langevin/gjf method not found");
break;
}
}
gjfc1 = (1.0 + gjfc2) / 2.0;
gjfc3 = (1.0 - gjfc2) * t_period / update->dt;
}
/* ----------------------------------------------------------------------
@ -268,10 +237,9 @@ void FixLangevin::init()
4. Velocity Choice in end_of_step()
------------------------------------------------------------------------- */
void FixLangevin::initial_integrate(int /* vflag */)
void FixLangevinGJF::initial_integrate(int /* vflag */)
{
double gamma1,gamma2;
// This function provides the integration of the GJ formulation 24a-e
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
@ -290,79 +258,21 @@ void FixLangevin::initial_integrate(int /* vflag */)
double dtf = 0.5 * dt * ftm2v;
double dtfm;
double c1sqrt = sqrt(gjfc1);
// NVE integrates position and velocity according to Eq. 8a, 8b
// This function embeds the GJF formulation into the NVE framework, which corresponds to the GJF case c1=c3.
double c1sq = sqrt(gjfc1);
double c3sq = sqrt(gjfc3);
double csq = sqrt(gjfc3 / gjfc1);
double m, beta;
//NVE
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
dtfm = dtf / rmass[i];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
x[i][0] += dt * v[i][0];
x[i][1] += dt * v[i][1];
x[i][2] += dt * v[i][2];
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
dtfm = dtf / mass[type[i]];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
x[i][0] += dt * v[i][0];
x[i][1] += dt * v[i][1];
x[i][2] += dt * v[i][2];
}
}
// The initial NVE integration should always use the on-site velocity. Therefore, a velocity correction
// must be done when using the half-step option.
//----------
// If user elected vhalf, v needs to be reassigned to onsite velocity for integration
if (!osflag) {
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
dtfm = dtf / rmass[i];
// Undo NVE integration
x[i][0] -= dt * v[i][0];
x[i][1] -= dt * v[i][1];
x[i][2] -= dt * v[i][2];
// Obtain Eq. 24a. lv[][] stores on-site velocity from previous timestep
v[i][0] = lv[i][0] + dtfm * f[i][0];
v[i][1] = lv[i][1] + dtfm * f[i][1];
v[i][2] = lv[i][2] + dtfm * f[i][2];
// Redo NVE integration with correct velocity
x[i][0] += dt * v[i][0];
x[i][1] += dt * v[i][1];
x[i][2] += dt * v[i][2];
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
dtfm = dtf / mass[type[i]];
// Undo NVE integration
x[i][0] -= dt * v[i][0];
x[i][1] -= dt * v[i][1];
x[i][2] -= dt * v[i][2];
// Obtain Eq. 24a. lv[][] stores on-site velocity from previous timestep
v[i][0] = lv[i][0] + dtfm * f[i][0];
v[i][1] = lv[i][1] + dtfm * f[i][1];
v[i][2] = lv[i][2] + dtfm * f[i][2];
// Redo NVE integration with correct velocity
x[i][0] += dt * v[i][0];
x[i][1] += dt * v[i][1];
x[i][2] += dt * v[i][2];
}
}
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
// lv is Eq. 24f from previous time step
v[i][0] = lv[i][0];
