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Updated GJ-VII, GJ-VIII

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This commit is contained in:
talinke
2025-04-11 20:07:25 -07:00
parent a30daec348
commit 09d3ac0a1b
2 changed files with 54 additions and 22 deletions
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7
examples/gjf/README
View File

@ -33,14 +33,13 @@ POTENTIAL ENERGY (eV)
Script Commands:
--
fix lang all langevin/gjf 10 10 1 26488
vs
--
fix nve all nve
fix lang all langevin 10 10 1 26488
--
vs
--
fix noho all nvt temp 10 10 1
--
vs
--
fix lang all langevin/gjf 10 10 1 26488
--

69
src/EXTRA-FIX/fix_langevin_gjf.cpp
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@ -41,8 +41,37 @@ using namespace FixConst;
enum { NOBIAS, BIAS };
enum { CONSTANT, EQUAL, ATOM };
static const char cite_langevin_gjf[] =
"Langevin GJF methods: doi:10.1007/s10955-024-03345-1\n\n"
"Langevin GJ methods: doi:10.1080/00268976.2019.1662506\n\n"
"@Article{gronbech-jensen_complete_2020,\n"
"title = {Complete set of stochastic Verlet-type thermostats for correct Langevin simulations},\n"
"volume = {118},\n"
"number = {8},\n"
"url = {https://www.tandfonline.com/doi/full/10.1080/00268976.2019.1662506},\n"
"doi = {10.1080/00268976.2019.1662506},\n"
"journal = {Molecular Physics},\n"
"author = {Grønbech-Jensen, Niels},\n"
"year = {2020},\n"
"}\n\n";
static const char cite_langevin_gjf_7[] =
"Langevin GJ-VII method: doi:10.1063/5.0066008\n\n"
"@Article{finkelstein_2021,\n"
"title = {Bringing discrete-time Langevin splitting methods into agreement with thermodynamics},\n"
"volume = {155},\n"
"number = {18},\n"
"url = {https://doi.org/10.1063/5.0066008},\n"
"doi = {10.1063/5.0066008},\n"
"urldate = {2021-11-14},\n"
"journal = {J. Chem. Phys.},\n"
"author = {Finkelstein, Joshua and Cheng, Chungho and Fiorin, Giacomo and Seibold, Benjamin and Grønbech-Jensen, Niels},\n"
"year = {2021},\n"
"pages = {184104}\n"
"}\n\n";
static const char cite_langevin_gjf_8[] =
"Langevin GJ-VIII method: doi:10.1007/s10955-024-03345-1\n\n"
"@Article{gronbech_jensen_2024,\n"
"title = {On the Definition of Velocity in Discrete-Time, Stochastic Langevin Simulations},\n"
"volume = {191},\n"
@ -55,7 +84,7 @@ static const char cite_langevin_gjf[] =
"year = {2024},\n"
"pages = {137}\n"
"}\n\n";
/* ---------------------------------------------------------------------- */
@ -109,10 +138,20 @@ FixLangevinGJF::FixLangevinGJF(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR, "Illegal fix langevin/gjf command");
iarg += 2;
} 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");
iarg += 2;
if (GJmethod = 7) {
if (iarg + 3 > narg) error->all(FLERR, "Illegal fix langevin/gjf command for GJ-VII");
gjfc2 = utils::numeric(FLERR, arg[iarg + 2], false, lmp);
if (gjfc2 < 0 || gjfc2 > 1) error->all(FLERR, "Choice of c2 in GJ-VII must be 0≤c2≤1");
iarg += 3;
if (lmp->citeme) lmp->citeme->add(cite_langevin_gjf_7);
}
else {
if (iarg + 2 > narg) error->all(FLERR, "Illegal fix langevin/gjf command");
if (GJmethod < 0 || GJmethod > GJmethods) error->all(FLERR, "Invalid GJ method choice in langevin/gjf command");
if (GJmethod = 8) if (lmp->citeme) lmp->citeme->add(cite_langevin_gjf_8);
iarg += 2;
}
} else
error->all(FLERR, "Illegal fix langevin/gjf command");
}
@ -218,10 +257,7 @@ void FixLangevinGJF::init()
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 = (1.0 - update->dt / 2.0 / t_period) / (1.0 + update->dt / 2.0 / t_period); //using GJ-I
gjfc1 = (1.0 + gjfc2) / 2.0;
gjfc3 = (1.0 - gjfc2) * t_period / update->dt;
gjfc2 = exp(-sqrt(gjfc3/gjfc1)*update->dt / t_period);
update->dt = (1.0 + gjfc2) / (1.0 - gjfc2) * log(gjfc2) * log(gjfc2) * 0.5 * t_period;
break;
case 8: // provided in Gronbech-Jensen (2024)
gjfc2 = sqrt( (update->dt / t_period) * (update->dt / t_period) + 1.0 ) - update->dt / t_period;
@ -238,11 +274,11 @@ void FixLangevinGJF::init()
}
/* ----------------------------------------------------------------------
integrate position and velocity according to the GJF method
integrate position and velocity according to the GJ methods
in Grønbech-Jensen, J Stat Phys 191, 137 (2024). The general workflow is
1. Langevin GJF Initial Integration
1. Langevin GJ Initial Integration
2. Force Update
3. Langevin GJF Final Integration
3. Langevin GJ Final Integration
4. Velocity Choice in end_of_step()
------------------------------------------------------------------------- */
@ -336,7 +372,6 @@ void FixLangevinGJF::final_integrate()
double dtf = 0.5 * dt * ftm2v;
double csq = sqrt(gjfc3 / gjfc1);
// update v of atoms in group
double **v = atom->v;
double **f = atom->f;
double *rmass = atom->rmass;
@ -346,6 +381,7 @@ void FixLangevinGJF::final_integrate()
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
// Calculate Eq. 24f.
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
@ -410,7 +446,7 @@ void FixLangevinGJF::compute_target()
}
/* ----------------------------------------------------------------------
select velocity for GJF
select velocity for GJ
------------------------------------------------------------------------- */
void FixLangevinGJF::end_of_step()
@ -472,10 +508,7 @@ void FixLangevinGJF::reset_dt()
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 = (1.0 - update->dt / 2.0 / t_period) / (1.0 + update->dt / 2.0 / t_period); //using GJ-I
gjfc1 = (1.0 + gjfc2) / 2.0;
gjfc3 = (1.0 - gjfc2) * t_period / update->dt;
gjfc2 = exp(-sqrt(gjfc3/gjfc1)*update->dt / t_period);
update->dt = (1.0 + gjfc2) / (1.0 - gjfc2) * log(gjfc2) * log(gjfc2) * 0.5 * t_period;
break;
case 8: // provided in Gronbech-Jensen (2024)
gjfc2 = sqrt( (update->dt / t_period)*(update->dt / t_period) + 1.0 ) - update->dt / t_period;