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Merge branch 'develop' into pair_style_tutorial

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This commit is contained in:
Axel Kohlmeyer
2023-03-23 01:23:36 -04:00
parent 91eb544979 12e0131abf
commit 0007b7c9fe
35 changed files with 582 additions and 791 deletions
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2
cmake/Modules/Packages/KIM.cmake
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@ -19,7 +19,7 @@ if(CURL_FOUND)
target_compile_definitions(lammps PRIVATE -DLMP_NO_SSL_CHECK)
endif()
endif()
set(KIM_EXTRA_UNITTESTS OFF CACHE STRING "Set extra unit tests verbose mode on/off. If on, extra tests are included.")
option(KIM_EXTRA_UNITTESTS "Enable extra unit tests for the KIM package." OFF)
mark_as_advanced(KIM_EXTRA_UNITTESTS)
find_package(PkgConfig QUIET)
set(DOWNLOAD_KIM_DEFAULT ON)

2
doc/src/Modify_gran_sub_mod.rst
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@ -25,7 +25,7 @@ specific implementation. For instance, from the GranSubModNormal class the
GranSubModNormalHooke, GranSubModNormalHertz, and GranSubModNormalJKR classes
are derived which calculate Hookean, Hertzian, or JKR normal forces,
respectively. This modular structure simplifies the addition of new granular
contact models as as one only needs to create a new GranSubMod class without
contact models as one only needs to create a new GranSubMod class without
having to modify the more complex PairGranular, FixGranWall, and GranularModel
classes. Most GranSubMod methods are also already defined by the parent classes
so new contact models typically only require edits to a few relevant methods

11
doc/src/bond_bpm_rotational.rst
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@ -10,7 +10,7 @@ Syntax
bond_style bpm/rotational keyword value attribute1 attribute2 ...
* optional keyword = *overlay/pair* or *store/local* or *smooth*
* optional keyword = *overlay/pair* or *store/local* or *smooth* or *break/no*
.. parsed-literal::
@ -30,6 +30,9 @@ Syntax
*smooth* value = *yes* or *no*
smooths bond forces near the breaking point
*break/no*
indicates that bonds should not break during a run
Examples
""""""""
@ -140,6 +143,12 @@ the *overlay/pair* keyword. These settings require specific
restrictions. Further details can be found in the `:doc: how to
<Howto_BPM>` page on BPMs.
.. versionadded:: TBD
If the *break/no* keyword is used, then LAMMPS assumes bonds should not break
during a simulation run. This will prevent some unnecessary calculation.
However, if a bond does break, it will trigger an error.
If the *store/local* keyword is used, an internal fix will track bonds that
break during the simulation. Whenever a bond breaks, data is processed
and transferred to an internal fix labeled *fix_ID*. This allows the

20
doc/src/bond_bpm_spring.rst
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@ -10,7 +10,7 @@ Syntax
bond_style bpm/spring keyword value attribute1 attribute2 ...
* optional keyword = *overlay/pair* or *store/local* or *smooth*
* optional keyword = *overlay/pair* or *store/local* or *smooth* or *break/no*
.. parsed-literal::
@ -30,6 +30,9 @@ Syntax
*smooth* value = *yes* or *no*
smooths bond forces near the breaking point
*break/no*
indicates that bonds should not break during a run
Examples
""""""""
@ -47,7 +50,7 @@ Description
.. versionadded:: 4May2022
The *bpm/spring* bond style computes forces and torques based on
The *bpm/spring* bond style computes forces based on
deviations from the initial reference state of the two atoms. The
reference state is stored by each bond when it is first computed in
the setup of a run. Data is then preserved across run commands and is
@ -56,7 +59,8 @@ the system will not reset the reference state of a bond.
This bond style only applies central-body forces which conserve the
translational and rotational degrees of freedom of a bonded set of
particles. The force has a magnitude of
particles based on a model described by Clemmer and Robbins
:ref:`(Clemmer) <fragment-Clemmer>`. The force has a magnitude of
.. math::
@ -105,6 +109,12 @@ the *overlay/pair* keyword. These settings require specific
restrictions. Further details can be found in the `:doc: how to
<Howto_BPM>` page on BPMs.
.. versionadded:: TBD
If the *break/no* keyword is used, then LAMMPS assumes bonds should not break
during a simulation run. This will prevent some unnecessary calculation.
However, if a bond does break, it will trigger an error.
If the *store/local* keyword is used, an internal fix will track bonds that
break during the simulation. Whenever a bond breaks, data is processed
and transferred to an internal fix labeled *fix_ID*. This allows the
@ -200,6 +210,10 @@ The option defaults are *smooth* = *yes*
----------
.. _fragment-Clemmer:
**(Clemmer)** Clemmer and Robbins, Phys. Rev. Lett. (2022).
.. _Groot4:
**(Groot)** Groot and Warren, J Chem Phys, 107, 4423-35 (1997).

1
doc/src/comm_modify.rst
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@ -69,6 +69,7 @@ For many systems this is an efficient algorithm, but for systems with
widely varying cutoffs for different type pairs, the *multi* or *multi/old* mode can
be faster. In *multi*, each atom is assigned to a collection which should
correspond to a set of atoms with similar interaction cutoffs.
See the :doc:`neighbor <neighbor>` command for a detailed description of collections.
In this case, each atom collection is assigned its own distance
cutoff for communication purposes, and fewer atoms will be
communicated. in *multi/old*, a similar technique is used but atoms

33
doc/src/neighbor.rst
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@ -59,9 +59,21 @@ long cutoff, but other type pairs have a much shorter cutoff. The
sized particles, where "size" may mean the physical size of the particle
or its cutoff distance for interacting with other particles. Different
sets of bins are then used to construct the neighbor lists as as further
described by Shire, Hanley, and Stratford :ref:`(Shire) <bytype-Shire>`.
This imposes some extra setup overhead, but the searches themselves may
be much faster. By default, each atom type defines a separate collection
described by Shire, Hanley, and Stratford :ref:`(Shire) <multi-Shire>`
and Monti et al. :ref:`(Monti) <multi-Monti>`. This imposes some extra
setup overhead, but the searches themselves may be much faster.
For instance in a dense binary system in d-dimensions with a ratio of the size
of the largest to smallest collection bin :math:`\lambda`, the computational
costs of building a default neighbor list grows as :math:`\lambda^{2d}` while
the costs for *multi* grows as :math:`\lambda^d`, equivalent to the cost
of force evaluations, as argued in Monti et al. :ref:`(Monti) <multi-Monti>`.
In other words, the neighboring costs of *multi* are expected to scale the
same as force calculations, such that its relative cost is independent of
the particle size ratio. This is not the case for the default style which
becomes substantially more expensive with increasing size ratios.
By default in *multi*, each atom type defines a separate collection
of particles. For systems where two or more atom types have the same
size (either physical size or cutoff distance), the definition of
collections can be customized, which can result in less overhead and
@ -75,8 +87,11 @@ An alternate style, *multi/old*, sets the bin size to 1/2 of the shortest
cutoff distance and multiple sets of bins are defined to search over for
different atom types. This algorithm used to be the default *multi*
algorithm in LAMMPS but was found to be significantly slower than the new
approach. For now we are keeping the old option in case there are use cases
where multi/old outperforms the new multi style.
approach. For the dense binary system, computational costs still grew as
:math:`\lambda^{2d}` at large enough :math:`\lambda`. This is equivalent
to the default style, albeit with a smaller prefactor. For now we are
keeping the old option in case there are use cases where multi/old
outperforms the new multi style.
.. note::
@ -118,6 +133,10 @@ Default
----------
.. _bytype-Shire:
.. _multi-Shire:
**(Shire)** Shire, Hanley and Stratford, Comp Part Mech, (2020).
**(Shire)** Shire, Hanley and Stratford, Comp. Part. Mech., (2020).
.. _multi-Monti:
**(Monti)** Monti, Clemmer, Srivastava, Silbert, Grest, and Lechman, Phys. Rev. E, (2022).

2
src/.gitignore vendored
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@ -56,6 +56,8 @@
/pair_lepton.cpp
/pair_lepton.h
/pair_lepton_coul.cpp
/pair_lepton_coul.h
/bond_lepton.cpp
/bond_lepton.h
/angle_lepton.cpp

16
src/BPM/bond_bpm.cpp
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@ -40,6 +40,7 @@ BondBPM::BondBPM(LAMMPS *_lmp) :
{
overlay_flag = 0;
prop_atom_flag = 0;
break_flag = 1;
nvalues = 0;
r0_max_estimate = 0.0;
@ -104,21 +105,21 @@ void BondBPM::init_style()
}
} else {
// Require atoms know about all of their bonds and if they break
if (force->newton_bond)
error->all(FLERR, "Without overlay/pair, BPM bond styles require Newton bond off");
if (force->newton_bond && break_flag)
error->all(FLERR, "Without overlay/pair or break/no, BPM bond styles require Newton bond off");
// special lj must be 0 1 1 to censor pair forces between bonded particles
// special coulomb must be 1 1 1 to ensure all pairs are included in the
// neighbor list and 1-3 and 1-4 special bond lists are skipped
if (force->special_lj[1] != 0.0 || force->special_lj[2] != 1.0 || force->special_lj[3] != 1.0)
error->all(FLERR,
"Without overlay/pair, BPM bond sytles requires special LJ weights = 0,1,1");
"Without overlay/pair, BPM bond styles requires special LJ weights = 0,1,1");
if (force->special_coul[1] != 1.0 || force->special_coul[2] != 1.0 ||
force->special_coul[3] != 1.0)
error->all(FLERR,
"Without overlay/pair, BPM bond sytles requires special Coulomb weights = 1,1,1");
"Without overlay/pair, BPM bond styles requires special Coulomb weights = 1,1,1");
if (id_fix_dummy) {
if (id_fix_dummy && break_flag) {
id_fix_update = utils::strdup("BPM_UPDATE_SPECIAL_BONDS");
fix_update_special_bonds = dynamic_cast<FixUpdateSpecialBonds *>(modify->replace_fix(
id_fix_dummy, fmt::format("{} all UPDATE_SPECIAL_BONDS", id_fix_update), 1));
@ -188,6 +189,9 @@ void BondBPM::settings(int narg, char **arg)
} else if (strcmp(arg[iarg], "overlay/pair") == 0) {
overlay_flag = 1;
iarg++;
} else if (strcmp(arg[iarg], "break/no") == 0) {
break_flag = 0;
iarg++;
} else {
leftover_iarg.push_back(iarg);
iarg++;
@ -328,6 +332,8 @@ void BondBPM::read_restart(FILE *fp)
void BondBPM::process_broken(int i, int j)
{
if (break_flag)
error->one(FLERR, "BPM bond broke with break/no option");
if (fix_store_local) {
for (int n = 0; n < nvalues; n++) (this->*pack_choice[n])(n, i, j);

2
src/BPM/bond_bpm.h
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@ -50,7 +50,7 @@ class BondBPM : public Bond {
FnPtrPack *pack_choice; // ptrs to pack functions
double *output_data;
int prop_atom_flag, nvalues, overlay_flag;
int prop_atom_flag, nvalues, overlay_flag, break_flag;
int index_x_ref, index_y_ref, index_z_ref;
void pack_id1(int, int, int);

43
src/KIM/fix_store_kim.cpp
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@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -69,11 +68,11 @@ using namespace FixConst;
/* ---------------------------------------------------------------------- */
FixStoreKIM::FixStoreKIM(LAMMPS *lmp, int narg, char **arg)
: Fix(lmp, narg, arg), simulator_model(nullptr), model_name(nullptr),
model_units(nullptr), user_units(nullptr)
FixStoreKIM::FixStoreKIM(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), simulator_model(nullptr), model_name(nullptr), model_units(nullptr),
user_units(nullptr)
{
if (narg != 3) error->all(FLERR,"Illegal fix STORE/KIM command");
if (narg != 3) error->all(FLERR, "Illegal fix STORE/KIM command");
}
/* ---------------------------------------------------------------------- */
@ -83,25 +82,25 @@ FixStoreKIM::~FixStoreKIM()
// free associated storage
if (simulator_model) {
auto sm = (KIM_SimulatorModel *)simulator_model;
auto sm = (KIM_SimulatorModel *) simulator_model;
KIM_SimulatorModel_Destroy(&sm);
simulator_model = nullptr;
}
if (model_name) {
auto mn = (char *)model_name;
auto mn = (char *) model_name;
delete[] mn;
model_name = nullptr;
}
if (model_units) {
auto mu = (char *)model_units;
auto mu = (char *) model_units;
delete[] mu;
model_units = nullptr;
}
if (user_units) {
auto uu = (char *)user_units;
auto uu = (char *) user_units;
delete[] uu;
user_units = nullptr;
}
@ -121,38 +120,44 @@ void FixStoreKIM::setptr(const std::string &name, void *ptr)
{
if (name == "simulator_model") {
if (simulator_model) {
auto sm = (KIM_SimulatorModel *)simulator_model;
auto sm = (KIM_SimulatorModel *) simulator_model;
KIM_SimulatorModel_Destroy(&sm);
}
simulator_model = ptr;
} else if (name == "model_name") {
if (model_name) {
auto mn = (char *)model_name;
auto mn = (char *) model_name;
delete[] mn;
}
model_name = ptr;
} else if (name == "model_units") {
if (model_units) {
auto mu = (char *)model_units;
auto mu = (char *) model_units;
delete[] mu;
}
model_units = ptr;
} else if (name == "user_units") {
if (user_units) {
auto uu = (char *)user_units;
auto uu = (char *) user_units;
delete[] uu;
}
user_units = ptr;
} else error->all(FLERR,"Unknown property in fix STORE/KIM");
} else
error->all(FLERR, "Unknown property in fix STORE/KIM");
}
/* ---------------------------------------------------------------------- */
void *FixStoreKIM::getptr(const std::string &name)
{
if (name == "simulator_model") return simulator_model;
else if (name == "model_name") return model_name;
else if (name == "model_units") return model_units;
else if (name == "user_units") return user_units;
else return nullptr;
if (name == "simulator_model")
return simulator_model;
else if (name == "model_name")
return model_name;
else if (name == "model_units")
return model_units;
else if (name == "user_units")
return user_units;
else
return nullptr;
}