v[i][1] = lv[i][1];
v[i][2] = lv[i][2];
}
}
//----------
compute_target();
@ -370,59 +280,58 @@ void FixLangevin::initial_integrate(int /* vflag */)
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
if (rmass) {
gamma2 = sqrt(rmass[i]) * sqrt(2.0*dt*boltz/t_period/mvv2e) / ftm2v;
gamma2 *= 1.0/sqrt(ratio[type[i]]) * tsqrt;
if (rmass) {
m = rmass[i];
beta = tsqrt * sqrt(2.0*dt*rmass[i]*boltz/t_period/mvv2e) / ftm2v;
} else {
gamma2 = gfactor2[type[i]] * tsqrt;
m = mass[type[i]];
beta = tsqrt * sqrt(2.0*dt*atom->mass[i]*boltz/t_period/mvv2e) / ftm2v;
}
fran[0] = gamma2*random->gaussian();
fran[1] = gamma2*random->gaussian();
fran[2] = gamma2*random->gaussian();
fran[0] = beta*random->gaussian();
fran[1] = beta*random->gaussian();
fran[2] = beta*random->gaussian();
// First integration delivers Eq. 24a and 24b:
dtfm = dtf / m;
v[i][0] += csq * dtfm * f[i][0];
v[i][1] += csq * dtfm * f[i][1];
v[i][2] += csq * dtfm * f[i][2];
x[i][0] += 0.5 * csq * dt * v[i][0];
x[i][1] += 0.5 * csq * dt * v[i][1];
x[i][2] += 0.5 * csq * dt * v[i][2];
// NVE integrator delivers Eq. 24a, but also overshoots position integration. Calculate Eq. 24b:
x[i][0] -= 0.5 * dt * v[i][0];
x[i][1] -= 0.5 * dt * v[i][1];
x[i][2] -= 0.5 * dt * v[i][2];
// Calculate Eq. 24c:
if (tbiasflag == BIAS)
temperature->remove_bias(i,v[i]);
if (rmass) {
lv[i][0] = c1sqrt*v[i][0] + ftm2v * (c1sqrt / (2.0 * rmass[i])) * fran[0];
lv[i][1] = c1sqrt*v[i][1] + ftm2v * (c1sqrt / (2.0 * rmass[i])) * fran[1];
lv[i][2] = c1sqrt*v[i][2] + ftm2v * (c1sqrt / (2.0 * rmass[i])) * fran[2];
} else {
lv[i][0] = c1sqrt*v[i][0] + ftm2v * (c1sqrt / (2.0 * mass[type[i]])) * fran[0];
lv[i][1] = c1sqrt*v[i][1] + ftm2v * (c1sqrt / (2.0 * mass[type[i]])) * fran[1];
lv[i][2] = c1sqrt*v[i][2] + ftm2v * (c1sqrt / (2.0 * mass[type[i]])) * fran[2];
}
lv[i][0] = c1sqrt*v[i][0] + ftm2v * (c3sqrt / (2.0 * m)) * fran[0];
lv[i][1] = c1sqrt*v[i][1] + ftm2v * (c3sqrt / (2.0 * m)) * fran[1];
lv[i][2] = c1sqrt*v[i][2] + ftm2v * (c3sqrt / (2.0 * m)) * fran[2];
if (tbiasflag == BIAS)
temperature->restore_bias(i,v[i]);
if (tbiasflag == BIAS)
temperature->restore_bias(i,lv[i]);
// Calculate Eq. 24d
if (tbiasflag == BIAS) temperature->remove_bias(i, lv[i]);
if (atom->rmass) {
v[i][0] = (gjfc2 / c1sqrt) * lv[i][0] + ftm2v * (0.5 / rmass[i]) * fran[0];
v[i][1] = (gjfc2 / c1sqrt) * lv[i][1] + ftm2v * (0.5 / rmass[i]) * fran[1];
v[i][2] = (gjfc2 / c1sqrt) * lv[i][2] + ftm2v * (0.5 / rmass[i]) * fran[2];
} else {
v[i][0] = (gjfc2 / c1sqrt) * lv[i][0] + ftm2v * (0.5 / mass[type[i]]) * fran[0];
v[i][1] = (gjfc2 / c1sqrt) * lv[i][1] + ftm2v * (0.5 / mass[type[i]]) * fran[1];
v[i][2] = (gjfc2 / c1sqrt) * lv[i][2] + ftm2v * (0.5 / mass[type[i]]) * fran[2];
}
if (tbiasflag == BIAS) temperature->restore_bias(i, lv[i]);
// Calculate Eq. 24e. NVE integrator then calculates Eq. 24f.
