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Merge pull request #3582 from athomps/sllod_variants

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Implement sllod variants
This commit is contained in:
Axel Kohlmeyer
2023-01-06 21:55:10 -05:00
committed by GitHub
parent be5cede69f 17e949df55
commit 6a8df032b6
17 changed files with 360 additions and 77 deletions
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52
doc/src/fix_nvt_sllod.rst
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@ -17,7 +17,15 @@ Syntax
* ID, group-ID are documented in :doc:`fix <fix>` command
* nvt/sllod = style name of this fix command
* additional thermostat related keyword/value pairs from the :doc:`fix nvt <fix_nh>` command can be appended
* zero or more keyword/value pairs may be appended
.. parsed-literal::
keyword = *psllod*
*psllod* value = *no* or *yes* = use SLLOD or p-SLLOD variant, respectively
* additional thermostat related keyword/value pairs from the :doc:`fix nvt <fix_nh>`
command can be appended
Examples
""""""""
@ -61,22 +69,27 @@ large x velocity. These velocities do not contribute to the thermal
consistent.
The SLLOD equations of motion, originally proposed by Hoover and Ladd
(see :ref:`(Evans and Morriss) <Evans3>`), were proven to be
equivalent to Newton's equations of motion for shear flow by
:ref:`(Evans and Morriss) <Evans3>`. They were later shown to generate
the desired velocity gradient and the correct production of work by
stresses for all forms of homogeneous flow by :ref:`(Daivis and Todd)
<Daivis>`.
The LAMMPS implementation corresponds to the p-SLLOD variant
of SLLOD. :ref:`(Edwards) <Edwards>`.
The equations of motion are coupled to a
(see :ref:`(Evans and Morriss) <Evans3>`), were proven to be equivalent
to Newton's equations of motion for shear flow by :ref:`(Evans and
Morriss) <Evans3>`. They were later shown to generate the desired
velocity gradient and the correct production of work by stresses for all
forms of homogeneous flow by :ref:`(Daivis and Todd) <Daivis>`.
.. versionchanged:: TBD
For the default (*psllod* = *no*), the LAMMPS implementation adheres to
the standard SLLOD equations of motion, as defined by :ref:`(Evans and
Morriss) <Evans3>`. The option *psllod* = *yes* invokes the slightly
different SLLOD variant first introduced by :ref:`(Tuckerman et al.)
<Tuckerman>` as g-SLLOD and later by :ref:`(Edwards) <Edwards>` as
p-SLLOD. In all cases, the equations of motion are coupled to a
Nose/Hoover chain thermostat in a velocity Verlet formulation, closely
following the implementation used for the :doc:`fix nvt <fix_nh>`
command.
.. note::
A recent (2017) book by :ref:`(Daivis and Todd) <Daivis-sllod>`
A recent (2017) book by :ref:`(Todd and Daivis) <Todd-sllod>`
discusses use of the SLLOD method and non-equilibrium MD (NEMD)
thermostatting generally, for both simple and complex fluids,
e.g. molecular systems. The latter can be tricky to do correctly.
@ -159,7 +172,7 @@ Restrictions
""""""""""""
This fix works best without Nose-Hoover chain thermostats, i.e. using
tchain = 1. Setting tchain to larger values can result in poor
*tchain* = 1. Setting *tchain* to larger values can result in poor
equilibration.
Related commands
@ -171,7 +184,7 @@ Related commands
Default
"""""""
Same as :doc:`fix nvt <fix_nh>`, except tchain = 1.
Same as :doc:`fix nvt <fix_nh>`, except *tchain* = 1, psllod = *no*.
----------
@ -183,11 +196,16 @@ Same as :doc:`fix nvt <fix_nh>`, except tchain = 1.
**(Daivis and Todd)** Daivis and Todd, J Chem Phys, 124, 194103 (2006).
.. _Todd-sllod:
**(Todd and Daivis)** Todd and Daivis, Nonequilibrium Molecular Dynamics (book),
Cambridge University Press, (2017) https://doi.org/10.1017/9781139017848.
.. _Tuckerman:
**(Tuckerman et al.)** Tuckerman, Mundy, Balasubramanian, and Klein, J Chem Phys 106, 5615 (1997).
.. _Edwards:
**(Edwards)** Edwards, Baig, and Keffer, J Chem Phys 124, 194104 (2006).
.. _Daivis-sllod:
**(Daivis and Todd)** Daivis and Todd, Nonequilibrium Molecular Dynamics (book),
Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).