58
src/KIM/kim_command.cpp
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@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -70,40 +69,40 @@
using namespace LAMMPS_NS;
static constexpr const char *const cite_openkim =
"OpenKIM Project: doi:10.1007/s11837-011-0102-6\n\n"
"@Article{tadmor:elliott:2011,\n"
" author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller "
"and C. A. Becker},\n"
" title = {The potential of atomistic simulations and the {K}nowledgebase of "
"{I}nteratomic {M}odels},\n"
" journal = {{JOM}},\n"
" year = 2011,\n"
" volume = 63,\n"
" number = 17,\n"
" pages = {17},\n"
" doi = {10.1007/s11837-011-0102-6}\n"
"}\n\n";
"OpenKIM Project: doi:10.1007/s11837-011-0102-6\n\n"
"@Article{tadmor:elliott:2011,\n"
" author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller "
"and C. A. Becker},\n"
" title = {The potential of atomistic simulations and the {K}nowledgebase of "
"{I}nteratomic {M}odels},\n"
" journal = {{JOM}},\n"
" year = 2011,\n"
" volume = 63,\n"
" number = 17,\n"
" pages = {17},\n"
" doi = {10.1007/s11837-011-0102-6}\n"
"}\n\n";
static constexpr const char *const cite_openkim_query =
"OpenKIM query: doi:10.1063/5.0014267\n\n"
"@Article{karls:bierbaum:2020,\n"
" author = {D. S. Karls and M. Bierbaum and A. A. Alemi and R. S. Elliott "
"and J. P. Sethna and E. B. Tadmor},\n"
" title = {The {O}pen{KIM} processing pipeline: {A} cloud-based automatic "
"material property computation engine},\n"
" journal = {{T}he {J}ournal of {C}hemical {P}hysics},\n"
" year = 2020,\n"
" volume = 153,\n"
" number = 6,\n"
" pages = {064104},\n"
" doi = {10.1063/5.0014267}\n"
"}\n\n";
"OpenKIM query: doi:10.1063/5.0014267\n\n"
"@Article{karls:bierbaum:2020,\n"
" author = {D. S. Karls and M. Bierbaum and A. A. Alemi and R. S. Elliott "
"and J. P. Sethna and E. B. Tadmor},\n"
" title = {The {O}pen{KIM} processing pipeline: {A} cloud-based automatic "
"material property computation engine},\n"
" journal = {{T}he {J}ournal of {C}hemical {P}hysics},\n"
" year = 2020,\n"
" volume = 153,\n"
" number = 6,\n"
" pages = {064104},\n"
" doi = {10.1063/5.0014267}\n"
"}\n\n";
/* ---------------------------------------------------------------------- */
void KimCommand::command(int narg, char **arg)
{
if (narg < 1) error->all(FLERR,"Illegal kim command");
if (narg < 1) error->all(FLERR, "Illegal kim command");
const std::string subcmd(arg[0]);
narg--;
@ -132,5 +131,6 @@ void KimCommand::command(int narg, char **arg)
auto cmd = new KimQuery(lmp);
cmd->command(narg, arg);
delete cmd;
} else error->all(FLERR,"Unknown kim subcommand {}", subcmd);
} else
error->all(FLERR, "Unknown kim subcommand {}", subcmd);
}

64
src/KIM/kim_init.cpp
View File

@ -76,6 +76,8 @@ extern "C" {
}
using namespace LAMMPS_NS;
using kim_units::get_kim_unit_names;
using kim_units::lammps_unit_conversion;
/* ---------------------------------------------------------------------- */
@ -96,7 +98,7 @@ void KimInit::command(int narg, char **arg)
error->all(FLERR,
"Illegal 'kim init' command.\n"
"The argument followed by unit_style {} is an optional argument and when "
"is used must be unit_conversion_mode",
"used must be unit_conversion_mode",
user_units);
}
} else
@ -109,58 +111,10 @@ void KimInit::command(int narg, char **arg)
if (universe->nprocs > 1) MPI_Barrier(universe->uworld);
determine_model_type_and_units(model_name, user_units, &model_units, pkim);
write_log_cite(lmp, model_type, model_name);
do_init(model_name, user_units, model_units, pkim);
}
/* ---------------------------------------------------------------------- */
namespace {
void get_kim_unit_names(char const *const system, KIM_LengthUnit &lengthUnit,
KIM_EnergyUnit &energyUnit, KIM_ChargeUnit &chargeUnit,
KIM_TemperatureUnit &temperatureUnit, KIM_TimeUnit &timeUnit, Error *error)
{
const std::string system_str(system);
if (system_str == "real") {
lengthUnit = KIM_LENGTH_UNIT_A;
energyUnit = KIM_ENERGY_UNIT_kcal_mol;
chargeUnit = KIM_CHARGE_UNIT_e;
temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_fs;
} else if (system_str == "metal") {
lengthUnit = KIM_LENGTH_UNIT_A;
energyUnit = KIM_ENERGY_UNIT_eV;
chargeUnit = KIM_CHARGE_UNIT_e;
temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_ps;
} else if (system_str == "si") {
lengthUnit = KIM_LENGTH_UNIT_m;
energyUnit = KIM_ENERGY_UNIT_J;
chargeUnit = KIM_CHARGE_UNIT_C;
temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_s;
} else if (system_str == "cgs") {
lengthUnit = KIM_LENGTH_UNIT_cm;
energyUnit = KIM_ENERGY_UNIT_erg;
chargeUnit = KIM_CHARGE_UNIT_statC;
temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_s;
} else if (system_str == "electron") {
lengthUnit = KIM_LENGTH_UNIT_Bohr;
energyUnit = KIM_ENERGY_UNIT_Hartree;
chargeUnit = KIM_CHARGE_UNIT_e;
temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_fs;
} else if ((system_str == "lj") || (system_str == "micro") || (system_str == "nano")) {
error->all(FLERR, "LAMMPS unit_style {} not supported by KIM models", system_str);
} else {
error->all(FLERR, "Unknown unit_style");
}
}
} // namespace
void KimInit::print_dirs(struct KIM_Collections *const collections) const
{
int kim_error = 0;
@ -312,12 +266,8 @@ void KimInit::do_init(char *model_name, char *user_units, char *model_units, KIM
{
// create storage proxy fix. delete existing fix, if needed.
int ifix = modify->find_fix("KIM_MODEL_STORE");
if (ifix >= 0) modify->delete_fix(ifix);
modify->add_fix("KIM_MODEL_STORE all STORE/KIM");
ifix = modify->find_fix("KIM_MODEL_STORE");
auto fix_store = dynamic_cast<FixStoreKIM *>(modify->fix[ifix]);
if (modify->get_fix_by_id("KIM_MODEL_STORE")) modify->delete_fix("KIM_MODEL_STORE");
auto fix_store = dynamic_cast<FixStoreKIM *>(modify->add_fix("KIM_MODEL_STORE all STORE/KIM"));
fix_store->setptr("model_name", (void *) model_name);
fix_store->setptr("user_units", (void *) user_units);
fix_store->setptr("model_units", (void *) model_units);
@ -471,9 +421,7 @@ void KimInit::do_variables(const std::string &from, const std::string &to)
}
ier = lammps_unit_conversion(units[i], from, to, conversion_factor);
if (ier != 0)
error->all(FLERR,
"Unable to obtain conversion factor: "
"unit = {}; from = {}; to = {}",
error->all(FLERR, "Unable to obtain conversion factor: unit = {}; from = {}; to = {}",
units[i], from, to);
variable->internal_set(v_unit, conversion_factor);

49
src/KIM/kim_interactions.cpp
View File

@ -85,11 +85,10 @@ using namespace LAMMPS_NS;
void KimInteractions::command(int narg, char **arg)
{
if (narg < 1) error->all(FLERR, "Illegal 'kim interactions' command");
if (narg < 1) utils::missing_cmd_args(FLERR, "kim interactions", error);
if (!domain->box_exist)
error->all(FLERR, "Must use 'kim interactions' command after "
"simulation box is defined");
error->all(FLERR, "Use of 'kim interactions' before simulation box is defined");
do_setup(narg, arg);
}
@ -103,11 +102,9 @@ void KimInteractions::do_setup(int narg, char **arg)
if ((narg == 1) && (arg_str == "fixed_types")) {
fixed_types = true;
} else if (narg != atom->ntypes) {
error->all(FLERR, "Illegal 'kim interactions' command.\nThe "
"LAMMPS simulation has {} atom type(s), but "
"{} chemical species passed to the "
"'kim interactions' command",
atom->ntypes, narg);
error->all(FLERR, "Illegal 'kim interactions' command.\nThe LAMMPS simulation has {} atom "
"type(s), but {} chemical species passed to the 'kim interactions' command",
atom->ntypes, narg);
} else {
fixed_types = false;
}
@ -119,16 +116,14 @@ void KimInteractions::do_setup(int narg, char **arg)
// retrieve model name and pointer to simulator model class instance.
// validate model name if not given as null pointer.
int ifix = modify->find_fix("KIM_MODEL_STORE");
if (ifix >= 0) {
auto fix_store = dynamic_cast<FixStoreKIM *>(modify->fix[ifix]);
auto fix_store = dynamic_cast<FixStoreKIM *>(modify->get_fix_by_id("KIM_MODEL_STORE"));
if (fix_store) {
model_name = (char *)fix_store->getptr("model_name");
simulatorModel = (KIM_SimulatorModel *)fix_store->getptr("simulator_model");
} else error->all(FLERR, "Must use 'kim init' before 'kim interactions'");
// Begin output to log file
input->write_echo("#=== BEGIN kim interactions ==========================="
"=======\n");
input->write_echo("#=== BEGIN kim interactions ==================================\n");
if (simulatorModel) {
auto first_visit = input->variable->find("kim_update");
@ -165,8 +160,8 @@ void KimInteractions::do_setup(int narg, char **arg)
if (atom_type_sym == sim_species) species_is_supported = true;
}
if (!species_is_supported) {
error->all(FLERR, "Species '{}' is not supported by this "
"KIM Simulator Model", atom_type_sym);
error->all(FLERR, "Species '{}' is not supported by this KIM Simulator Model",
atom_type_sym);
}
}
} else {
@ -179,18 +174,15 @@ void KimInteractions::do_setup(int narg, char **arg)
const char *sim_field, *sim_value;
KIM_SimulatorModel_GetNumberOfSimulatorFields(simulatorModel, &sim_fields);
for (int i = 0; i < sim_fields; ++i) {
KIM_SimulatorModel_GetSimulatorFieldMetadata(
simulatorModel, i, &sim_lines, &sim_field);
KIM_SimulatorModel_GetSimulatorFieldMetadata(simulatorModel, i, &sim_lines, &sim_field);
const std::string sim_field_str(sim_field);
if (sim_field_str == "units") {
KIM_SimulatorModel_GetSimulatorFieldLine(
simulatorModel, i, 0, &sim_value);
KIM_SimulatorModel_GetSimulatorFieldLine(simulatorModel, i, 0, &sim_value);
const std::string sim_value_str(sim_value);
const std::string unit_style_str(update->unit_style);
if (sim_value_str != unit_style_str)
error->all(FLERR, "Incompatible units for KIM Simulator Model");
if (strcmp(sim_value, update->unit_style) != 0)
error->all(FLERR, "Incompatible units for KIM Simulator Model: {} vs {}",
sim_value, update->unit_style);
}
}
@ -217,8 +209,7 @@ void KimInteractions::do_setup(int narg, char **arg)
no_model_definition = false;
for (int j = 0; j < sim_lines; ++j) {
KIM_SimulatorModel_GetSimulatorFieldLine(
simulatorModel, i, j, &sim_value);
KIM_SimulatorModel_GetSimulatorFieldLine(simulatorModel, i, j, &sim_value);
if (utils::strmatch(sim_value, "^KIM_SET_TYPE_PARAMETERS")) {
// Notes regarding the KIM_SET_TYPE_PARAMETERS command
// * This is an INTERNAL command.
@ -264,8 +255,7 @@ void KimInteractions::do_setup(int narg, char **arg)
}
// End output to log file
input->write_echo("#=== END kim interactions ============================="
"=======\n\n");
input->write_echo("#=== END kim interactions ====================================\n\n");
}
/* ---------------------------------------------------------------------- */
@ -276,8 +266,7 @@ void KimInteractions::KIM_SET_TYPE_PARAMETERS(const std::string &input_line) con
const std::string key = words[1];
if (key != "pair" && key != "charge")
error->one(FLERR, "Unrecognized KEY {} for "
"KIM_SET_TYPE_PARAMETERS command", key);
error->one(FLERR, "Unrecognized KEY {} for KIM_SET_TYPE_PARAMETERS command", key);
std::string filename = words[2];
std::vector<std::string> species(words.begin() + 3, words.end());
@ -287,7 +276,7 @@ void KimInteractions::KIM_SET_TYPE_PARAMETERS(const std::string &input_line) con
FILE *fp = nullptr;
if (comm->me == 0) {
fp = fopen(filename.c_str(), "r");
if (fp == nullptr) error->one(FLERR, "Parameter file not found");
if (fp == nullptr) error->one(FLERR, "Parameter file {} not found", filename);
}
char line[MAXLINE], *ptr;

76
src/KIM/kim_param.cpp
View File

@ -63,6 +63,7 @@
#include "fix_store_kim.h"
#include "force.h"
#include "input.h"
#include "kim_units.h"
#include "modify.h"
#include "pair_kim.h"
#include "variable.h"
@ -77,61 +78,7 @@ extern "C"
}
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
namespace
{
void get_kim_unit_names(
char const *const system,
KIM_LengthUnit &lengthUnit,
KIM_EnergyUnit &energyUnit,
KIM_ChargeUnit &chargeUnit,
KIM_TemperatureUnit &temperatureUnit,
KIM_TimeUnit &timeUnit,
Error *error)
{
const std::string system_str(system);
if (system_str == "real") {
lengthUnit = KIM_LENGTH_UNIT_A;
energyUnit = KIM_ENERGY_UNIT_kcal_mol;
chargeUnit = KIM_CHARGE_UNIT_e;
temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_fs;
} else if (system_str == "metal") {
lengthUnit = KIM_LENGTH_UNIT_A;
energyUnit = KIM_ENERGY_UNIT_eV;
chargeUnit = KIM_CHARGE_UNIT_e;
temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_ps;
} else if (system_str == "si") {
lengthUnit = KIM_LENGTH_UNIT_m;
energyUnit = KIM_ENERGY_UNIT_J;
chargeUnit = KIM_CHARGE_UNIT_C;
temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_s;
} else if (system_str == "cgs") {
lengthUnit = KIM_LENGTH_UNIT_cm;
energyUnit = KIM_ENERGY_UNIT_erg;
chargeUnit = KIM_CHARGE_UNIT_statC;
temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_s;
} else if (system_str == "electron") {
lengthUnit = KIM_LENGTH_UNIT_Bohr;
energyUnit = KIM_ENERGY_UNIT_Hartree;
chargeUnit = KIM_CHARGE_UNIT_e;
temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_fs;
} else if ((system_str == "lj") ||
(system_str == "micro") ||
(system_str == "nano")) {
error->all(FLERR, "LAMMPS unit_style {} not supported "
"by KIM models", system_str);
} else {
error->all(FLERR, "Unknown unit_style");
}
}
} // namespace
using kim_units::get_kim_unit_names;
/* ---------------------------------------------------------------------- */
@ -159,20 +106,17 @@ void KimParam::command(int narg, char **arg)
error->all(FLERR, "Incorrect arguments in 'kim param' command.\n"
"'kim param get/set' is mandatory");
int const ifix = modify->find_fix("KIM_MODEL_STORE");
if (ifix >= 0) {
auto fix_store = reinterpret_cast<FixStoreKIM *>(modify->fix[ifix]);
KIM_SimulatorModel *simulatorModel =
reinterpret_cast<KIM_SimulatorModel *>(
fix_store->getptr("simulator_model"));
auto fix_store = dynamic_cast<FixStoreKIM *>(modify->get_fix_by_id("KIM_MODEL_STORE"));
if (fix_store) {
auto *simulatorModel = reinterpret_cast<KIM_SimulatorModel *>(
fix_store->getptr("simulator_model"));
if (simulatorModel)
error->all(FLERR, "'kim param' can only be used with a KIM Portable Model");
}
input->write_echo(fmt::format("#=== BEGIN kim param {} ==================="
"==================\n", kim_param_get_set));
input->write_echo(fmt::format("#=== BEGIN kim param {} =====================================\n",
kim_param_get_set));
KIM_Model *pkim = nullptr;
@ -431,6 +375,6 @@ void KimParam::command(int narg, char **arg)
} else
error->all(FLERR, "This model has No mutable parameters");
input->write_echo(fmt::format("#=== END kim param {} ====================="
"==================\n", kim_param_get_set));
input->write_echo(fmt::format("#=== END kim param {} =======================================\n",
kim_param_get_set));
}