x[i][0] += 0.5 * dt * v[i][0];
x[i][1] += 0.5 * dt * v[i][1];
x[i][2] += 0.5 * dt * v[i][2];
if (tbiasflag == BIAS) temperature->remove_bias(i, v[i]);
v[i][0] = (gjfc2 / c1sqrt) * lv[i][0] + ftm2v * csq * (0.5 / m) * fran[0];
v[i][1] = (gjfc2 / c1sqrt) * lv[i][1] + ftm2v * csq * (0.5 / m) * fran[1];
v[i][2] = (gjfc2 / c1sqrt) * lv[i][2] + ftm2v * csq * (0.5 / m) * fran[2];
if (tbiasflag == BIAS) temperature->restore_bias(i, v[i]);
// Calculate Eq. 24e. Final integrator then calculates Eq. 24f after force update.
x[i][0] += 0.5 * csq * dt * v[i][0];
x[i][1] += 0.5 * csq * dt * v[i][1];
x[i][2] += 0.5 * csq * dt * v[i][2];
}
}
}
void FixLangevin::final_integrate()
void FixLangevinGJF::final_integrate()
{
double dtfm;
double dt = update->dt;
@ -444,18 +353,18 @@ void FixLangevin::final_integrate()
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
dtfm = dtf / rmass[i];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
v[i][0] += csq * dtfm * f[i][0];
v[i][1] += csq * dtfm * f[i][1];
v[i][2] += csq * dtfm * f[i][2];
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
dtfm = dtf / mass[type[i]];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
v[i][0] += csq * dtfm * f[i][0];
v[i][1] += csq * dtfm * f[i][1];
v[i][2] += csq * dtfm * f[i][2];
}
}
}
@ -464,7 +373,7 @@ void FixLangevin::final_integrate()
set current t_target and t_sqrt
------------------------------------------------------------------------- */
void FixLangevin::compute_target()
void FixLangevinGJF::compute_target()
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
@ -483,7 +392,7 @@ void FixLangevin::compute_target()
if (tstyle == EQUAL) {
t_target = input->variable->compute_equal(tvar);
if (t_target < 0.0)
error->one(FLERR, "Fix langevin variable returned negative temperature");
error->one(FLERR, "Fix langevin/gjf variable returned negative temperature");
tsqrt = sqrt(t_target);
} else {
if (atom->nmax > maxatom2) {
@ -495,86 +404,94 @@ void FixLangevin::compute_target()
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (tforce[i] < 0.0)
error->one(FLERR, "Fix langevin variable returned negative temperature");
error->one(FLERR, "Fix langevin/gjf variable returned negative temperature");
}
modify->addstep_compute(update->ntimestep + 1);
}
}
/* ----------------------------------------------------------------------
tally energy transfer to thermal reservoir, select velocity for GJF
select velocity for GJF
------------------------------------------------------------------------- */
void FixLangevin::end_of_step()
void FixLangevinGJF::end_of_step()
{
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
energy_onestep = 0.0;
if (tallyflag) {
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 += energy_onestep*update->dt;
// After the NVE integrator delivers 24f, either the on-site or half-step
// After the final integrator delivers 24f, either the on-site or half-step
// velocity is used in remaining simulation tasks, depending on user input
if (gjfflag && !osflag) {
double tmp[3];
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
// v is Eq. 24f
tmp[0] = v[i][0];
tmp[1] = v[i][1];
tmp[2] = v[i][2];
// Move on with half-step velocity
v[i][0] = lv[i][0];
v[i][1] = lv[i][1];
v[i][2] = lv[i][2];
// store Eq. 24f in lv for next timestep
lv[i][0] = tmp[0];
lv[i][1] = tmp[1];
lv[i][2] = tmp[2];
}
}
double tmp[3];
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
// v is Eq. 24f
tmp[0] = v[i][0];
tmp[1] = v[i][1];
tmp[2] = v[i][2];
// Move on with half-step velocity
v[i][0] = lv[i][0];
v[i][1] = lv[i][1];
v[i][2] = lv[i][2];