24
doc/src/fix_nvt_sllod_eff.rst
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@ -12,7 +12,15 @@ Syntax
* ID, group-ID are documented in :doc:`fix <fix>` command
* nvt/sllod/eff = style name of this fix command
* additional thermostat related keyword/value pairs from the :doc:`fix nvt/eff <fix_nh_eff>` command can be appended
* zero or more keyword/value pairs may be appended
.. parsed-literal::
keyword = *psllod*
*psllod* value = *no* or *yes* = use SLLOD or p-SLLOD variant, respectively
* additional thermostat related keyword/value pairs from the :doc:`fix
nvt/eff <fix_nh_eff>` command may be appended, too.
Examples
""""""""
@ -25,18 +33,20 @@ Examples
Description
"""""""""""
Perform constant NVT integration to update positions and velocities
each timestep for nuclei and electrons in the group for the :doc:`electron force field <pair_eff>` model, using a Nose/Hoover temperature
Perform constant NVT integration to update positions and velocities each
timestep for nuclei and electrons in the group for the :doc:`electron
force field <pair_eff>` model, using a Nose/Hoover temperature
thermostat. V is volume; T is temperature. This creates a system
trajectory consistent with the canonical ensemble.
The operation of this fix is exactly like that described by the :doc:`fix nvt/sllod <fix_nvt_sllod>` command, except that the radius and
The operation of this fix is exactly like that described by the
:doc:`fix nvt/sllod <fix_nvt_sllod>` command, except that the radius and
radial velocity of electrons are also updated and thermostatted.
Likewise the temperature calculated by the fix, using the compute it
creates (as discussed in the :doc:`fix nvt, npt, and nph <fix_nh>` doc
page), is performed with a :doc:`compute temp/deform/eff <compute_temp_deform_eff>` command that includes
the eFF contribution to the temperature from the electron radial
velocity.
page), is performed with a :doc:`compute temp/deform/eff
<compute_temp_deform_eff>` command that includes the eFF contribution to
the temperature from the electron radial velocity.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

1
doc/utils/sphinx-config/false_positives.txt
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@ -2854,6 +2854,7 @@ pscrozi
Pseudocode
pseudodynamics
pseudopotential
psllod
pSp
pSPICA
Pstart

2
src/EFF/fix_nh_eff.cpp
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@ -33,7 +33,7 @@ enum{NOBIAS,BIAS};
FixNHEff::FixNHEff(LAMMPS *lmp, int narg, char **arg) : FixNH(lmp, narg, arg)
{
if (!atom->electron_flag)
error->all(FLERR,"Fix nvt/nph/npt/eff requires atom style electron");
error->all(FLERR,"Fix {} requires atom style electron", style);
}
/* ----------------------------------------------------------------------

16
src/EFF/fix_nvt_sllod_eff.cpp
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@ -42,8 +42,21 @@ FixNVTSllodEff::FixNVTSllodEff(LAMMPS *lmp, int narg, char **arg) :
// default values
psllod_flag = 0;
if (mtchain_default_flag) mtchain = 1;
// select SLLOD/p-SLLOD/g-SLLOD variant
int iarg = 3;
while (iarg < narg) {
if (strcmp(arg[iarg],"psllod") == 0) {
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix nvt/sllod/eff psllod", error);
psllod_flag = utils::logical(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else iarg++;
}
// create a new compute temp style
// id = fix-ID + temp
@ -108,10 +121,11 @@ void FixNVTSllodEff::nh_v_temp()
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
temperature->remove_bias(i,v[i]);
if (!psllod_flag) temperature->remove_bias(i,v[i]);
vdelu[0] = h_two[0]*v[i][0] + h_two[5]*v[i][1] + h_two[4]*v[i][2];
vdelu[1] = h_two[1]*v[i][1] + h_two[3]*v[i][2];
vdelu[2] = h_two[2]*v[i][2];
if (psllod_flag) temperature->remove_bias(i,v[i]);
v[i][0] = v[i][0]*factor_eta - dthalf*vdelu[0];
v[i][1] = v[i][1]*factor_eta - dthalf*vdelu[1];
v[i][2] = v[i][2]*factor_eta - dthalf*vdelu[2];