2
src/KIM/kim_param.h
View File

@ -67,7 +67,5 @@ class KimParam : protected Pointers {
KimParam(class LAMMPS *lmp);
void command(int, char **);
};
} // namespace LAMMPS_NS
#endif

68
src/KIM/kim_property.cpp
View File

@ -85,14 +85,13 @@ void KimProperty::command(int narg, char **arg)
{
#if LMP_PYTHON
#if PY_MAJOR_VERSION >= 3
if (narg < 2) error->all(FLERR, "Invalid 'kim property' command");
if (narg < 2) utils::missing_cmd_args(FLERR, "kim property", error);
const std::string subcmd(arg[0]);
if ((subcmd != "create") && (subcmd != "destroy") && (subcmd != "modify") &&
(subcmd != "remove") && (subcmd != "dump")) {
std::string msg("Incorrect arguments in 'kim property' command.\n");
msg += "'kim property create/destroy/modify/remove/dump' is mandatory";
error->all(FLERR, msg);
error->all(FLERR, "Incorrect first argument {} to 'kim property' command.\n"
"One of create, destroy, modify, remove, or dump is mandatory", subcmd);
}
input->write_echo("#=== kim property ====================================="
@ -117,12 +116,11 @@ void KimProperty::command(int narg, char **arg)
kim_property = PyImport_Import(obj);
if (!kim_property) {
PyGILState_Release(gstate);
std::string msg("Unable to import Python kim_property module!");
msg += "\nkim-property Python package can be installed with pip:\n";
msg += "'pip install kim-property'\nSee the installation instructions ";
msg += "at\nhttps://github.com/openkim/kim-property#installing-kim-";
msg += "property\nfor detailed information";
error->all(FLERR, msg);
error->all(FLERR, "Unable to import Python kim_property module!\n"
"kim-property Python package can be installed with pip:\n"
"'pip install kim-property'\nSee the installation instructions at\n"
"https://github.com/openkim/kim-property#installing-kim-property\n"
"for detailed information");
}
// Decrementing of the reference count
@ -147,9 +145,8 @@ void KimProperty::command(int narg, char **arg)
PyObject_GetAttrString(kim_property, "kim_property_create");
if (!pFunc) {
PyGILState_Release(gstate);
std::string msg("Unable to get an attribute named ");
msg += "'kim_property_create' from a kim_property object";
error->all(FLERR, msg);
error->all(FLERR, "Unable to get an attribute named 'kim_property_create' from "
"a kim_property object");
}
// Decrementing of the reference count
@ -182,16 +179,13 @@ void KimProperty::command(int narg, char **arg)
if (!pValue) {
PyErr_Print();
PyGILState_Release(gstate);
std::string msg("Python 'kim_property_create' function ");
msg += "evaluation failed";
error->one(FLERR, msg);
error->all(FLERR, "Python 'kim_property_create' function evaluation failed");
}
// Python function returned a string value
const char *pystr = PyUnicode_AsUTF8(pValue);
if (kim_str) input->variable->set_string("kim_property_str", pystr);
else
input->variable->set(fmt::format("kim_property_str string '{}'", pystr));
else input->variable->set(fmt::format("kim_property_str string '{}'", pystr));
Py_XDECREF(pArgs);
Py_XDECREF(pFunc);
@ -216,9 +210,8 @@ void KimProperty::command(int narg, char **arg)
PyObject_GetAttrString(kim_property, "kim_property_destroy");
if (!pFunc) {
PyGILState_Release(gstate);
std::string msg("Unable to get an attribute named ");
msg += "'kim_property_destroy' from a kim_property object";
error->all(FLERR, msg);
error->all(FLERR, "Unable to get an attribute named 'kim_property_destroy' "
"from a kim_property object");
}
// Decrementing of the reference count
@ -244,9 +237,7 @@ void KimProperty::command(int narg, char **arg)
if (!pValue) {
PyErr_Print();
PyGILState_Release(gstate);
std::string msg("Python 'kim_property_destroy' function ");
msg += "evaluation failed";
error->one(FLERR, msg);
error->all(FLERR, "Python 'kim_property_destroy' function evaluation failed");
}
// Python function returned a string value
@ -276,9 +267,8 @@ void KimProperty::command(int narg, char **arg)
PyObject_GetAttrString(kim_property, "kim_property_modify");
if (!pFunc) {
PyGILState_Release(gstate);
std::string msg("Unable to get an attribute named ");
msg += "'kim_property_modify' from a kim_property object";
error->all(FLERR, msg);
error->all(FLERR, "Unable to get an attribute named 'kim_property_modify' "
"from a kim_property object");
}
// Decrementing of the reference count
@ -309,9 +299,7 @@ void KimProperty::command(int narg, char **arg)
if (!pValue) {
PyErr_Print();
PyGILState_Release(gstate);
std::string msg("Python 'kim_property_modify' function ");
msg += "evaluation failed";
error->one(FLERR, msg);
error->all(FLERR, "Python 'kim_property_modify' function evaluation failed");
}
// Python function returned a string value
@ -341,9 +329,8 @@ void KimProperty::command(int narg, char **arg)
PyObject_GetAttrString(kim_property, "kim_property_remove");
if (!pFunc) {
PyGILState_Release(gstate);
std::string msg("Unable to get an attribute named ");
msg += "'kim_property_remove' from a kim_property object";
error->all(FLERR, msg);
error->all(FLERR, "Unable to get an attribute named "
"'kim_property_remove' from a kim_property object");
}
// Decrementing of the reference count
@ -374,9 +361,7 @@ void KimProperty::command(int narg, char **arg)
if (!pValue) {
PyErr_Print();
PyGILState_Release(gstate);
std::string msg("Python 'kim_property_remove' function ");
msg += "evaluation failed";
error->one(FLERR, msg);
error->all(FLERR, "Python 'kim_property_remove' function evaluation failed");
}
// Python function returned a string value
@ -404,9 +389,8 @@ void KimProperty::command(int narg, char **arg)
PyObject_GetAttrString(kim_property, "kim_property_dump");
if (!pFunc) {
PyGILState_Release(gstate);
std::string msg("Unable to get an attribute named ");
msg += "'kim_property_dump' from a kim_property object";
error->all(FLERR, msg);
error->all(FLERR, "Unable to get an attribute named "
"'kim_property_dump' from a kim_property object");
}
// Decrementing of the reference count
@ -428,14 +412,12 @@ void KimProperty::command(int narg, char **arg)
if (comm->me == 0) {
// call the Python kim_property_dump function
// error check with one() since only some procs may fail
// error check with one() since only root process calls.
pValue = PyObject_CallObject(pFunc, pArgs);
if (!pValue) {
PyErr_Print();
PyGILState_Release(gstate);
std::string msg("Python 'kim_property_dump' function ");
msg += "evaluation failed";
error->one(FLERR, msg);
error->one(FLERR, "Python 'kim_property_dump' function evaluation failed");
}
} else
pValue = nullptr;

41
src/KIM/kim_query.cpp
View File

@ -136,11 +136,9 @@ void KimQuery::command(int narg, char **arg)
// check the query_args format (a series of keyword=value pairs)
for (int i = 2; i < narg; ++i) {
if (!utils::strmatch(arg[i], "[=][\\[].*[\\]]"))
error->all(FLERR, "Illegal query format.\nInput argument "
"of `{}` to 'kim query' is wrong. The "
"query format is the keyword=[value], "
"where value is always an array of one or "
"more comma-separated items", arg[i]);
error->all(FLERR, "Illegal query format.\nInput argument of `{}` to 'kim query' is wrong. "
"The query format is the keyword=[value], where value is always an array of one "
"or more comma-separated items", arg[i]);
}
if (query_function != "get_available_models") {
@ -156,15 +154,13 @@ void KimQuery::command(int narg, char **arg)
// if the model name is not provided by the user
if (model_name.empty()) {
// check if we had a kim init command by finding fix STORE/KIM
const int ifix = modify->find_fix("KIM_MODEL_STORE");
if (ifix >= 0) {
auto fix_store = dynamic_cast<FixStoreKIM *>(modify->fix[ifix]);
auto fix_store = dynamic_cast<FixStoreKIM *>(modify->get_fix_by_id("KIM_MODEL_STORE"));
if (fix_store) {
char *model_name_c = (char *) fix_store->getptr("model_name");
model_name = model_name_c;
} else {
error->all(FLERR, "Illegal query format.\nMust use 'kim init' "
"before 'kim query' or must provide the model name "
"after query function with the format of "
error->all(FLERR, "Illegal query format.\nMust use 'kim init' before 'kim query' "
"or must provide the model name after query function with the format of "
"'model=[model_name]'");
}
}
@ -179,16 +175,14 @@ void KimQuery::command(int narg, char **arg)
// and then the error message that was returned by the web server
if (strlen(value) == 0) {
auto msg = fmt::format("OpenKIM query failed: {}", value + 1);
delete [] value;
error->all(FLERR, msg);
error->all(FLERR, "OpenKIM query failed: {}", value + 1);
delete[] value;
} else if (strcmp(value, "EMPTY") == 0) {
delete [] value;
delete[] value;
error->all(FLERR, "OpenKIM query returned no results");
}
input->write_echo("#=== BEGIN kim-query =================================="
"=======\n");
input->write_echo("#=== BEGIN kim-query =========================================\n");
// trim list of models to those that are installed on the system
if (query_function == "get_available_models") {
Tokenizer vals(value, ", \"");
@ -199,7 +193,7 @@ void KimQuery::command(int narg, char **arg)
KIM_CollectionItemType typ;
if (KIM_Collections_Create(&collections)) {
delete [] value;
delete[] value;
error->all(FLERR, "Unable to access KIM Collections to find Model");
}
@ -219,7 +213,7 @@ void KimQuery::command(int narg, char **arg)
fmt::format("# Missing OpenKIM models: {}\n\n", missing));
if (available.empty()) {
delete [] value;
delete[] value;
error->all(FLERR,"There are no matching OpenKIM models installed on the system");
}
@ -262,13 +256,12 @@ void KimQuery::command(int narg, char **arg)
input->variable->set(setcmd);
input->write_echo(fmt::format("variable {}\n", setcmd));
}
input->write_echo("#=== END kim-query ===================================="
"=======\n\n");
input->write_echo("#=== END kim-query ===========================================\n\n");
delete [] value;
delete[] value;
#else
error->all(FLERR, "Cannot use 'kim query' command when KIM package "
"is compiled without support for libcurl");
error->all(FLERR, "Cannot use 'kim query' command when KIM package is compiled without "
"support for libcurl");
#endif
}