// store Eq. 24f in lv for next timestep
lv[i][0] = tmp[0];
lv[i][1] = tmp[1];
lv[i][2] = tmp[2];
}
}
// clang-format on
/* ---------------------------------------------------------------------- */
void FixLangevin::reset_target(double t_new)
void FixLangevinGJF::reset_target(double t_new)
{
t_target = t_start = t_stop = t_new;
}
/* ---------------------------------------------------------------------- */
void FixLangevin::reset_dt()
void FixLangevinGJF::reset_dt()
{
if (atom->mass) {
for (int i = 1; i <= atom->ntypes; i++) {
gfactor2[i] = sqrt(atom->mass[i]) / force->ftm2v;
if (gjfflag)
gfactor2[i] *= sqrt(2.0 * update->dt * force->boltz / t_period / force->mvv2e); // sqrt(2*alpha*kT*dt)
else
gfactor2[i] *= sqrt(24.0 * force->boltz / t_period / update->dt / force->mvv2e);
gfactor2[i] *= 1.0 / sqrt(ratio[i]);
}
}
if (gjfflag) {
gjfc2 = (1.0 - update->dt / 2.0 / t_period) / (1.0 + update->dt / 2.0 / t_period);
gjfc1 = 1.0 / (1.0 + update->dt / 2.0 / t_period);
// Complete set of thermostats is given in Gronbech-Jensen, Molecular Physics, 118 (2020)
switch (GJmethod) {
case 1:
gjfc2 = (1.0 - update->dt / 2.0 / t_period) / (1.0 + update->dt / 2.0 / t_period);
break;
case 2:
gjfc2 = exp(-update->dt / t_period);
break;
case 3:
gjfc2 = 1.0 - update->dt / t_period;
break;
case 4:
gjfc2 = ( sqrt(1.0 + 4.0 * (update->dt / t_period) ) - 1.0 ) / ( 2.0 * update->dt / t_period );
break;
case 5:
gjfc2 = 1.0 / (1.0 + update->dt / t_period);
break;
case 6:
gjfc2 = (1.0 / (1.0 + update->dt / 2.0 / t_period)) * (1.0 / (1.0 + update->dt / 2.0 / t_period));
break;
case 7: // provided in Finkelstein (2021)
gjfc2 = 1; // TODO: correct this
break;
case 8: // provided in Gronbech-Jensen (2024)
gjfc2 = sqrt( (update->dt / t_period)*(update->dt / t_period) + 1.0 ) - update->dt / t_period;
break;
case 0:
gjfc2 = 0.0;
break;
default:
error->all(FLERR, "Fix langevin/gjf method not found");
break;
}
gjfc1 = (1.0 + gjfc2) / 2.0;
gjfc3 = (1.0 - gjfc2) * t_period / update->dt;
}
/* ---------------------------------------------------------------------- */
int FixLangevin::modify_param(int narg, char **arg)
int FixLangevinGJF::modify_param(int narg, char **arg)
{
if (strcmp(arg[0], "temp") == 0) {
if (narg < 2) utils::missing_cmd_args(FLERR, "fix_modify", error);
@ -594,52 +511,11 @@ int FixLangevin::modify_param(int narg, char **arg)
return 0;
}
/* ---------------------------------------------------------------------- */
double FixLangevin::compute_scalar()
{
if (!tallyflag || !flangevin_allocated) return 0.0;
// capture the very first energy transfer to thermal reservoir
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (update->ntimestep == update->beginstep) {
energy_onestep = 0.0;
if (!gjfflag) {
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;
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (tbiasflag) temperature->remove_bias(i, lv[i]);
energy_onestep +=
flangevin[i][0] * lv[i][0] + flangevin[i][1] * lv[i][1] + flangevin[i][2] * lv[i][2];
if (tbiasflag) temperature->restore_bias(i, lv[i]);
}
energy = -0.5 * energy_onestep * update->dt;
}
}
// convert midstep energy back to previous fullstep energy
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);
return -energy_all;
}
/* ----------------------------------------------------------------------
extract thermostat properties
------------------------------------------------------------------------- */
void *FixLangevin::extract(const char *str, int &dim)
void *FixLangevinGJF::extract(const char *str, int &dim)
{
dim = 0;
if (strcmp(str, "t_target") == 0) { return &t_target; }