1
src/EFF/fix_nvt_sllod_eff.h
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@ -31,6 +31,7 @@ class FixNVTSllodEff : public FixNHEff {
private:
int nondeformbias;
int psllod_flag;
void nh_v_temp() override;
};

37
src/INTEL/fix_nvt_sllod_intel.cpp
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@ -35,14 +35,26 @@ FixNVTSllodIntel::FixNVTSllodIntel(LAMMPS *lmp, int narg, char **arg) :
FixNHIntel(lmp, narg, arg)
{
if (!tstat_flag)
error->all(FLERR,"Temperature control must be used with fix nvt/sllod");
error->all(FLERR,"Temperature control must be used with fix nvt/sllod/intel");
if (pstat_flag)
error->all(FLERR,"Pressure control can not be used with fix nvt/sllod");
error->all(FLERR,"Pressure control can not be used with fix nvt/sllod/intel");
// default values
psllod_flag = 0;
if (mtchain_default_flag) mtchain = 1;
// select SLLOD/p-SLLOD/g-SLLOD variant
int iarg = 3;
while (iarg < narg) {
if (strcmp(arg[iarg],"psllod") == 0) {
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix nvt/sllod/intel psllod", error);
psllod_flag = utils::logical(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else iarg++;
}
// create a new compute temp style
// id = fix-ID + temp
@ -61,23 +73,21 @@ void FixNVTSllodIntel::init()
FixNHIntel::init();
if (!temperature->tempbias)
error->all(FLERR,"Temperature for fix nvt/sllod does not have a bias");
error->all(FLERR,"Temperature for fix nvt/sllod/intel does not have a bias");
nondeformbias = 0;
if (strcmp(temperature->style,"temp/deform") != 0) nondeformbias = 1;
// check fix deform remap settings
int i;
for (i = 0; i < modify->nfix; i++)
if (strncmp(modify->fix[i]->style,"deform",6) == 0) {
if ((dynamic_cast<FixDeform *>(modify->fix[i]))->remapflag != Domain::V_REMAP)
error->all(FLERR,"Using fix nvt/sllod with inconsistent fix deform "
"remap option");
break;
auto deform = modify->get_fix_by_style("^deform");
if (deform.size() < 1) error->all(FLERR,"Using fix nvt/sllod/intel with no fix deform defined");
for (auto ifix : deform) {
auto f = dynamic_cast<FixDeform *>(ifix);
if (f && (f->remapflag != Domain::V_REMAP))
error->all(FLERR,"Using fix nvt/sllod/intel with inconsistent fix deform remap option");
}
if (i == modify->nfix)
error->all(FLERR,"Using fix nvt/sllod with no fix deform defined");
}
/* ----------------------------------------------------------------------
@ -105,10 +115,11 @@ void FixNVTSllodIntel::nh_v_temp()
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (!psllod_flag) temperature->remove_bias(i,v[i]);
vdelu[0] = h_two[0]*v[i][0] + h_two[5]*v[i][1] + h_two[4]*v[i][2];
vdelu[1] = h_two[1]*v[i][1] + h_two[3]*v[i][2];
vdelu[2] = h_two[2]*v[i][2];
temperature->remove_bias(i,v[i]);
if (psllod_flag) temperature->remove_bias(i,v[i]);
v[i][0] = v[i][0]*factor_eta - dthalf*vdelu[0];
v[i][1] = v[i][1]*factor_eta - dthalf*vdelu[1];
v[i][2] = v[i][2]*factor_eta - dthalf*vdelu[2];

1
src/INTEL/fix_nvt_sllod_intel.h
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@ -36,6 +36,7 @@ class FixNVTSllodIntel : public FixNHIntel {
private:
int nondeformbias;
int psllod_flag; // 0 for SLLOD, 1 for p-SLLOD
void nh_v_temp() override;
};