425
src/KIM/kim_units.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -54,179 +53,182 @@
Designed for use with the kim-api-2.0.2 (and newer) package
------------------------------------------------------------------------- */
#include "kim_units.h"
#include "error.h"
#include <cmath>
#include <map>
#include <string>
#include <utility>
using namespace std;
namespace
{
using namespace LAMMPS_NS;
using namespace kim_units;
// Constants of nature and basic conversion factors
// Source: https://physics.nist.gov/cuu/Constants/Table/allascii.txt
// Working with NIST values even when there are newer values for
// compatibility with LAMMPS
// clang-format off
/*----------------------
Fundamental constants
------------------------ */
double const boltz_si = 1.38064852e-23; // [J K^-1] Boltzmann's factor
// (NIST value)
double const Nav = 6.022140857e23; // [unitless] Avogadro's number
// (NIST value)
// double const Nav = 6.02214076e23; // [unitless] Avogadro's number
// (official value May 2019)
double const me_si = 9.10938356e-31; // [kg] electron rest mass
// (NIST value)
// double me_si = 9.10938291e-31; // [kg] electron rest mass
double const e_si = 1.6021766208e-19; // [C] elementary charge
// (charge of an electron/proton)
// (NIST value)
static double constexpr boltz_si = 1.38064852e-23; // [J K^-1] Boltzmann's factor
// (NIST value)
static double constexpr Nav = 6.022140857e23; // [unitless] Avogadro's number (NIST value)
// static double constexp Nav = 6.02214076e23; // [unitless] Avogadro's number
// (official value May 2019)
static double constexpr me_si = 9.10938356e-31; // [kg] electron rest mass (NIST value)
// static double constexpr me_si = 9.10938291e-31; // [kg] electron rest mass
static double constexpr e_si = 1.6021766208e-19; // [C] elementary charge
// (charge of an electron/proton)
// (NIST value)
/*----------------------
Distance units
------------------------ */
double const bohr_si = 5.2917721067e-11; // [m] Bohr unit (distance between
// nucleus and electron in H)
// (NIST value)
double const angstrom_si = 1e-10; // [m] Angstrom
double const centimeter_si = 1e-2; // [m] centimeter
double const micrometer_si = 1e-6; // [m] micrometer (micron)
double const nanometer_si = 1e-9; // [m] nanometer
static double constexpr bohr_si = 5.2917721067e-11; // [m] Bohr unit (distance between
// nucleus and electron in H) (NIST value)
static double constexpr angstrom_si = 1e-10; // [m] Angstrom
static double constexpr centimeter_si = 1e-2; // [m] centimeter
static double constexpr micrometer_si = 1e-6; // [m] micrometer (micron)
static double constexpr nanometer_si = 1e-9; // [m] nanometer
/*----------------------
Mass units
------------------------ */
double const gram_per_mole_si = 1e-3/Nav; // [kg] gram per mole
double const amu_si = 1e-3/Nav; // [kg] atomic mass unit (molecular
// weight) For example, the mean
// molecular weight of water
// is 18.015 atomic mass units
// (amu), so one mole of water
// weight 18.015 grams.
double const gram_si = 1e-3; // [kg] gram
double const picogram_si = 1e-15; // [kg] picogram
double const attogram_si = 1e-21; // [kg[ attogram
static double constexpr gram_per_mole_si = 1e-3/Nav; // [kg] gram per mole
static double constexpr amu_si = 1e-3/Nav; // [kg] atomic mass unit (molecular
// weight) For example, the mean
// molecular weight of water
// is 18.015 atomic mass units
// (amu), so one mole of water
// weight 18.015 grams.
static double constexpr gram_si = 1e-3; // [kg] gram
static double constexpr picogram_si = 1e-15; // [kg] picogram
static double constexpr attogram_si = 1e-21; // [kg[ attogram
/*----------------------
Time units
------------------------ */
double const atu_si = 2.418884326509e-17; // [s] atomic time unit
// ( = hbar/E_h where E_h is the
// Hartree energy) (NIST value)
double const atu_electron_si = atu_si*sqrt(amu_si/me_si);
// [s] atomic time unit
// used in electron system (see https://sourceforge.net/p/lammps/mailman/lammps-users/thread/BCA2BDB2-BA03-4280-896F-1E6120EF47B2%40caltech.edu/)
double const microsecond_si = 1e-6; // [s] microsecond
double const nanosecond_si = 1e-9; // [s] nanosecond
double const picosecond_si = 1e-12; // [s] picosecond
double const femtosecond_si = 1e-15; // [s] femtosecond
static double constexpr atu_si = 2.418884326509e-17; // [s] atomic time unit
// ( = hbar/E_h where E_h is the
// Hartree energy) (NIST value)
static double constexpr atu_electron_si = 5153034.567408186; // must not use sqrt() in constexpr
// static double constexpr atu_electron_si = atu_si*sqrt(amu_si/me_si);
// [s] atomic time unit
// used in electron system (see https://sourceforge.net/p/lammps/mailman/lammps-users/thread/BCA2BDB2-BA03-4280-896F-1E6120EF47B2%40caltech.edu/)
static double constexpr microsecond_si = 1e-6; // [s] microsecond
static double constexpr nanosecond_si = 1e-9; // [s] nanosecond
static double constexpr picosecond_si = 1e-12; // [s] picosecond
static double constexpr femtosecond_si = 1e-15; // [s] femtosecond
/*----------------------
Density units
------------------------ */
double const gram_per_centimetercu_si =
gram_si/pow(centimeter_si,3); // [kg/m^3] gram/centimeter^3
double const amu_per_bohrcu_si = amu_si/pow(bohr_si,3); // [kg/m^3] amu/bohr^3
double const picogram_per_micrometercu_si =
picogram_si/pow(micrometer_si,3); // [kg/m^3] picogram/micrometer^3
double const attogram_per_nanometercu_si =
attogram_si/pow(nanometer_si,3); // [kg/m^3] attogram/nanometer^3
static double constexpr gram_per_centimetercu_si =
gram_si/centimeter_si/centimeter_si/centimeter_si; // [kg/m^3] gram/centimeter^3
static double constexpr amu_per_bohrcu_si = amu_si/bohr_si/bohr_si/bohr_si; // [kg/m^3] amu/bohr^3
static double constexpr picogram_per_micrometercu_si =
picogram_si/micrometer_si/micrometer_si/micrometer_si; // [kg/m^3] picogram/micrometer^3
static double constexpr attogram_per_nanometercu_si =
attogram_si/nanometer_si/nanometer_si/nanometer_si; // [kg/m^3] attogram/nanometer^3
/*----------------------
Energy/torque units
------------------------ */
double const kcal_si = 4184.0; // [J] kilocalorie (heat energy
// involved in warming up one
// kilogram of water by one
// degree Kelvin)
double const ev_si = 1.6021766208e-19; // [J] electron volt (amount of
// energy gained or lost by the
// charge of a single electron
// moving across an electric
// potential difference of one
// volt.) (NIST value)
double const hartree_si = 4.359744650e-18; // [J] Hartree (approximately the
// electric potential energy of
// the hydrogen atom in its
// ground state) (NIST value)
double const kcal_per_mole_si = kcal_si/Nav;// [J] kcal/mole
double const erg_si = 1e-7; // [J] erg
double const dyne_centimeter_si = 1e-7; // [J[ dyne*centimeter
double const picogram_micrometersq_per_microsecondsq_si =
picogram_si*pow(micrometer_si,2)/pow(microsecond_si,2);
// [J] picogram*micrometer^2/
// microsecond^2
double const attogram_nanometersq_per_nanosecondsq_si =
attogram_si*pow(nanometer_si,2)/pow(nanosecond_si,2);
// [J] attogram*nanometer^2/
// nanosecond^2
static double constexpr kcal_si = 4184.0; // [J] kilocalorie (heat energy
// involved in warming up one
// kilogram of water by one
// degree Kelvin)
static double constexpr ev_si = 1.6021766208e-19; // [J] electron volt (amount of
// energy gained or lost by the
// charge of a single electron
// moving across an electric
// potential difference of one
// volt.) (NIST value)
static double constexpr hartree_si = 4.359744650e-18; // [J] Hartree (approximately the
// electric potential energy of
// the hydrogen atom in its
// ground state) (NIST value)
static double constexpr kcal_per_mole_si = kcal_si/Nav;// [J] kcal/mole
static double constexpr erg_si = 1e-7; // [J] erg
static double constexpr dyne_centimeter_si = 1e-7; // [J[ dyne*centimeter
static double constexpr picogram_micrometersq_per_microsecondsq_si =
picogram_si*micrometer_si/microsecond_si*micrometer_si/microsecond_si;
// [J] picogram*micrometer^2/
// microsecond^2
static double constexpr attogram_nanometersq_per_nanosecondsq_si =
attogram_si*nanometer_si/nanosecond_si*nanometer_si/nanosecond_si;
// [J] attogram*nanometer^2/
// nanosecond^2
/*----------------------
Velocity units
------------------------ */
double const angstrom_per_femtosecond_si =
static double constexpr angstrom_per_femtosecond_si =
angstrom_si/femtosecond_si; // [m/s] Angstrom/femtosecond
double const angstrom_per_picosecond_si =
static double constexpr angstrom_per_picosecond_si =
angstrom_si/picosecond_si; // [m/s] Angstrom/picosecond
double const micrometer_per_microsecond_si =
static double constexpr micrometer_per_microsecond_si =
micrometer_si/microsecond_si; // [m/s] micrometer/microsecond
double const nanometer_per_nanosecond_si =
static double constexpr nanometer_per_nanosecond_si =
nanometer_si/nanosecond_si; // [m/s] nanometer/nanosecond
double const centimeter_per_second_si =
static double constexpr centimeter_per_second_si =
centimeter_si; // [m/s] centimeter/second
double const bohr_per_atu_electron_si =
static double constexpr bohr_per_atu_electron_si =
bohr_si/atu_electron_si; // [m/s] bohr/atu
/*----------------------
Force units
------------------------ */
double const kcal_per_mole_angstrom_si =
static double constexpr kcal_per_mole_angstrom_si =
kcal_per_mole_si/angstrom_si; // [N] kcal/(mole*Angstrom)
double const ev_per_angstrom_si =
static double constexpr ev_per_angstrom_si =
ev_si/angstrom_si; // [N] eV/Angstrom
double const dyne_si =
static double constexpr dyne_si =
dyne_centimeter_si/centimeter_si; // [N] dyne
double const hartree_per_bohr_si =
static double constexpr hartree_per_bohr_si =
hartree_si/bohr_si; // [N] hartree/bohr
double const picogram_micrometer_per_microsecondsq_si =
picogram_si*micrometer_si/pow(microsecond_si,2);
static double constexpr picogram_micrometer_per_microsecondsq_si =
picogram_si*micrometer_si/microsecond_si/microsecond_si;
// [N] picogram*micrometer/
// microsecond^2
double const attogram_nanometer_per_nanosecondsq_si =
attogram_si*nanometer_si/pow(nanosecond_si,2);
static double constexpr attogram_nanometer_per_nanosecondsq_si =
attogram_si*nanometer_si/nanosecond_si/nanosecond_si;
// [N] attogram*nanometer/
// nanosecond^2
/*----------------------
Pressure units
------------------------ */
double const atmosphere_si = 101325.0; // [Pa] standard atmosphere (NIST value)
double const bar_si = 1e5; // [Pa] bar
double const dyne_per_centimetersq_si =
dyne_centimeter_si/pow(centimeter_si,3);
static double constexpr atmosphere_si = 101325.0; // [Pa] standard atmosphere (NIST value)
static double constexpr bar_si = 1e5; // [Pa] bar
static double constexpr dyne_per_centimetersq_si =
dyne_centimeter_si/centimeter_si/centimeter_si/centimeter_si;
// [Pa] dyne/centimeter^2
double const picogram_per_micrometer_microsecondsq_si =
picogram_si/(micrometer_si*pow(microsecond_si,2));
static double constexpr picogram_per_micrometer_microsecondsq_si =
picogram_si/(micrometer_si*microsecond_si*microsecond_si);
// [Pa] picogram/(micrometer*
// microsecond^2)
double const attogram_per_nanometer_nanosecondsq_si =
attogram_si/(nanometer_si*pow(nanosecond_si,2));
static double constexpr attogram_per_nanometer_nanosecondsq_si =
attogram_si/(nanometer_si*nanosecond_si*nanosecond_si);
// [Pa] attogram/(nanometer*nanosecond^2)
/*----------------------
Viscosity units
------------------------ */
double const poise_si = 0.1; // [Pa*s] Poise
double const amu_per_bohr_femtosecond_si =
static double constexpr poise_si = 0.1; // [Pa*s] Poise
static double constexpr amu_per_bohr_femtosecond_si =
amu_si/(bohr_si*femtosecond_si); // [Pa*s] amu/(bohr*femtosecond)
double const picogram_per_micrometer_microsecond_si =
static double constexpr picogram_per_micrometer_microsecond_si =
picogram_si/(micrometer_si*microsecond_si);
// [Pa*s] picogram/(micrometer*
// microsecond)
double const attogram_per_nanometer_nanosecond_si =
static double constexpr attogram_per_nanometer_nanosecond_si =
attogram_si/(nanometer_si*nanosecond_si);
// [Pa*s] attogram/(nanometer*
// nanosecond)
@ -234,39 +236,41 @@ double const attogram_per_nanometer_nanosecond_si =
/*----------------------
Charge units
------------------------ */
double const echarge_si = e_si; // [C] electron charge unit
double const statcoulomb_si = e_si/4.8032044e-10; // [C] Statcoulomb or esu
static double constexpr echarge_si = e_si; // [C] electron charge unit
static double constexpr statcoulomb_si = e_si/4.8032044e-10; // [C] Statcoulomb or esu
// (value from LAMMPS units
// documentation)
double const picocoulomb_si = 1e-12; // [C] picocoulomb
static double constexpr picocoulomb_si = 1e-12; // [C] picocoulomb
/*----------------------
Dipole units
------------------------ */
double const electron_angstrom_si = echarge_si*angstrom_si;
static double constexpr electron_angstrom_si = echarge_si*angstrom_si;
// [C*m] electron*angstrom
double const statcoulomb_centimeter_si = statcoulomb_si*centimeter_si;
static double constexpr statcoulomb_centimeter_si = statcoulomb_si*centimeter_si;
// [C*m] statcoulomb*centimeter
double const debye_si = 1e-18*statcoulomb_centimeter_si;
static double constexpr debye_si = 1e-18*statcoulomb_centimeter_si;
// [C*m] Debye
double const picocoulomb_micrometer_si = picocoulomb_si*micrometer_si;
static double constexpr picocoulomb_micrometer_si = picocoulomb_si*micrometer_si;
// [C*m] picocoulomb*micrometer
double const electron_nanometer_si = echarge_si*nanometer_si;
static double constexpr electron_nanometer_si = echarge_si*nanometer_si;
// [C*m] electron*nanometer
/*----------------------
Electric field units
------------------------ */
double const volt_per_angstrom_si = 1.0/angstrom_si;// [V/m] volt/angstrom
double const statvolt_per_centimeter_si =
static double constexpr volt_per_angstrom_si = 1.0/angstrom_si;// [V/m] volt/angstrom
static double constexpr statvolt_per_centimeter_si =
erg_si/(statcoulomb_si*centimeter_si); // [V/m] statvolt/centimeter
double const volt_per_centimeter_si =
static double constexpr volt_per_centimeter_si =
1.0/centimeter_si; // [V/m] volt/centimeter
double const volt_per_micrometer_si =
static double constexpr volt_per_micrometer_si =
1.0/micrometer_si; // [V/m] volt/micrometer
double const volt_per_nanometer_si =
static double constexpr volt_per_nanometer_si =
1.0/nanometer_si; // [V/m] volt/nanometer
namespace LAMMPS_NS {
namespace kim_units {
// Define enumerations
enum sys_type
{
@ -388,20 +392,42 @@ enum units
attogram_per_nanometercu = 1405
};
void initialize_dictionaries();
units get_lammps_system_unit(sys_type system_enum, unit_type unit_type_enum);
double get_mass_conversion_factor(units from_unit_enum, units to_unit_enum);
double get_distance_conversion_factor(units from_unit_enum, units to_unit_enum);
double get_time_conversion_factor(units from_unit_enum, units to_unit_enum);
double get_energy_conversion_factor(units from_unit_enum, units to_unit_enum);
double get_velocity_conversion_factor(units from_unit_enum, units to_unit_enum);
double get_force_conversion_factor(units from_unit_enum, units to_unit_enum);
double get_torque_conversion_factor(units from_unit_enum, units to_unit_enum);
double get_temperature_conversion_factor(units from_unit_enum, units to_unit_enum);
double get_pressure_conversion_factor(units from_unit_enum, units to_unit_enum);
double get_viscosity_conversion_factor(units from_unit_enum, units to_unit_enum);
double get_charge_conversion_factor(units from_unit_enum, units to_unit_enum);
double get_dipole_conversion_factor(units from_unit_enum, units to_unit_enum);
double get_efield_conversion_factor(units from_unit_enum, units to_unit_enum);
double get_density_conversion_factor(units from_unit_enum, units to_unit_enum);
double get_unit_conversion_factor(unit_type &unit_type_enum, sys_type from_system_enum,
sys_type to_system_enum);
}
}
// Define dictionaries
map<string, sys_type> system_dic;
map<string, unit_type> unit_dic;
map<unit_type, units> units_real_dic;
map<unit_type, units> units_metal_dic;
map<unit_type, units> units_si_dic;
map<unit_type, units> units_cgs_dic;
map<unit_type, units> units_electron_dic;
map<unit_type, units> units_micro_dic;
map<unit_type, units> units_nano_dic;
static map<string, sys_type> system_dic;
static map<string, unit_type> unit_dic;
static map<unit_type, units> units_real_dic;
static map<unit_type, units> units_metal_dic;
static map<unit_type, units> units_si_dic;
static map<unit_type, units> units_cgs_dic;
static map<unit_type, units> units_electron_dic;
static map<unit_type, units> units_micro_dic;
static map<unit_type, units> units_nano_dic;
/* ---------------------------------------------------------------------- */
void initialize_dictionaries()
void kim_units::initialize_dictionaries()
{
system_dic["real"] = real;
system_dic["metal"] = metal;
@ -537,7 +563,7 @@ void initialize_dictionaries()
// Get the enumeration for the unit of type `unit_type_enum`
// for LAMMPS system `system_enum`.
units get_lammps_system_unit(sys_type system_enum, unit_type unit_type_enum)
units kim_units::get_lammps_system_unit(sys_type system_enum, unit_type unit_type_enum)
{
switch(system_enum) {
case real :
@ -561,7 +587,7 @@ units get_lammps_system_unit(sys_type system_enum, unit_type unit_type_enum)
/* ---------------------------------------------------------------------- */
// Mass conversion
double get_mass_conversion_factor(units from_unit_enum, units to_unit_enum)
double kim_units::get_mass_conversion_factor(units from_unit_enum, units to_unit_enum)
{
map<units, map<units, double> > conv;
double to_si;
@ -619,7 +645,7 @@ double get_mass_conversion_factor(units from_unit_enum, units to_unit_enum)
/* ---------------------------------------------------------------------- */
// Distance conversion
double get_distance_conversion_factor(units from_unit_enum, units to_unit_enum)
double kim_units::get_distance_conversion_factor(units from_unit_enum, units to_unit_enum)
{
map<units, map<units, double> > conv;
double to_si;
@ -677,7 +703,7 @@ double get_distance_conversion_factor(units from_unit_enum, units to_unit_enum)
/* ---------------------------------------------------------------------- */
// Time conversion
double get_time_conversion_factor(units from_unit_enum, units to_unit_enum)
double kim_units::get_time_conversion_factor(units from_unit_enum, units to_unit_enum)
{
map<units, map<units, double> > conv;
double to_si;
@ -722,7 +748,7 @@ double get_time_conversion_factor(units from_unit_enum, units to_unit_enum)
/* ---------------------------------------------------------------------- */
// Energy conversion
double get_energy_conversion_factor(units from_unit_enum, units to_unit_enum)
double kim_units::get_energy_conversion_factor(units from_unit_enum, units to_unit_enum)
{
map<units, map<units, double> > conv;
@ -796,7 +822,7 @@ double get_energy_conversion_factor(units from_unit_enum, units to_unit_enum)
/* ---------------------------------------------------------------------- */
// Velocity conversion
double get_velocity_conversion_factor(units from_unit_enum, units to_unit_enum)
double kim_units::get_velocity_conversion_factor(units from_unit_enum, units to_unit_enum)
{
map<units, map<units, double> > conv;
double to_si;
@ -869,7 +895,7 @@ double get_velocity_conversion_factor(units from_unit_enum, units to_unit_enum)
/* ---------------------------------------------------------------------- */
// Force conversion
double get_force_conversion_factor(units from_unit_enum, units to_unit_enum)
double kim_units::get_force_conversion_factor(units from_unit_enum, units to_unit_enum)
{
map<units, map<units, double> > conv;
double to_si;
@ -942,7 +968,7 @@ double get_force_conversion_factor(units from_unit_enum, units to_unit_enum)
/* ---------------------------------------------------------------------- */
// Torque conversion
double get_torque_conversion_factor(units from_unit_enum, units to_unit_enum)
double kim_units::get_torque_conversion_factor(units from_unit_enum, units to_unit_enum)
{
map<units, map<units, double> > conv;
double to_si;
@ -1015,7 +1041,7 @@ double get_torque_conversion_factor(units from_unit_enum, units to_unit_enum)
/* ---------------------------------------------------------------------- */
// Temperature conversion
double get_temperature_conversion_factor(units from_unit_enum, units to_unit_enum)
double kim_units::get_temperature_conversion_factor(units from_unit_enum, units to_unit_enum)
{
map<units, map<units, double> > conv;
@ -1026,7 +1052,7 @@ double get_temperature_conversion_factor(units from_unit_enum, units to_unit_enu
/* ---------------------------------------------------------------------- */
// Pressure conversion
double get_pressure_conversion_factor(units from_unit_enum, units to_unit_enum)
double kim_units::get_pressure_conversion_factor(units from_unit_enum, units to_unit_enum)
{
map<units, map<units, double> > conv;
double to_si;
@ -1084,7 +1110,7 @@ double get_pressure_conversion_factor(units from_unit_enum, units to_unit_enum)
/* ---------------------------------------------------------------------- */
// Viscosity conversion
double get_viscosity_conversion_factor(units from_unit_enum, units to_unit_enum)
double kim_units::get_viscosity_conversion_factor(units from_unit_enum, units to_unit_enum)
{
map<units, map<units, double> > conv;
double to_si;
@ -1129,7 +1155,7 @@ double get_viscosity_conversion_factor(units from_unit_enum, units to_unit_enum)
/* ---------------------------------------------------------------------- */
// Charge conversion
double get_charge_conversion_factor(units from_unit_enum, units to_unit_enum)
double kim_units::get_charge_conversion_factor(units from_unit_enum, units to_unit_enum)
{
map<units, map<units, double> > conv;
double to_si;
@ -1163,7 +1189,7 @@ double get_charge_conversion_factor(units from_unit_enum, units to_unit_enum)
/* ---------------------------------------------------------------------- */
// Dipole conversion
double get_dipole_conversion_factor(units from_unit_enum, units to_unit_enum)
double kim_units::get_dipole_conversion_factor(units from_unit_enum, units to_unit_enum)
{
map<units, map<units, double> > conv;
double to_si;
@ -1221,7 +1247,7 @@ double get_dipole_conversion_factor(units from_unit_enum, units to_unit_enum)
/* ---------------------------------------------------------------------- */
// Electric field conversion
double get_efield_conversion_factor(units from_unit_enum, units to_unit_enum)
double kim_units::get_efield_conversion_factor(units from_unit_enum, units to_unit_enum)
{
map<units, map<units, double> > conv;
double to_si;
@ -1278,8 +1304,8 @@ double get_efield_conversion_factor(units from_unit_enum, units to_unit_enum)
/* ---------------------------------------------------------------------- */
// Demsity conversion
double get_density_conversion_factor(units from_unit_enum, units to_unit_enum)
// Density conversion
double kim_units::get_density_conversion_factor(units from_unit_enum, units to_unit_enum)
{
map<units, map<units, double> > conv;
double to_si;
@ -1325,9 +1351,9 @@ double get_density_conversion_factor(units from_unit_enum, units to_unit_enum)
// This routine returns the unit conversion factor between the
// `from_system_enum` to the `to_system_enum` for the `unit_type_enum`.
double get_unit_conversion_factor(unit_type &unit_type_enum,
sys_type from_system_enum,
sys_type to_system_enum)
double kim_units::get_unit_conversion_factor(unit_type &unit_type_enum,
sys_type from_system_enum,
sys_type to_system_enum)
{
units from_unit = get_lammps_system_unit(from_system_enum, unit_type_enum);
units to_unit = get_lammps_system_unit(to_system_enum, unit_type_enum);
@ -1364,48 +1390,87 @@ double get_unit_conversion_factor(unit_type &unit_type_enum,
}
}
} // end of anonymous name space
/* ---------------------------------------------------------------------- */
// clang-format on
// Wrapper to the routine that gets the unit conversion. Translates strings
// to enumerations and then call get_unit_conversion_factor()
int lammps_unit_conversion(const string &unit_type_str,
const string &from_system_str,
const string &to_system_str,
double &conversion_factor)
int kim_units::lammps_unit_conversion(const string &unit_type_str, const string &from_system_str,
const string &to_system_str, double &conversion_factor)
{
// initialize
conversion_factor = 0.0;
initialize_dictionaries();
// initialize
conversion_factor = 0.0;
initialize_dictionaries();
// convert input to enumeration
unit_type unit_type_enum;
{
map<string, unit_type>::const_iterator itr = unit_dic.find(unit_type_str);
if (itr != unit_dic.end()) unit_type_enum = itr->second;
else return 1; // error
}
sys_type from_system_enum;
{
map<string, sys_type>::const_iterator
itr = system_dic.find(from_system_str);
if (itr != system_dic.end()) from_system_enum = itr->second;
else return 1; // error
}
sys_type to_system_enum;
{
map<string, sys_type>::const_iterator
itr = system_dic.find(to_system_str);
if (itr != system_dic.end()) to_system_enum = itr->second;
else return 1;
}
// convert input to enumeration
unit_type unit_type_enum;
{
map<string, unit_type>::const_iterator itr = unit_dic.find(unit_type_str);
if (itr != unit_dic.end())
unit_type_enum = itr->second;
else
return 1; // error
}
sys_type from_system_enum;
{
map<string, sys_type>::const_iterator itr = system_dic.find(from_system_str);
if (itr != system_dic.end())
from_system_enum = itr->second;
else
return 1; // error
}
sys_type to_system_enum;
{
map<string, sys_type>::const_iterator itr = system_dic.find(to_system_str);
if (itr != system_dic.end())
to_system_enum = itr->second;
else
return 1;
}
// process unit conversions
conversion_factor = get_unit_conversion_factor(unit_type_enum,
from_system_enum,
to_system_enum);
return 0;
// process unit conversions
conversion_factor = get_unit_conversion_factor(unit_type_enum, from_system_enum, to_system_enum);
return 0;
}
void kim_units::get_kim_unit_names(char const *const system, KIM_LengthUnit &lengthUnit,
KIM_EnergyUnit &energyUnit, KIM_ChargeUnit &chargeUnit,
KIM_TemperatureUnit &temperatureUnit, KIM_TimeUnit &timeUnit,
Error *error)
{
const std::string system_str(system);
if (system_str == "real") {
lengthUnit = KIM_LENGTH_UNIT_A;
energyUnit = KIM_ENERGY_UNIT_kcal_mol;
chargeUnit = KIM_CHARGE_UNIT_e;
temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_fs;
} else if (system_str == "metal") {
lengthUnit = KIM_LENGTH_UNIT_A;
energyUnit = KIM_ENERGY_UNIT_eV;
chargeUnit = KIM_CHARGE_UNIT_e;
temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_ps;
} else if (system_str == "si") {
lengthUnit = KIM_LENGTH_UNIT_m;
energyUnit = KIM_ENERGY_UNIT_J;
chargeUnit = KIM_CHARGE_UNIT_C;
temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_s;
} else if (system_str == "cgs") {
lengthUnit = KIM_LENGTH_UNIT_cm;
energyUnit = KIM_ENERGY_UNIT_erg;
chargeUnit = KIM_CHARGE_UNIT_statC;
temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_s;
} else if (system_str == "electron") {
lengthUnit = KIM_LENGTH_UNIT_Bohr;
energyUnit = KIM_ENERGY_UNIT_Hartree;
chargeUnit = KIM_CHARGE_UNIT_e;
temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_fs;
} else if ((system_str == "lj") || (system_str == "micro") || (system_str == "nano")) {
error->all(FLERR, "LAMMPS unit_style {} not supported by KIM models", system_str);
} else {
error->all(FLERR, "Unknown unit_style {}", system_str);
}
}

