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Merge pull request #942 from tootea/nhfixes 

Fix discrepancies between fix_nh and papers
This commit is contained in:
Steve Plimpton 2018-08-02 11:16:54 -06:00 committed by GitHub
parent fb03924e83 e37ee02eed
commit 1b0a8fdc9b
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GPG Key ID: 4AEE18F83AFDEB23
3 changed files with 56 additions and 27 deletions
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2
src/KOKKOS/fix_nh_kokkos.cpp
View File

@ -148,7 +148,7 @@ void FixNHKokkos<DeviceType>::setup(int vflag)
if (pstat_flag) {
double kt = boltz * t_target;
double nkt = atom->natoms * kt;
double nkt = (atom->natoms + 1) * kt;
for (int i = 0; i < 3; i++)
if (p_flag[i])

45
src/USER-BOCS/fix_bocs.cpp
View File

@ -846,7 +846,7 @@ void FixBocs::setup(int vflag)
if (pstat_flag) {
double kt = boltz * t_target;
double nkt = atom->natoms * kt;
double nkt = (atom->natoms + 1) * kt;
for (int i = 0; i < 3; i++)
if (p_flag[i])
@ -1508,7 +1508,7 @@ double FixBocs::compute_scalar()
double volume;
double energy;
double kt = boltz * t_target;
double lkt_press = kt;
double lkt_press = 0.0;
int ich;
if (dimension == 3) volume = domain->xprd * domain->yprd * domain->zprd;
else volume = domain->xprd * domain->yprd;
@ -1539,15 +1539,21 @@ double FixBocs::compute_scalar()
// sum is over barostatted dimensions
if (pstat_flag) {
for (i = 0; i < 3; i++)
if (p_flag[i])
for (i = 0; i < 3; i++) {
if (p_flag[i]) {
energy += 0.5*omega_dot[i]*omega_dot[i]*omega_mass[i] +
p_hydro*(volume-vol0) / (pdim*nktv2p);
lkt_press += kt;
}
}
if (pstyle == TRICLINIC) {
for (i = 3; i < 6; i++)
if (p_flag[i])
for (i = 3; i < 6; i++) {
if (p_flag[i]) {
energy += 0.5*omega_dot[i]*omega_dot[i]*omega_mass[i];
lkt_press += kt;
}
}
}
// extra contributions from thermostat chain for barostat
@ -1880,15 +1886,14 @@ void FixBocs::nhc_temp_integrate()
void FixBocs::nhc_press_integrate()
{
int ich,i;
int ich,i,pdof;
double expfac,factor_etap,kecurrent;
double kt = boltz * t_target;
double lkt_press = kt;
// Update masses, to preserve initial freq, if flag set
if (omega_mass_flag) {
double nkt = atom->natoms * kt;
double nkt = (atom->natoms + 1) * kt;
for (int i = 0; i < 3; i++)
if (p_flag[i])
omega_mass[i] = nkt/(p_freq[i]*p_freq[i]);
@ -1912,14 +1917,24 @@ void FixBocs::nhc_press_integrate()
}
kecurrent = 0.0;
for (i = 0; i < 3; i++)
if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
if (pstyle == TRICLINIC) {
for (i = 3; i < 6; i++)
if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
pdof = 0;
for (i = 0; i < 3; i++) {
if (p_flag[i]) {
kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
pdof++;
}
}
if (pstyle == TRICLINIC) {
for (i = 3; i < 6; i++) {
if (p_flag[i]) {
kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
pdof++;
}
}
}
double lkt_press = pdof * kt;
etap_dotdot[0] = (kecurrent - lkt_press)/etap_mass[0];
double ncfac = 1.0/nc_pchain;

36
src/fix_nh.cpp
View File

@ -798,7 +798,7 @@ void FixNH::setup(int vflag)
if (pstat_flag) {
double kt = boltz * t_target;
double nkt = atom->natoms * kt;
double nkt = (atom->natoms + 1) * kt;
for (int i = 0; i < 3; i++)
if (p_flag[i])
@ -1446,7 +1446,7 @@ double FixNH::compute_scalar()
double volume;
double energy;
double kt = boltz * t_target;
double lkt_press = kt;
double lkt_press = 0.0;
int ich;
if (dimension == 3) volume = domain->xprd * domain->yprd * domain->zprd;
else volume = domain->xprd * domain->yprd;
@ -1477,15 +1477,21 @@ double FixNH::compute_scalar()
// sum is over barostatted dimensions
if (pstat_flag) {
for (i = 0; i < 3; i++)
if (p_flag[i])
for (i = 0; i < 3; i++) {
if (p_flag[i]) {
energy += 0.5*omega_dot[i]*omega_dot[i]*omega_mass[i] +
p_hydro*(volume-vol0) / (pdim*nktv2p);
lkt_press += kt;
}
}
if (pstyle == TRICLINIC) {
for (i = 3; i < 6; i++)
if (p_flag[i])
for (i = 3; i < 6; i++) {
if (p_flag[i]) {
energy += 0.5*omega_dot[i]*omega_dot[i]*omega_mass[i];
lkt_press += kt;
}
}
}
// extra contributions from thermostat chain for barostat
@ -1818,15 +1824,15 @@ void FixNH::nhc_temp_integrate()
void FixNH::nhc_press_integrate()
{
int ich,i;
int ich,i,pdof;
double expfac,factor_etap,kecurrent;
double kt = boltz * t_target;
double lkt_press = kt;
double lkt_press;
// Update masses, to preserve initial freq, if flag set
if (omega_mass_flag) {
double nkt = atom->natoms * kt;
double nkt = (atom->natoms + 1) * kt;
for (int i = 0; i < 3; i++)
if (p_flag[i])
omega_mass[i] = nkt/(p_freq[i]*p_freq[i]);
@ -1850,14 +1856,22 @@ void FixNH::nhc_press_integrate()
}
kecurrent = 0.0;
pdof = 0;
for (i = 0; i < 3; i++)
if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
if (p_flag[i]) {
kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
pdof++;
}
if (pstyle == TRICLINIC) {
for (i = 3; i < 6; i++)
if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
if (p_flag[i]) {
kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
pdof++;
}
}
lkt_press = pdof * kt;
etap_dotdot[0] = (kecurrent - lkt_press)/etap_mass[0];
double ncfac = 1.0/nc_pchain;