55
src/KOKKOS/fix_nvt_sllod_kokkos.cpp
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@ -47,12 +47,25 @@ FixNVTSllodKokkos<DeviceType>::FixNVTSllodKokkos(LAMMPS *lmp, int narg, char **a
this->domainKK = (DomainKokkos *) this->domain;
if (!this->tstat_flag)
this->error->all(FLERR,"Temperature control must be used with fix nvt/kk");
this->error->all(FLERR,"Temperature control must be used with fix nvt/sllod/kk");
if (this->pstat_flag)
this->error->all(FLERR,"Pressure control can not be used with fix nvt/kk");
this->error->all(FLERR,"Pressure control can not be used with fix nvt/sllod/kk");
this->psllod_flag = 0;
if (this->mtchain_default_flag) this->mtchain = 1;
// select SLLOD/p-SLLOD/g-SLLOD variant
int iarg = 3;
while (iarg < narg) {
if (strcmp(arg[iarg],"psllod") == 0) {
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix nvt/sllod/kk psllod", this->error);
this->psllod_flag = utils::logical(FLERR,arg[iarg+1],false,this->lmp);
iarg += 2;
} else iarg++;
}
this->id_temp = utils::strdup(std::string(this->id)+"_temp");
this->modify->add_compute(fmt::format("{} all temp/deform/kk",this->id_temp));
this->tcomputeflag = 1;
@ -67,22 +80,22 @@ void FixNVTSllodKokkos<DeviceType>::init()
FixNHKokkos<DeviceType>::init();
if (!this->temperature->tempbias)
this->error->all(FLERR,"Temperature for fix nvt/sllod does not have a bias");
this->error->all(FLERR,"Temperature for fix nvt/sllod/kk does not have a bias");
nondeformbias = 0;
if (utils::strmatch(this->temperature->style,"^temp/deform")) nondeformbias = 1;
// check fix deform remap settings
int i;
for (i = 0; i < this->modify->nfix; i++)
if (utils::strmatch(this->modify->fix[i]->style,"^deform")) {
if (((FixDeform *) this->modify->fix[i])->remapflag != Domain::V_REMAP)
this->error->all(FLERR,"Using fix nvt/sllod with inconsistent fix deform remap option");
break;
auto deform = this->modify->get_fix_by_style("^deform");
if (deform.size() < 1)
this->error->all(FLERR,"Using fix nvt/sllod/kk with no fix deform defined");
for (auto ifix : deform) {
auto f = dynamic_cast<FixDeform *>(ifix);
if (f && (f->remapflag != Domain::V_REMAP))
this->error->all(FLERR,"Using fix ntv/sllod/kk with inconsistent fix deform remap option");
}
if (i == this->modify->nfix)
this->error->all(FLERR,"Using fix nvt/sllod with no fix deform defined");
}
/* ----------------------------------------------------------------------
@ -104,6 +117,7 @@ void FixNVTSllodKokkos<DeviceType>::nh_v_temp()
this->temperature->compute_scalar();
atomKK->modified(this->temperature->execution_space,this->temperature->datamask_modify);
}
v = atomKK->k_v.view<DeviceType>();
mask = atomKK->k_mask.view<DeviceType>();
int nlocal = atomKK->nlocal;
@ -117,17 +131,35 @@ void FixNVTSllodKokkos<DeviceType>::nh_v_temp()
if (vdelu.extent(0) < atomKK->nmax)
vdelu = typename AT::t_v_array(Kokkos::NoInit("nvt/sllod/kk:vdelu"), atomKK->nmax);
if (!this->psllod_flag) {
atomKK->sync(this->temperature->execution_space,this->temperature->datamask_read);
this->temperature->remove_bias_all();
atomKK->modified(this->temperature->execution_space,this->temperature->datamask_modify);
}
atomKK->sync(this->execution_space,V_MASK | MASK_MASK);
this->copymode = 1;
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagFixNVTSllod_temp1>(0,nlocal),*this);
this->copymode = 0;
if (this->psllod_flag) {
atomKK->sync(this->temperature->execution_space,this->temperature->datamask_read);
this->temperature->remove_bias_all();
atomKK->modified(this->temperature->execution_space,this->temperature->datamask_modify);
}
atomKK->sync(this->execution_space,V_MASK | MASK_MASK);
this->copymode = 1;
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagFixNVTSllod_temp2>(0,nlocal),*this);
this->copymode = 0;
atomKK->modified(this->execution_space,V_MASK);
atomKK->sync(this->temperature->execution_space,this->temperature->datamask_read);
this->temperature->restore_bias_all();
atomKK->modified(this->temperature->execution_space,this->temperature->datamask_modify);
}
template<class DeviceType>
@ -157,4 +189,3 @@ template class FixNVTSllodKokkos<LMPHostType>;
#endif
}