17
src/KIM/kim_units.h
View File

@ -56,7 +56,20 @@
#define LMP_KIM_UNITS_H
#include <string>
extern "C" {
#include "KIM_SimulatorHeaders.h"
}
int lammps_unit_conversion(const std::string &unit_type_str, const std::string &from_system_str,
const std::string &to_system_str, double &conversion_factor);
namespace LAMMPS_NS {
class Error;
namespace kim_units {
int lammps_unit_conversion(const std::string &unit_type_str, const std::string &from_system_str,
const std::string &to_system_str, double &conversion_factor);
void get_kim_unit_names(char const *const system, KIM_LengthUnit &lengthUnit,
KIM_EnergyUnit &energyUnit, KIM_ChargeUnit &chargeUnit,
KIM_TemperatureUnit &temperatureUnit, KIM_TimeUnit &timeUnit,
Error *error);
} // namespace kim_units
} // namespace LAMMPS_NS
#endif

21
src/KIM/pair_kim.cpp
View File

@ -218,8 +218,7 @@ void PairKIM::compute(int eflag, int vflag)
kim_particleSpecies);
memory->create(kim_particleContributing,lmps_maxalloc,
"pair:kim_particleContributing");
kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerInteger(
pargs,
kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerInteger(pargs,
KIM_COMPUTE_ARGUMENT_NAME_particleContributing,
kim_particleContributing);
if (kimerror)
@ -248,7 +247,7 @@ void PairKIM::compute(int eflag, int vflag)
// compute via KIM model
int kimerror = KIM_Model_Compute(pkim, pargs);
if (kimerror) error->all(FLERR,"KIM Compute returned error");
if (kimerror) error->all(FLERR,"KIM Compute returned error {}", kimerror);
// compute virial before reverse comm!
if (vflag_global)
@ -454,7 +453,7 @@ void PairKIM::coeff(int narg, char **arg)
kimerror = KIM_Model_GetParameterMetadata(pkim, param_index, &kim_DataType,
&extent, &str_name, &str_desc);
if (kimerror)
error->all(FLERR,"KIM GetParameterMetadata returned error");
error->all(FLERR,"KIM GetParameterMetadata returned error {}", kimerror);
const std::string str_name_str(str_name);
if (paramname == str_name_str) break;
@ -484,8 +483,8 @@ void PairKIM::coeff(int narg, char **arg)
nubound = atoi(words[1].c_str());
if ((nubound < 1) || (nubound > extent) || (nlbound < 1) || (nlbound > nubound))
error->all(FLERR,"Illegal index_range '{}-{}' for '{}' parameter with the extent of '{}'",
nlbound, nubound, paramname, extent);
error->all(FLERR,"Illegal index_range '{}-{}' for '{}' parameter with the extent "
"of '{}'", nlbound, nubound, paramname, extent);
} else {
nlbound = atoi(argtostr.c_str());
@ -975,7 +974,7 @@ void PairKIM::set_lmps_flags()
// determine if running with pair hybrid
if (force->pair_match("hybrid",0))
error->all(FLERR,"pair_kim does not support hybrid");
error->all(FLERR,"Pair style must not be used as a hybrid sub-style");
const std::string unit_style_str(update->unit_style);
@ -1018,10 +1017,9 @@ void PairKIM::set_lmps_flags()
} else if ((unit_style_str == "lj") ||
(unit_style_str == "micro") ||
(unit_style_str == "nano")) {
error->all(FLERR,"LAMMPS unit_style {} not supported "
"by KIM models", unit_style_str);
error->all(FLERR,"LAMMPS unit_style {} not supported by KIM models", unit_style_str);
} else {
error->all(FLERR,"Unknown unit_style");
error->all(FLERR,"Unknown unit_style {}", unit_style_str);
}
}
@ -1100,7 +1098,8 @@ void PairKIM::set_kim_model_has_flags()
if (comm->me == 0) {
if (KIM_SupportStatus_Equal(kim_model_support_for_energy, KIM_SUPPORT_STATUS_notSupported))
error->warning(FLERR,"KIM Model does not provide 'partialEnergy'; Potential energy will be zero");
error->warning(FLERR,"KIM Model does not provide 'partialEnergy'; "
"Potential energy will be zero");
if (KIM_SupportStatus_Equal(kim_model_support_for_forces,
KIM_SUPPORT_STATUS_notSupported))