@ -650,11 +526,10 @@ void *FixLangevin::extract(const char *str, int &dim)
memory usage of tally array
------------------------------------------------------------------------- */
double FixLangevin::memory_usage()
double FixLangevinGJF::memory_usage()
{
double bytes = 0.0;
if (gjfflag) bytes += (double) atom->nmax * 3 * sizeof(double);
if (tallyflag || osflag) bytes += (double) atom->nmax * 3 * sizeof(double);
bytes += (double) atom->nmax * 3 * sizeof(double);
if (tforce) bytes += (double) atom->nmax * sizeof(double);
return bytes;
}
@ -663,16 +538,16 @@ double FixLangevin::memory_usage()
allocate atom-based array for lv
------------------------------------------------------------------------- */
void FixLangevin::grow_arrays(int nmax)
void FixLangevinGJF::grow_arrays(int nmax)
{
memory->grow(lv, nmax, 3, "fix_langevin:lv");
memory->grow(lv, nmax, 3, "fix_langevin_gjf:lv");
}
/* ----------------------------------------------------------------------
copy values within local atom-based array
------------------------------------------------------------------------- */
void FixLangevin::copy_arrays(int i, int j, int /*delflag*/)
void FixLangevinGJF::copy_arrays(int i, int j, int /*delflag*/)
{
lv[j][0] = lv[i][0];
lv[j][1] = lv[i][1];
@ -683,7 +558,7 @@ void FixLangevin::copy_arrays(int i, int j, int /*delflag*/)
pack values in local atom-based array for exchange with another proc
------------------------------------------------------------------------- */
int FixLangevin::pack_exchange(int i, double *buf)
int FixLangevinGJF::pack_exchange(int i, double *buf)
{
int n = 0;
buf[n++] = lv[i][0];
@ -696,7 +571,7 @@ int FixLangevin::pack_exchange(int i, double *buf)
unpack values in local atom-based array from exchange with another proc
------------------------------------------------------------------------- */
int FixLangevin::unpack_exchange(int nlocal, double *buf)
int FixLangevinGJF::unpack_exchange(int nlocal, double *buf)
{
int n = 0;
lv[nlocal][0] = buf[n++];

25
src/EXTRA-FIX/fix_langevin_gjf.h
View File

@ -24,21 +24,19 @@ FixStyle(langevin,FixLangevin);
namespace LAMMPS_NS {
class FixLangevin : public Fix {
class FixLangevinGJF : public Fix {
public:
FixLangevin(class LAMMPS *, int, char **);
~FixLangevin() override;
FixLangevinGJF(class LAMMPS *, int, char **);
~FixLangevinGJF() override;
int setmask() override;
void init() override;
void setup(int) override;
void initial_integrate(int) override;
void post_force(int) override;
void post_force_respa(int, int, int) override;
void final_integrate() override;
void end_of_step() override;
void reset_target(double) override;
void reset_dt() override;
int modify_param(int, char **) override;
double compute_scalar() override;
double memory_usage() override;
void *extract(const char *, int &) override;
void grow_arrays(int) override;
@ -48,19 +46,13 @@ class FixLangevin : public Fix {
protected:
int osflag, GJmethod;
int flangevin_allocated;
double t_start, t_stop, t_period, t_target;
double *gfactor1, *gfactor2, *ratio;
double energy, energy_onestep;
double *gfactor2;
double tsqrt;
double gjfc1, gjfc2;
double gjfc1, gjfc2, gjfc3;
int tstyle, tvar;
char *tstr;
class AtomVecEllipsoid *avec;
int maxatom1, maxatom2;
double **flangevin;
double *tforce;
double **lv; //half step velocity
@ -71,11 +63,6 @@ class FixLangevin : public Fix {
class RanMars *random;
int seed;
template <int Tp_TSTYLEATOM, int Tp_TALLY, int Tp_BIAS, int Tp_RMASS, int Tp_ZERO>
void post_force_templated();
void omega_thermostat();
void angmom_thermostat();
void compute_target();
};