1
src/KOKKOS/fix_nvt_sllod_kokkos.h
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@ -50,6 +50,7 @@ class FixNVTSllodKokkos : public FixNHKokkos<DeviceType> {
private:
int nondeformbias;
int psllod_flag;
void nh_v_temp() override;

32
src/OPENMP/fix_nvt_sllod_omp.cpp
View File

@ -43,14 +43,26 @@ FixNVTSllodOMP::FixNVTSllodOMP(LAMMPS *lmp, int narg, char **arg) :
FixNHOMP(lmp, narg, arg)
{
if (!tstat_flag)
error->all(FLERR,"Temperature control must be used with fix nvt/sllod");
error->all(FLERR,"Temperature control must be used with fix nvt/sllod/omp");
if (pstat_flag)
error->all(FLERR,"Pressure control can not be used with fix nvt/sllod");
error->all(FLERR,"Pressure control can not be used with fix nvt/sllod/omp");
// default values
psllod_flag = 0;
if (mtchain_default_flag) mtchain = 1;
// select SLLOD/p-SLLOD/g-SLLOD variant
int iarg = 3;
while (iarg < narg) {
if (strcmp(arg[iarg],"psllod") == 0) {
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix nvt/sllod/omp psllod", error);
psllod_flag = utils::logical(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else iarg++;
}
// create a new compute temp style
// id = fix-ID + temp
@ -75,15 +87,14 @@ void FixNVTSllodOMP::init()
// check fix deform remap settings
int i;
for (i = 0; i < modify->nfix; i++)
if (utils::strmatch(modify->fix[i]->style,"^deform")) {
if ((dynamic_cast<FixDeform *>(modify->fix[i]))->remapflag != Domain::V_REMAP)
auto deform = modify->get_fix_by_style("^deform");
if (deform.size() < 1) error->all(FLERR,"Using fix nvt/sllod/omp with no fix deform defined");
for (auto ifix : deform) {
auto f = dynamic_cast<FixDeform *>(ifix);
if (f && (f->remapflag != Domain::V_REMAP))
error->all(FLERR,"Using fix nvt/sllod/omp with inconsistent fix deform remap option");
break;
}
if (i == modify->nfix)
error->all(FLERR,"Using fix nvt/sllod/omp with no fix deform defined");
}
/* ----------------------------------------------------------------------
@ -114,10 +125,11 @@ void FixNVTSllodOMP::nh_v_temp()
for (int i = 0; i < nlocal; i++) {
double vdelu0,vdelu1,vdelu2,buf[3];
if (mask[i] & groupbit) {
if (!psllod_flag) temperature->remove_bias_thr(i,&v[i].x,buf);
vdelu0 = h_two[0]*v[i].x + h_two[5]*v[i].y + h_two[4]*v[i].z;
vdelu1 = h_two[1]*v[i].y + h_two[3]*v[i].z;
vdelu2 = h_two[2]*v[i].z;
temperature->remove_bias_thr(i,&v[i].x,buf);
if (psllod_flag) temperature->remove_bias_thr(i,&v[i].x,buf);
v[i].x = v[i].x*factor_eta - dthalf*vdelu0;
v[i].y = v[i].y*factor_eta - dthalf*vdelu1;
v[i].z = v[i].z*factor_eta - dthalf*vdelu2;

1
src/OPENMP/fix_nvt_sllod_omp.h
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@ -31,6 +31,7 @@ class FixNVTSllodOMP : public FixNHOMP {
private:
int nondeformbias;
int psllod_flag; // 0 for SLLOD, 1 for p-SLLOD
void nh_v_temp() override;
};