38
src/KOKKOS/fix_property_atom_kokkos.cpp
View File

@ -24,8 +24,6 @@
using namespace LAMMPS_NS;
using namespace FixConst;
enum{MOLECULE,CHARGE,RMASS,INTEGER,DOUBLE};
/* ---------------------------------------------------------------------- */
FixPropertyAtomKokkos::FixPropertyAtomKokkos(LAMMPS *lmp, int narg, char **arg) :
@ -44,33 +42,45 @@ FixPropertyAtomKokkos::FixPropertyAtomKokkos(LAMMPS *lmp, int narg, char **arg)
void FixPropertyAtomKokkos::grow_arrays(int nmax)
{
for (int m = 0; m < nvalue; m++) {
if (styles[m] == MOLECULE) {
for (int nv = 0; nv < nvalue; nv++) {
if (styles[nv] == MOLECULE) {
memory->grow(atom->molecule,nmax,"atom:molecule");
size_t nbytes = (nmax-nmax_old) * sizeof(tagint);
memset(&atom->molecule[nmax_old],0,nbytes);
} else if (styles[m] == CHARGE) {
} else if (styles[nv] == CHARGE) {
memory->grow(atom->q,nmax,"atom:q");
size_t nbytes = (nmax-nmax_old) * sizeof(double);
memset(&atom->q[nmax_old],0,nbytes);
} else if (styles[m] == RMASS) {
} else if (styles[nv] == RMASS) {
memory->grow(atom->rmass,nmax,"atom:rmass");
size_t nbytes = (nmax-nmax_old) * sizeof(double);
memset(&atom->rmass[nmax_old],0,nbytes);
} else if (styles[m] == INTEGER) {
memory->grow(atom->ivector[index[m]],nmax,"atom:ivector");
} else if (styles[nv] == TEMPERATURE) {
memory->grow(atom->temperature, nmax, "atom:temperature");
size_t nbytes = (nmax - nmax_old) * sizeof(double);
memset(&atom->temperature[nmax_old], 0, nbytes);
} else if (styles[nv] == HEATFLOW) {
memory->grow(atom->heatflow, nmax, "atom:heatflow");
size_t nbytes = (nmax - nmax_old) * sizeof(double);
memset(&atom->heatflow[nmax_old], 0, nbytes);
} else if (styles[nv] == IVEC) {
memory->grow(atom->ivector[index[nv]],nmax,"atom:ivector");
size_t nbytes = (nmax-nmax_old) * sizeof(int);
memset(&atom->ivector[index[m]][nmax_old],0,nbytes);
} else if (styles[m] == DOUBLE) {
memset(&atom->ivector[index[nv]][nmax_old],0,nbytes);
} else if (styles[nv] == DVEC) {
atomKK->sync(Device,DVECTOR_MASK);
memoryKK->grow_kokkos(atomKK->k_dvector,atomKK->dvector,atomKK->k_dvector.extent(0),nmax,
"atom:dvector");
atomKK->modified(Device,DVECTOR_MASK);
//memory->grow(atom->dvector[index[m]],nmax,"atom:dvector");
//size_t nbytes = (nmax-nmax_old) * sizeof(double);
//memset(&atom->dvector[index[m]][nmax_old],0,nbytes);
} else if (styles[nv] == IARRAY) {
memory->grow(atom->iarray[index[nv]], nmax, cols[nv], "atom:iarray");
size_t nbytes = (size_t) (nmax - nmax_old) * cols[nv] * sizeof(int);
if (nbytes) memset(&atom->iarray[index[nv]][nmax_old][0], 0, nbytes);
} else if (styles[nv] == DARRAY) {
memory->grow(atom->darray[index[nv]], nmax, cols[nv], "atom:darray");
size_t nbytes = (size_t) (nmax - nmax_old) * cols[nv] * sizeof(double);
if (nbytes) memset(&atom->darray[index[nv]][nmax_old][0], 0, nbytes);
}
}
nmax_old = nmax;
}

215
src/KOKKOS/fix_rx_kokkos.cpp
View File

@ -74,23 +74,17 @@ FixRxKokkos<DeviceType>::FixRxKokkos(LAMMPS *lmp, int narg, char **arg) :
datamask_modify = EMPTY_MASK;
k_error_flag = DAT::tdual_int_scalar("FixRxKokkos::k_error_flag");
//printf("Inside FixRxKokkos::FixRxKokkos\n");
}
template <typename DeviceType>
FixRxKokkos<DeviceType>::~FixRxKokkos()
{
//printf("Inside FixRxKokkos::~FixRxKokkos copymode= %d\n", copymode);
if (copymode) return;
if (localTempFlag)
memoryKK->destroy_kokkos(k_dpdThetaLocal, dpdThetaLocal);
memoryKK->destroy_kokkos(k_sumWeights, sumWeights);
//memoryKK->destroy_kokkos(k_sumWeights);
//delete [] scratchSpace;
memoryKK->destroy_kokkos(d_scratchSpace);
memoryKK->destroy_kokkos(k_cutsq);
@ -147,7 +141,6 @@ void FixRxKokkos<DeviceType>::init()
template <typename DeviceType>
void FixRxKokkos<DeviceType>::init_list(int, class NeighList* ptr)
{
//printf("Inside FixRxKokkos::init_list\n");
this->list = ptr;
}
@ -551,7 +544,6 @@ void FixRxKokkos<DeviceType>::k_rkf45(const int neq, const double t_stop, Vector
nfe += 6;
if (maxIters && nit > maxIters) {
//fprintf(stderr,"atom[%d] took too many iterations in rkf45 %d %e %e\n", id, nit, t, t_stop);
counter.nFails ++;
break;
// We should set an error here so that the solution is not used!
@ -562,8 +554,6 @@ void FixRxKokkos<DeviceType>::k_rkf45(const int neq, const double t_stop, Vector
counter.nSteps += nst;
counter.nIters += nit;
counter.nFuncs += nfe;
//printf("id= %d nst= %d nit= %d\n", id, nst, nit);
}
/* ---------------------------------------------------------------------- */
@ -733,9 +723,6 @@ int FixRxKokkos<DeviceType>::rkf45_h0(const int neq, const double t, const doubl
yddnrm = sqrt( yddnrm / double(neq) );
//std::cout << "iter " << _iter << " hg " << hg << " y'' " << yddnrm << std::endl;
//std::cout << "ydot " << ydot[neq-1] << std::endl;
// should we accept this?
if (hnew_is_ok || iter == max_iters) {
hnew = hg;
@ -760,8 +747,6 @@ int FixRxKokkos<DeviceType>::rkf45_h0(const int neq, const double t, const doubl
hnew_is_ok = true;
}
//printf("iter=%d, yddnrw=%e, hnew=%e, hmin=%e, hmax=%e\n", iter, yddnrm, hnew, hmin, hmax);
hg = hnew;
iter ++;
}
@ -805,13 +790,9 @@ void FixRxKokkos<DeviceType>::rkf45(const int neq, const double t_stop, double *
double t = 0.0;
if (h < h_min) {
//fprintf(stderr,"hin not implemented yet\n");
//exit(-1);
nfe = rkf45_h0 (neq, t, t_stop, h_min, h_max, h, y, rwork, v_param);
}
//printf("t= %e t_stop= %e h= %e\n", t, t_stop, h);
// Integrate until we reach the end time.
while (fabs(t - t_stop) > tround) {
double *yout = rwork;
@ -865,7 +846,6 @@ void FixRxKokkos<DeviceType>::rkf45(const int neq, const double t_stop, double *
nfe += 6;
if (maxIters && nit > maxIters) {
//fprintf(stderr,"atom[%d] took too many iterations in rkf45 %d %e %e\n", id, nit, t, t_stop);
counter.nFails ++;
break;
// We should set an error here so that the solution is not used!
@ -876,8 +856,6 @@ void FixRxKokkos<DeviceType>::rkf45(const int neq, const double t_stop, double *
counter.nSteps += nst;
counter.nIters += nit;
counter.nFuncs += nfe;
//printf("id= %d nst= %d nit= %d\n", id, nst, nit);
}
/* ---------------------------------------------------------------------- */
@ -902,9 +880,6 @@ int FixRxKokkos<DeviceType>::rhs_dense(double /*t*/, const double *y, double *dy
double *rxnRateLaw = userData->rxnRateLaw;
double *kFor = userData->kFor;
//const double VDPD = domain->xprd * domain->yprd * domain->zprd / atom->natoms;
//const int nspecies = atom->nspecies_dpd;
for (int ispecies=0; ispecies<nspecies; ispecies++)
dydt[ispecies] = 0.0;
@ -915,7 +890,6 @@ int FixRxKokkos<DeviceType>::rhs_dense(double /*t*/, const double *y, double *dy
for (int ispecies=0; ispecies<nspecies; ispecies++) {
const double concentration = y[ispecies]/VDPD;
rxnRateLawForward *= pow( concentration, d_kineticsData.stoichReactants(jrxn,ispecies) );
//rxnRateLawForward *= pow(concentration,stoichReactants[jrxn][ispecies]);
}
rxnRateLaw[jrxn] = rxnRateLawForward;
}
@ -925,7 +899,6 @@ int FixRxKokkos<DeviceType>::rhs_dense(double /*t*/, const double *y, double *dy
for (int jrxn=0; jrxn<nreactions; jrxn++)
{
dydt[ispecies] += d_kineticsData.stoich(jrxn,ispecies) *VDPD*rxnRateLaw[jrxn];
//dydt[ispecies] += stoich[jrxn][ispecies]*VDPD*rxnRateLaw[jrxn];
}
return 0;
@ -938,8 +911,6 @@ int FixRxKokkos<DeviceType>::rhs_sparse(double /*t*/, const double *y, double *d
{
UserRHSData *userData = (UserRHSData *) v_params;
//const double VDPD = domain->xprd * domain->yprd * domain->zprd / atom->natoms;
#define kFor (userData->kFor)
#define kRev (nullptr)
#define rxnRateLaw (userData->rxnRateLaw)
@ -964,7 +935,6 @@ int FixRxKokkos<DeviceType>::rhs_sparse(double /*t*/, const double *y, double *d
for (int kk = 1; kk < maxReactants; ++kk) {
const int k = nuk(i,kk);
if (k == SparseKinetics_invalidIndex) break;
//if (k != SparseKinetics_invalidIndex)
rxnRateLawForward *= powint( conc[k], inu(i,kk) );
}
} else {
@ -972,7 +942,6 @@ int FixRxKokkos<DeviceType>::rhs_sparse(double /*t*/, const double *y, double *d
for (int kk = 1; kk < maxReactants; ++kk) {
const int k = nuk(i,kk);
if (k == SparseKinetics_invalidIndex) break;
//if (k != SparseKinetics_invalidIndex)
rxnRateLawForward *= pow( conc[k], nu(i,kk) );
}
}
@ -991,7 +960,6 @@ int FixRxKokkos<DeviceType>::rhs_sparse(double /*t*/, const double *y, double *d
for (int kk = 1; kk < maxReactants; ++kk) {
const int k = nuk(i,kk);
if (k == SparseKinetics_invalidIndex) break;
//if (k != SparseKinetics_invalidIndex)
dydt[k] -= nu(i,kk) * rxnRateLaw[i];
}
@ -1000,7 +968,6 @@ int FixRxKokkos<DeviceType>::rhs_sparse(double /*t*/, const double *y, double *d
for (int kk = maxReactants+1; kk < maxSpecies; ++kk) {
const int k = nuk(i,kk);
if (k == SparseKinetics_invalidIndex) break;
//if (k != SparseKinetics_invalidIndex)
dydt[k] += nu(i,kk) * rxnRateLaw[i];
}
}
@ -1048,9 +1015,6 @@ int FixRxKokkos<DeviceType>::k_rhs_dense(double /*t*/, const VectorType& y, Vect
#define rxnRateLaw (userData.rxnRateLaw)
#define kFor (userData.kFor )
//const double VDPD = domain->xprd * domain->yprd * domain->zprd / atom->natoms;
//const int nspecies = atom->nspecies_dpd;
for (int ispecies=0; ispecies<nspecies; ispecies++)
dydt[ispecies] = 0.0;
@ -1061,7 +1025,6 @@ int FixRxKokkos<DeviceType>::k_rhs_dense(double /*t*/, const VectorType& y, Vect
for (int ispecies=0; ispecies<nspecies; ispecies++) {
const double concentration = y[ispecies]/VDPD;
rxnRateLawForward *= pow( concentration, d_kineticsData.stoichReactants(jrxn,ispecies) );
//rxnRateLawForward *= pow(concentration,stoichReactants[jrxn][ispecies]);
}
rxnRateLaw[jrxn] = rxnRateLawForward;
}
@ -1071,7 +1034,6 @@ int FixRxKokkos<DeviceType>::k_rhs_dense(double /*t*/, const VectorType& y, Vect
for (int jrxn=0; jrxn<nreactions; jrxn++)
{
dydt[ispecies] += d_kineticsData.stoich(jrxn,ispecies) *VDPD*rxnRateLaw[jrxn];
//dydt[ispecies] += stoich[jrxn][ispecies]*VDPD*rxnRateLaw[jrxn];
}
#undef rxnRateLaw
@ -1111,7 +1073,6 @@ int FixRxKokkos<DeviceType>::k_rhs_sparse(double /*t*/, const VectorType& y, Vec
for (int kk = 1; kk < maxReactants; ++kk) {
const int k = nuk(i,kk);
if (k == SparseKinetics_invalidIndex) break;
//if (k != SparseKinetics_invalidIndex)
rxnRateLawForward *= powint( conc[k], inu(i,kk) );
}
} else {
@ -1119,7 +1080,6 @@ int FixRxKokkos<DeviceType>::k_rhs_sparse(double /*t*/, const VectorType& y, Vec
for (int kk = 1; kk < maxReactants; ++kk) {
const int k = nuk(i,kk);
if (k == SparseKinetics_invalidIndex) break;
//if (k != SparseKinetics_invalidIndex)
rxnRateLawForward *= pow( conc[k], nu(i,kk) );
}
}
@ -1138,7 +1098,6 @@ int FixRxKokkos<DeviceType>::k_rhs_sparse(double /*t*/, const VectorType& y, Vec
for (int kk = 1; kk < maxReactants; ++kk) {
const int k = nuk(i,kk);
if (k == SparseKinetics_invalidIndex) break;
//if (k != SparseKinetics_invalidIndex)
dydt[k] -= nu(i,kk) * rxnRateLaw[i];
}
@ -1147,7 +1106,6 @@ int FixRxKokkos<DeviceType>::k_rhs_sparse(double /*t*/, const VectorType& y, Vec
for (int kk = maxReactants+1; kk < maxSpecies; ++kk) {
const int k = nuk(i,kk);
if (k == SparseKinetics_invalidIndex) break;
//if (k != SparseKinetics_invalidIndex)
dydt[k] += nu(i,kk) * rxnRateLaw[i];
}
}
@ -1215,8 +1173,6 @@ void FixRxKokkos<DeviceType>::operator()(SolverType, const int &i) const
template <typename DeviceType>
void FixRxKokkos<DeviceType>::create_kinetics_data()
{
//printf("Inside FixRxKokkos::create_kinetics_data\n");
memoryKK->create_kokkos( d_kineticsData.Arr, h_kineticsData.Arr, nreactions, "KineticsType::Arr");
memoryKK->create_kokkos( d_kineticsData.nArr, h_kineticsData.nArr, nreactions, "KineticsType::nArr");
memoryKK->create_kokkos( d_kineticsData.Ea, h_kineticsData.Ea, nreactions, "KineticsType::Ea");
@ -1296,8 +1252,6 @@ void FixRxKokkos<DeviceType>::create_kinetics_data()
template <typename DeviceType>
void FixRxKokkos<DeviceType>::setup_pre_force(int vflag)
{
//printf("Inside FixRxKokkos<DeviceType>::setup_pre_force restartFlag= %d\n", my_restartFlag);
if (my_restartFlag)
my_restartFlag = 0;
else
@ -1309,8 +1263,6 @@ void FixRxKokkos<DeviceType>::setup_pre_force(int vflag)
template <typename DeviceType>
void FixRxKokkos<DeviceType>::pre_force(int vflag)
{
//printf("Inside FixRxKokkos<DeviceType>::pre_force localTempFlag= %d\n", localTempFlag);
this->solve_reactions( vflag, true );
}
@ -1407,8 +1359,6 @@ void FixRxKokkos<DeviceType>::operator()(Tag_FixRxKokkos_solveSystems<ZERO_RATES
template <typename DeviceType>
void FixRxKokkos<DeviceType>::solve_reactions(const int /*vflag*/, const bool isPreForce)
{
//printf("Inside FixRxKokkos<DeviceType>::solve_reactions localTempFlag= %d isPreForce= %s\n", localTempFlag, isPreForce ? "True" : "false");
copymode = 1;
if (update_kinetics_data)
@ -1416,7 +1366,6 @@ void FixRxKokkos<DeviceType>::solve_reactions(const int /*vflag*/, const bool is
//TimerType timer_start = getTimeStamp();
//const int nlocal = atom->nlocal;
this->nlocal = atom->nlocal;
const int nghost = atom->nghost;
const int newton_pair = force->newton_pair;
@ -1477,9 +1426,6 @@ void FixRxKokkos<DeviceType>::solve_reactions(const int /*vflag*/, const bool is
// ...
// Local references to the atomKK objects.
//typename ArrayTypes<DeviceType>::t_efloat_1d d_dpdTheta = atomKK->k_dpdTheta.view<DeviceType>();
//typename ArrayTypes<DeviceType>::t_float_2d d_dvector = atomKK->k_dvector.view<DeviceType>();
//typename ArrayTypes<DeviceType>::t_int_1d d_mask = atomKK->k_mask.view<DeviceType>();
this->d_dpdTheta = atomKK->k_dpdTheta.view<DeviceType>();
this->d_dvector = atomKK->k_dvector.view<DeviceType>();
this->d_mask = atomKK->k_mask.view<DeviceType>();
@ -1488,8 +1434,6 @@ void FixRxKokkos<DeviceType>::solve_reactions(const int /*vflag*/, const bool is
atomKK->sync( execution_space, MASK_MASK | DVECTOR_MASK | DPDTHETA_MASK );
// Set some constants outside of the parallel_for
//const double boltz = force->boltz;
//const double t_stop = update->dt; // DPD time-step and integration length.
this->boltz = force->boltz;
this->t_stop = update->dt; // DPD time-step and integration length.
@ -1505,13 +1449,6 @@ void FixRxKokkos<DeviceType>::solve_reactions(const int /*vflag*/, const bool is
d_diagnosticCounterPerODEnFuncs = k_diagnosticCounterPerODEnFuncs.template view<DeviceType>();
Kokkos::parallel_for ( Kokkos::RangePolicy<DeviceType, Tag_FixRxKokkos_zeroCounterViews>(0,nlocal), *this);
//Kokkos::parallel_for ( nlocal,
// LAMMPS_LAMBDA(const int i)
// {
// d_diagnosticCounterPerODEnSteps(i) = 0;
// d_diagnosticCounterPerODEnFuncs(i) = 0;
// }
// );
}
// Error flag for any failures.
@ -1523,116 +1460,17 @@ void FixRxKokkos<DeviceType>::solve_reactions(const int /*vflag*/, const bool is
k_error_flag.template sync<DeviceType>();
// Create scratch array space.
//const size_t scratchSpaceSize = (8*nspecies + 2*nreactions);
this->scratchSpaceSize = (8*nspecies + 2*nreactions);
//double *scratchSpace = new double[ scratchSpaceSize * nlocal ];
//typename ArrayTypes<DeviceType>::t_double_1d d_scratchSpace("d_scratchSpace", scratchSpaceSize * nlocal);
if (nlocal*scratchSpaceSize > d_scratchSpace.extent(0)) {
memoryKK->destroy_kokkos (d_scratchSpace);
memoryKK->create_kokkos (d_scratchSpace, nlocal*scratchSpaceSize, "FixRxKokkos::d_scratchSpace");
}
#if 0
Kokkos::parallel_reduce( nlocal, LAMMPS_LAMBDA(int i, CounterType &counter)
{
if (d_mask(i) & groupbit)
{
//double *y = new double[8*nspecies];
//double *rwork = y + nspecies;
//StridedArrayType<double,1> _y( y );
//StridedArrayType<double,1> _rwork( rwork );
StridedArrayType<double,1> y( d_scratchSpace.data() + scratchSpaceSize * i );
StridedArrayType<double,1> rwork( &y[nspecies] );
//UserRHSData userData;
//userData.kFor = new double[nreactions];
//userData.rxnRateLaw = new double[nreactions];
//UserRHSDataKokkos<1> userDataKokkos;
//userDataKokkos.kFor.m_data = userData.kFor;
//userDataKokkos.rxnRateLaw.m_data = userData.rxnRateLaw;
UserRHSDataKokkos<1> userData;
userData.kFor.m_data = &( rwork[7*nspecies] );
userData.rxnRateLaw.m_data = &( userData.kFor[ nreactions ] );
CounterType counter_i;
const double theta = (localTempFlag) ? d_dpdThetaLocal(i) : d_dpdTheta(i);
//Compute the reaction rate constants
for (int irxn = 0; irxn < nreactions; irxn++)
{
if (setRatesToZero)
userData.kFor[irxn] = 0.0;
else
{
userData.kFor[irxn] = d_kineticsData.Arr(irxn) *
pow(theta, d_kineticsData.nArr(irxn)) *
exp(-d_kineticsData.Ea(irxn) / boltz / theta);
}
}
// Update ConcOld and initialize the ODE solution vector y[].
for (int ispecies = 0; ispecies < nspecies; ispecies++)
{
const double tmp = d_dvector(ispecies, i);
d_dvector(ispecies+nspecies, i) = tmp;
y[ispecies] = tmp;
}
// Solver the ODE system.
if (odeIntegrationFlag == ODE_LAMMPS_RK4)
{
k_rk4(t_stop, y, rwork, userData);
}
else if (odeIntegrationFlag == ODE_LAMMPS_RKF45)
{
k_rkf45(nspecies, t_stop, y, rwork, userData, counter_i);
if (diagnosticFrequency == 1)
{
d_diagnosticCounterPerODEnSteps(i) = counter_i.nSteps;
d_diagnosticCounterPerODEnFuncs(i) = counter_i.nFuncs;
}
}
// Store the solution back in dvector.
for (int ispecies = 0; ispecies < nspecies; ispecies++)
{
if (y[ispecies] < -1.0e-10)
{
//error->one(FLERR,"Computed concentration in RK solver is < -1.0e-10");
k_error_flag.template view<DeviceType>()() = 2;
// This should be an atomic update.
}
else if (y[ispecies] < MY_EPSILON)
y[ispecies] = 0.0;
d_dvector(ispecies,i) = y[ispecies];
}
//delete [] y;
//delete [] userData.kFor;
//delete [] userData.rxnRateLaw;
// Update the iteration statistics counter. Is this unique for each iteration?
counter += counter_i;
} // if
} // parallel_for lambda-body
, TotalCounters // reduction value for all iterations.
);
#else
if (setRatesToZero)
Kokkos::parallel_reduce( Kokkos::RangePolicy<DeviceType, Tag_FixRxKokkos_solveSystems<true > >(0,nlocal), *this, TotalCounters);
else
Kokkos::parallel_reduce( Kokkos::RangePolicy<DeviceType, Tag_FixRxKokkos_solveSystems<false> >(0,nlocal), *this, TotalCounters);
#endif
TimerType timer_ODE = getTimeStamp();
@ -1652,16 +1490,8 @@ void FixRxKokkos<DeviceType>::solve_reactions(const int /*vflag*/, const bool is
atomKK->modified ( Host, DVECTOR_MASK );
//TimerType timer_stop = getTimeStamp();
double time_ODE = getElapsedTime(timer_localTemperature, timer_ODE);
//printf("me= %d kokkos total= %g temp= %g ode= %g comm= %g nlocal= %d nfc= %d %d\n", comm->me,
// getElapsedTime(timer_start, timer_stop),
// getElapsedTime(timer_start, timer_localTemperature),
// getElapsedTime(timer_localTemperature, timer_ODE),
// getElapsedTime(timer_ODE, timer_stop), nlocal, TotalCounters.nFuncs, TotalCounters.nSteps);
// Warn the user if a failure was detected in the ODE solver.
if (TotalCounters.nFails > 0) {
char sbuf[128];
@ -1731,7 +1561,6 @@ void FixRxKokkos<DeviceType>::odeDiagnostics()
// Compute counters per dpd time-step.
for (int i = 0; i < numCounters; ++i) {
my_vals[i] = this->diagnosticCounter[i] / nTimes;
//printf("my sum[%d] = %f %d\n", i, my_vals[i], comm->me);
}
MPI_Allreduce (my_vals, sums, numCounters, MPI_DOUBLE, MPI_SUM, world);
@ -1770,7 +1599,6 @@ void FixRxKokkos<DeviceType>::odeDiagnostics()
double my_max[numCounters], my_min[numCounters];
//const int nlocal = atom->nlocal;
nlocal = atom->nlocal;
HAT::t_int_1d h_mask = atomKK->k_mask.h_view;
@ -1980,9 +1808,6 @@ template <typename DeviceType>
template <int WT_FLAG, int LOCAL_TEMP_FLAG, bool NEWTON_PAIR, int NEIGHFLAG>
void FixRxKokkos<DeviceType>::computeLocalTemperature()
{
//typename ArrayTypes<DeviceType>::t_x_array_randomread d_x = atomKK->k_x.view<DeviceType>();
//typename ArrayTypes<DeviceType>::t_int_1d_randomread d_type = atomKK->k_type.view<DeviceType>();
//typename ArrayTypes<DeviceType>::t_efloat_1d d_dpdTheta = atomKK->k_dpdTheta.view<DeviceType>();
d_x = atomKK->k_x.view<DeviceType>();
d_type = atomKK->k_type.view<DeviceType>();
d_dpdTheta = atomKK->k_dpdTheta.view<DeviceType>();
@ -1993,21 +1818,9 @@ void FixRxKokkos<DeviceType>::computeLocalTemperature()
nlocal = atom->nlocal;
const int nghost = atom->nghost;
//printf("Inside FixRxKokkos::computeLocalTemperature: %d %d %d %d %d %d %d\n", WT_FLAG, LOCAL_TEMP_FLAG, NEWTON_PAIR, (int)lmp->kokkos->neighflag, NEIGHFLAG, nlocal, nghost);
// Pull from pairDPDE. The pairDPDEKK objects are protected so recreate here for now.
//pairDPDEKK->k_cutsq.template sync<DeviceType>();
//typename ArrayTypes<DeviceType>::t_ffloat_2d d_cutsq = pairDPDEKK->k_cutsq.template view<DeviceType();
//!< Copies pulled from pairDPDE for local use since pairDPDEKK's objects are protected.
//typename ArrayTypes<DeviceType>::tdual_ffloat_2d k_cutsq;
//typename ArrayTypes<DeviceType>::t_ffloat_2d d_cutsq;
//double **h_cutsq;
{
const int ntypes = atom->ntypes;
//memoryKK->create_kokkos (k_cutsq, h_cutsq, ntypes+1, ntypes+1, "pair:cutsq");
if (ntypes+1 > (int) k_cutsq.extent(0)) {
memoryKK->destroy_kokkos (k_cutsq);
memoryKK->create_kokkos (k_cutsq, ntypes+1, ntypes+1, "FixRxKokkos::k_cutsq");
@ -2028,7 +1841,6 @@ void FixRxKokkos<DeviceType>::computeLocalTemperature()
// Initialize the local temperature weight array
int sumWeightsCt = nlocal + (NEWTON_PAIR ? nghost : 0);
//memoryKK->create_kokkos (k_sumWeights, sumWeights, sumWeightsCt, "FixRxKokkos::sumWeights");
if (sumWeightsCt > (int)k_sumWeights.template view<DeviceType>().extent(0)) {
memoryKK->destroy_kokkos(k_sumWeights, sumWeights);
memoryKK->create_kokkos (k_sumWeights, sumWeightsCt, "FixRxKokkos::sumWeights");
@ -2036,14 +1848,6 @@ void FixRxKokkos<DeviceType>::computeLocalTemperature()
h_sumWeights = k_sumWeights.h_view;
}
// Initialize the accumulator to zero ...
//Kokkos::parallel_for (sumWeightsCt,
// LAMMPS_LAMBDA(const int i)
// {
// d_sumWeights(i) = 0.0;
// }
// );
Kokkos::parallel_for (Kokkos::RangePolicy<DeviceType, Tag_FixRxKokkos_zeroTemperatureViews>(0, sumWeightsCt), *this);
// Local list views. (This isn't working!)
@ -2051,9 +1855,6 @@ void FixRxKokkos<DeviceType>::computeLocalTemperature()
if (!list->kokkos)
error->one(FLERR,"list is not a Kokkos list\n");
//typename ArrayTypes<DeviceType>::t_neighbors_2d d_neighbors = k_list->d_neighbors;
//typename ArrayTypes<DeviceType>::t_int_1d d_ilist = k_list->d_ilist;
//typename ArrayTypes<DeviceType>::t_int_1d d_numneigh = k_list->d_numneigh;
d_neighbors = k_list->d_neighbors;
d_ilist = k_list->d_ilist;
d_numneigh = k_list->d_numneigh;
@ -2067,7 +1868,6 @@ void FixRxKokkos<DeviceType>::computeLocalTemperature()
{
// Create an atomic view of sumWeights and dpdThetaLocal. Only needed
// for Half/thread scenarios.
//typedef Kokkos::View< E_FLOAT*, typename DAT::t_efloat_1d::array_layout, typename KKDevice<DeviceType>::value, Kokkos::MemoryTraits< AtomicF< NEIGHFLAG >::value> > AtomicViewType;
typedef Kokkos::View< E_FLOAT*, typename DAT::t_efloat_1d::array_layout, typename KKDevice<DeviceType>::value, Kokkos::MemoryTraits< AtomicF< NEIGHFLAG >::value> > AtomicViewType;
AtomicViewType a_dpdThetaLocal = d_dpdThetaLocal;
@ -2174,8 +1974,6 @@ void FixRxKokkos<DeviceType>::computeLocalTemperature()
template <typename DeviceType>
int FixRxKokkos<DeviceType>::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/)
{
//printf("inside FixRxKokkos::pack_forward_comm %d\n", comm->me);
HAT::t_float_2d h_dvector = atomKK->k_dvector.h_view;
int m = 0;
@ -2186,9 +1984,6 @@ int FixRxKokkos<DeviceType>::pack_forward_comm(int n, int *list, double *buf, in
buf[m++] = h_dvector(ispecies+nspecies,jj);
}
}
//printf("done with FixRxKokkos::pack_forward_comm %d\n", comm->me);
return m;
}
@ -2197,8 +1992,6 @@ int FixRxKokkos<DeviceType>::pack_forward_comm(int n, int *list, double *buf, in
template <typename DeviceType>
void FixRxKokkos<DeviceType>::unpack_forward_comm(int n, int first, double *buf)
{
//printf("inside FixRxKokkos::unpack_forward_comm %d\n", comm->me);
HAT::t_float_2d h_dvector = atomKK->k_dvector.h_view;
const int last = first + n ;
@ -2209,8 +2002,6 @@ void FixRxKokkos<DeviceType>::unpack_forward_comm(int n, int first, double *buf)
h_dvector(ispecies+nspecies,ii) = buf[m++];
}
}
//printf("done with FixRxKokkos::unpack_forward_comm %d\n", comm->me);
}
/* ---------------------------------------------------------------------- */
@ -2218,7 +2009,6 @@ void FixRxKokkos<DeviceType>::unpack_forward_comm(int n, int first, double *buf)
template <typename DeviceType>
int FixRxKokkos<DeviceType>::pack_reverse_comm(int n, int first, double *buf)
{
//printf("inside FixRxKokkos::pack_reverse_comm %d %d %d\n", comm->me, first, n);
// Sync the host view.
k_dpdThetaLocal.template sync<LMPHostType>();
k_sumWeights. template sync<LMPHostType>();
@ -2230,8 +2020,6 @@ int FixRxKokkos<DeviceType>::pack_reverse_comm(int n, int first, double *buf)
buf[m++] = h_dpdThetaLocal(i);
buf[m++] = h_sumWeights(i);
}
//printf("done with FixRxKokkos::pack_reverse_comm %d\n", comm->me);
return m;
}
@ -2240,7 +2028,6 @@ int FixRxKokkos<DeviceType>::pack_reverse_comm(int n, int first, double *buf)
template <typename DeviceType>
void FixRxKokkos<DeviceType>::unpack_reverse_comm(int n, int *list, double *buf)
{
// printf("inside FixRxKokkos::unpack_reverse_comm %d\n", comm->me);
int m = 0;
for (int i = 0; i < n; i++) {
const int j = list[i];
@ -2252,8 +2039,6 @@ void FixRxKokkos<DeviceType>::unpack_reverse_comm(int n, int *list, double *buf)
// Signal that the host view has been modified.
k_dpdThetaLocal.template modify<LMPHostType>();
k_sumWeights. template modify<LMPHostType>();
// printf("done with FixRxKokkos::unpack_reverse_comm %d\n", comm->me);
}
namespace LAMMPS_NS {