5
src/fix_nh.cpp
View File

@ -359,6 +359,11 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"ext") == 0) {
iarg += 2;
// keyword psllod is parsed in fix/nvt/sllod
} else if (strcmp(arg[iarg],"psllod") == 0) {
iarg += 2;
} else error->all(FLERR,"Unknown fix nvt/npt/nph keyword: {}", arg[iarg]);
}

32
src/fix_nvt_sllod.cpp
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@ -44,8 +44,20 @@ FixNVTSllod::FixNVTSllod(LAMMPS *lmp, int narg, char **arg) :
// default values
psllod_flag = 0;
if (mtchain_default_flag) mtchain = 1;
// select SLLOD/p-SLLOD/g-SLLOD variant
int iarg = 3;
while (iarg < narg) {
if (strcmp(arg[iarg],"psllod") == 0) {
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix nvt/sllod psllod", error);
psllod_flag = utils::logical(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else iarg++;
}
// create a new compute temp style
// id = fix-ID + temp
@ -63,22 +75,21 @@ void FixNVTSllod::init()
FixNH::init();
if (!temperature->tempbias)
error->all(FLERR,"Temperature for fix nvt/sllod does not have a bias");
error->all(FLERR,"Temperature for fix {} does not have a bias", style);
nondeformbias = 0;
if (strcmp(temperature->style,"temp/deform") != 0) nondeformbias = 1;
// check fix deform remap settings
int i;
for (i = 0; i < modify->nfix; i++)
if (strncmp(modify->fix[i]->style,"deform",6) == 0) {
if ((dynamic_cast<FixDeform *>(modify->fix[i]))->remapflag != Domain::V_REMAP)
error->all(FLERR,"Using fix nvt/sllod with inconsistent fix deform remap option");
break;
auto deform = modify->get_fix_by_style("^deform");
if (deform.size() < 1) error->all(FLERR,"Using fix {} with no fix deform defined", style);
for (auto ifix : deform) {
auto f = dynamic_cast<FixDeform *>(ifix);
if (f && (f->remapflag != Domain::V_REMAP))
error->all(FLERR,"Using fix {} with inconsistent fix deform remap option", style);
}
if (i == modify->nfix)
error->all(FLERR,"Using fix nvt/sllod with no fix deform defined");
}
/* ----------------------------------------------------------------------
@ -106,10 +117,11 @@ void FixNVTSllod::nh_v_temp()
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (!psllod_flag) temperature->remove_bias(i,v[i]);
vdelu[0] = h_two[0]*v[i][0] + h_two[5]*v[i][1] + h_two[4]*v[i][2];
vdelu[1] = h_two[1]*v[i][1] + h_two[3]*v[i][2];
vdelu[2] = h_two[2]*v[i][2];
temperature->remove_bias(i,v[i]);
if (psllod_flag) temperature->remove_bias(i,v[i]);
v[i][0] = v[i][0]*factor_eta - dthalf*vdelu[0];
v[i][1] = v[i][1]*factor_eta - dthalf*vdelu[1];
v[i][2] = v[i][2]*factor_eta - dthalf*vdelu[2];

1
src/fix_nvt_sllod.h
View File

@ -32,6 +32,7 @@ class FixNVTSllod : public FixNH {
private:
int nondeformbias;
int psllod_flag; // 0 for SLLOD, 1 for p-SLLOD
void nh_v_temp() override;
};

82
unittest/force-styles/tests/fix-timestep-nvt-psllod.yaml Normal file
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@ -0,0 +1,82 @@
---
lammps_version: 22 Dec 2022
date_generated: Tue Jan 3 17:19:09 2023
epsilon: 5e-12
skip_tests:
prerequisites: ! |
atom full
fix nvt/sllod
pre_commands: ! ""
post_commands: ! |
change_box all triclinic
variable gamma index 0.05
variable vx atom y*${gamma}
if $(step)==0 then "velocity all set v_vx NULL NULL sum yes"
fix all all deform 2 xy erate ${gamma} remap v
fix test all nvt/sllod temp 50.0 ${t_target} 1.0 psllod yes
input_file: in.fourmol
natoms: 29
global_scalar: 2854867.1697558644
global_vector: ! |-
12 1167.0668964303359 582.8541838571305 19481.306509850383 2835385.863246014 0 0 0 0 0 0 0 0
run_pos: ! |2
1 7.3766923105571358e-01 2.4745425115631381e+00 -1.7150321559212145e-01
2 1.3664612528682669e+00 2.9513079914030929e+00 -8.5728427260886253e-01
3 1.9844034438342817e-01 1.2423847783028510e+00 -6.2275616693380798e-01
4 -6.5919858368017614e-01 1.4910537181348680e+00 -1.2483715460591922e+00
5 -3.3421547180145339e-02 9.3441475316631362e-01 4.0189034091250875e-01
6 1.0791403982726226e+00 2.3587900895167735e-01 -1.2773831741505397e+00
7 1.1086458909800943e+00 -1.0907385860336127e-02 -2.4728565776108500e+00
8 1.8864879896626023e+00 -4.8393570832815591e-01 -6.6998265853493333e-01
9 2.1216439487920260e+00 -2.5289625793938608e-01 2.7015879660912390e-01
10 2.6502404066034719e+00 -1.4343374038132586e+00 -9.6995371157599219e-01
11 2.3630358464762002e+00 -1.9872831599030887e+00 -1.8838953155606841e+00
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29 -9.0154250196648267e-01 -3.5993683848967324e+00 2.2680257402204091e+00
run_vel: ! |2
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20 5.6879641471194298e-01 -1.5609359591659303e-35 8.8070498729597009e-36
21 1.8088744775485388e-01 1.9173821972353103e-36 6.7827061363565996e-38
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29 2.0467857431672881e-01 -1.3393001700153206e-35 -3.6636010064204463e-36
...

82
unittest/force-styles/tests/fix-timestep-nvt-sllod.yaml Normal file
View File

@ -0,0 +1,82 @@
---
lammps_version: 22 Dec 2022
date_generated: Tue Jan 3 17:19:09 2023
epsilon: 5e-12
skip_tests:
prerequisites: ! |
atom full
fix nvt/sllod
pre_commands: ! ""
post_commands: ! |
change_box all triclinic
variable gamma index 0.05
variable vx atom y*${gamma}
if $(step)==0 then "velocity all set v_vx NULL NULL sum yes"
fix all all deform 2 xy erate ${gamma} remap v
fix test all nvt/sllod temp 50.0 ${t_target} 1.0 psllod no
input_file: in.fourmol
natoms: 29
global_scalar: 2854867.1697558644
global_vector: ! |-
12 1167.0668964303359 582.8541838571305 19481.306509850383 2835385.863246014 0 0 0 0 0 0 0 0
run_pos: ! |2
1 7.3766923105571358e-01 2.4745425115631381e+00 -1.7150321559212145e-01
2 1.3664612528682669e+00 2.9513079914030929e+00 -8.5728427260886253e-01
3 1.9844034438342817e-01 1.2423847783028510e+00 -6.2275616693380798e-01
4 -6.5919858368017614e-01 1.4910537181348680e+00 -1.2483715460591922e+00
5 -3.3421547180145339e-02 9.3441475316631362e-01 4.0189034091250875e-01
6 1.0791403982726226e+00 2.3587900895167735e-01 -1.2773831741505397e+00
7 1.1086458909800943e+00 -1.0907385860336127e-02 -2.4728565776108500e+00
8 1.8864879896626023e+00 -4.8393570832815591e-01 -6.6998265853493333e-01
9 2.1216439487920260e+00 -2.5289625793938608e-01 2.7015879660912390e-01
10 2.6502404066034719e+00 -1.4343374038132586e+00 -9.6995371157599219e-01
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29 -9.0154250196648267e-01 -3.5993683848967324e+00 2.2680257402204091e+00
run_vel: ! |2
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2 5.3221189005127478e-01 -1.1568811919842230e-35 -3.5425288652190980e-36
3 4.4676818218962833e-01 -2.0462738591065681e-35 -1.9816457116709468e-36
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...