3
src/MANYBODY/pair_eam.cpp
View File

@ -852,8 +852,7 @@ double PairEAM::single(int i, int j, int itype, int jtype,
/* ---------------------------------------------------------------------- */
int PairEAM::pack_forward_comm(int n, int *list, double *buf,
int /*pbc_flag*/, int * /*pbc*/)
int PairEAM::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;

34
src/RIGID/fix_rigid.cpp
View File

@ -2523,9 +2523,17 @@ int FixRigid::pack_exchange(int i, double *buf)
buf[2] = displace[i][0];
buf[3] = displace[i][1];
buf[4] = displace[i][2];
if (!extended) return 5;
// must also pack vatom if per-atom virial calculated on this timestep
// since vatom is calculated before and after atom migration
int m = 5;
if (vflag_atom)
for (int k = 0; k < 6; k++)
buf[m++] = vatom[i][k];
if (!extended) return m;
buf[m++] = eflags[i];
for (int j = 0; j < orientflag; j++)
buf[m++] = orient[i][j];
@ -2535,13 +2543,6 @@ int FixRigid::pack_exchange(int i, double *buf)
buf[m++] = dorient[i][2];
}
// must also pack vatom if per-atom virial calculated on this timestep
// since vatom is calculated before and after atom migration
if (vflag_atom)
for (int k = 0; k < 6; k++)
buf[m++] = vatom[i][k];
return m;
}
@ -2556,9 +2557,17 @@ int FixRigid::unpack_exchange(int nlocal, double *buf)
displace[nlocal][0] = buf[2];
displace[nlocal][1] = buf[3];
displace[nlocal][2] = buf[4];
if (!extended) return 5;
// must also unpack vatom if per-atom virial calculated on this timestep
// since vatom is calculated before and after atom migration
int m = 5;
if (vflag_atom)
for (int k = 0; k < 6; k++)
vatom[nlocal][k] = buf[m++];
if (!extended) return m;
eflags[nlocal] = static_cast<int> (buf[m++]);
for (int j = 0; j < orientflag; j++)
orient[nlocal][j] = buf[m++];
@ -2568,13 +2577,6 @@ int FixRigid::unpack_exchange(int nlocal, double *buf)
dorient[nlocal][2] = buf[m++];
}
// must also unpack vatom if per-atom virial calculated on this timestep
// since vatom is calculated before and after atom migration
if (vflag_atom)
for (int k = 0; k < 6; k++)
vatom[nlocal][k] = buf[m++];
return m;
}

5
src/compute_chunk_atom.cpp
View File

@ -691,9 +691,10 @@ void ComputeChunkAtom::compute_ichunk()
if (invoked_ichunk == update->ntimestep) return;
// if old IDs persist via storage in fixstore, then just retrieve them
// yes if idsflag = ONCE, and already done once
// restore = yes if idsflag = ONCE, and already done once
// or if idsflag = NFREQ and lock is in place and are on later timestep
// else proceed to recalculate per-atom chunk assignments
// if restoring, update invoked_ichunk only for NFREQ case
const int nlocal = atom->nlocal;
int restore = 0;
@ -701,7 +702,7 @@ void ComputeChunkAtom::compute_ichunk()
if (idsflag == NFREQ && lockfix && update->ntimestep > lockstart) restore = 1;
if (restore) {
invoked_ichunk = update->ntimestep;
if (idsflag == NFREQ) invoked_ichunk = update->ntimestep;
double *vstore = fixstore->vstore;
for (i = 0; i < nlocal; i++) ichunk[i] = static_cast<int>(vstore[i]);
return;

70
src/fix_adapt.cpp
View File

@ -48,9 +48,9 @@ FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), nadapt(0), anypair(0), anybond(0), anyangle(0),
id_fix_diam(nullptr), id_fix_chg(nullptr), adapt(nullptr)
{
if (narg < 5) error->all(FLERR,"Illegal fix adapt command");
if (narg < 5) utils::missing_cmd_args(FLERR,"fix adapt", error);
nevery = utils::inumeric(FLERR,arg[3],false,lmp);
if (nevery < 0) error->all(FLERR,"Illegal fix adapt command");
if (nevery < 0) error->all(FLERR,"Illegal fix adapt every value {}", nevery);
dynamic_group_allow = 1;
create_attribute = 1;
@ -62,29 +62,29 @@ FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) :
int iarg = 4;
while (iarg < narg) {
if (strcmp(arg[iarg],"pair") == 0) {
if (iarg+6 > narg) error->all(FLERR,"Illegal fix adapt command");
if (iarg+6 > narg) utils::missing_cmd_args(FLERR,"fix adapt pair", error);
nadapt++;
iarg += 6;
} else if (strcmp(arg[iarg],"kspace") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix adapt command");
if (iarg+2 > narg) utils::missing_cmd_args(FLERR,"fix adapt kspace", error);
nadapt++;
iarg += 2;
} else if (strcmp(arg[iarg],"atom") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix adapt command");
if (iarg+3 > narg) utils::missing_cmd_args(FLERR,"fix adapt atom", error);
nadapt++;
iarg += 3;
} else if (strcmp(arg[iarg],"bond") == 0) {
if (iarg+5 > narg) error->all(FLERR,"Illegal fix adapt command");
if (iarg+5 > narg) utils::missing_cmd_args(FLERR,"fix adapt bond", error);
nadapt++;
iarg += 5;
} else if (strcmp(arg[iarg],"angle") == 0) {
if (iarg+5 > narg) error->all(FLERR,"Illegal fix adapt command");
if (iarg+5 > narg) utils::missing_cmd_args(FLERR,"fix adapt angle", error);
nadapt++;
iarg += 5;
} else break;
}
if (nadapt == 0) error->all(FLERR,"Illegal fix adapt command");
if (nadapt == 0) error->all(FLERR,"Nothing to adapt in fix adapt command");
adapt = new Adapt[nadapt];
// parse keywords
@ -96,7 +96,6 @@ FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) :
iarg = 4;
while (iarg < narg) {
if (strcmp(arg[iarg],"pair") == 0) {
if (iarg+6 > narg) error->all(FLERR,"Illegal fix adapt command");
adapt[nadapt].which = PAIR;
adapt[nadapt].pair = nullptr;
adapt[nadapt].pstyle = utils::strdup(arg[iarg+1]);
@ -107,12 +106,11 @@ FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) :
adapt[nadapt].jlo,adapt[nadapt].jhi,error);
if (utils::strmatch(arg[iarg+5],"^v_")) {
adapt[nadapt].var = utils::strdup(arg[iarg+5]+2);
} else error->all(FLERR,"Illegal fix adapt command");
} else error->all(FLERR,"Argument #{} must be variable not {}", iarg+6, arg[iarg+5]);
nadapt++;
iarg += 6;
} else if (strcmp(arg[iarg],"bond") == 0) {
if (iarg+5 > narg) error->all(FLERR, "Illegal fix adapt command");
adapt[nadapt].which = BOND;
adapt[nadapt].bond = nullptr;
adapt[nadapt].bstyle = utils::strdup(arg[iarg+1]);
@ -121,12 +119,11 @@ FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) :
adapt[nadapt].ilo,adapt[nadapt].ihi,error);
if (utils::strmatch(arg[iarg+4],"^v_")) {
adapt[nadapt].var = utils::strdup(arg[iarg+4]+2);
} else error->all(FLERR,"Illegal fix adapt command");
} else error->all(FLERR,"Argument #{} must be variable not {}", iarg+5, arg[iarg+4]);
nadapt++;
iarg += 5;
} else if (strcmp(arg[iarg],"angle") == 0) {
if (iarg+5 > narg) error->all(FLERR, "Illegal fix adapt command");
adapt[nadapt].which = ANGLE;
adapt[nadapt].angle = nullptr;
adapt[nadapt].astyle = utils::strdup(arg[iarg+1]);
@ -135,21 +132,19 @@ FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) :
adapt[nadapt].ilo,adapt[nadapt].ihi,error);
if (utils::strmatch(arg[iarg+4],"^v_")) {
adapt[nadapt].var = utils::strdup(arg[iarg+4]+2);
} else error->all(FLERR,"Illegal fix adapt command");
} else error->all(FLERR,"Argument #{} must be variable not {}", iarg+5, arg[iarg+4]);
nadapt++;
iarg += 5;
} else if (strcmp(arg[iarg],"kspace") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix adapt command");
adapt[nadapt].which = KSPACE;
if (utils::strmatch(arg[iarg+1],"^v_")) {
adapt[nadapt].var = utils::strdup(arg[iarg+1]+2);
} else error->all(FLERR,"Illegal fix adapt command");
} else error->all(FLERR,"Argument #{} must be variable not {}", iarg+2, arg[iarg+1]);
nadapt++;
iarg += 2;
} else if (strcmp(arg[iarg],"atom") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix adapt command");
adapt[nadapt].which = ATOM;
if (strcmp(arg[iarg+1],"diameter") == 0 ||
strcmp(arg[iarg+1],"diameter/disc") == 0) {
@ -160,10 +155,10 @@ FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg+1],"charge") == 0) {
adapt[nadapt].atomparam = CHARGE;
chgflag = 1;
} else error->all(FLERR,"Illegal fix adapt command");
} else error->all(FLERR,"Unsupported per-atom property {} for fix adapt", arg[iarg+1]);
if (utils::strmatch(arg[iarg+2],"^v_")) {
adapt[nadapt].var = utils::strdup(arg[iarg+2]+2);
} else error->all(FLERR,"Illegal fix adapt command");
} else error->all(FLERR,"Argument #{} must be variable not {}", iarg+3, arg[iarg+2]);
nadapt++;
iarg += 3;
} else break;
@ -177,18 +172,18 @@ FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) :
while (iarg < narg) {
if (strcmp(arg[iarg],"reset") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix adapt command");
if (iarg+2 > narg) utils::missing_cmd_args(FLERR,"fix adapt reset", error);
resetflag = utils::logical(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else if (strcmp(arg[iarg],"scale") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix adapt command");
if (iarg+2 > narg) utils::missing_cmd_args(FLERR,"fix adapt scale", error);
scaleflag = utils::logical(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else if (strcmp(arg[iarg],"mass") == 0) {
if (iarg+2 > narg)error->all(FLERR,"Illegal fix adapt command");
if (iarg+2 > narg) utils::missing_cmd_args(FLERR,"fix adapt mass", error);
massflag = utils::logical(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else error->all(FLERR,"Illegal fix adapt command");
} else error->all(FLERR,"Unknown fix adapt keyword {}", arg[iarg]);
}
// if scaleflag set with diameter or charge adaptation,
@ -202,22 +197,19 @@ FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) :
int n = atom->ntypes;
for (int m = 0; m < nadapt; m++)
if (adapt[m].which == PAIR)
memory->create(adapt[m].array_orig,n+1,n+1,"adapt:array_orig");
if (adapt[m].which == PAIR) memory->create(adapt[m].array_orig,n+1,n+1,"adapt:array_orig");
// allocate bond style arrays:
n = atom->nbondtypes;
for (int m = 0; m < nadapt; ++m)
if (adapt[m].which == BOND)
memory->create(adapt[m].vector_orig,n+1,"adapt:vector_orig");
if (adapt[m].which == BOND) memory->create(adapt[m].vector_orig,n+1,"adapt:vector_orig");
// allocate angle style arrays:
n = atom->nbondtypes;
for (int m = 0; m < nadapt; ++m)
if (adapt[m].which == ANGLE)
memory->create(adapt[m].vector_orig,n+1,"adapt:vector_orig");
if (adapt[m].which == ANGLE) memory->create(adapt[m].vector_orig,n+1,"adapt:vector_orig");
}
/* ---------------------------------------------------------------------- */
@ -324,7 +316,7 @@ void FixAdapt::init()
if (group->dynamic[igroup])
for (i = 0; i < nadapt; i++)
if (adapt[i].which == ATOM)
error->all(FLERR,"Cannot use dynamic group with fix adapt atom");
error->all(FLERR,"Cannot use dynamic group {} with fix adapt atom", group->names[igroup]);
// setup and error checks
@ -337,9 +329,9 @@ void FixAdapt::init()
ad->ivar = input->variable->find(ad->var);
if (ad->ivar < 0)
error->all(FLERR,"Variable name for fix adapt does not exist");
error->all(FLERR,"Variable name {} for fix adapt does not exist", ad->var);
if (!input->variable->equalstyle(ad->ivar))
error->all(FLERR,"Variable for fix adapt is invalid style");
error->all(FLERR,"Variable {} for fix adapt is invalid style", ad->var);
if (ad->which == PAIR) {
anypair = 1;
@ -368,13 +360,13 @@ void FixAdapt::init()
void *ptr = ad->pair->extract(ad->pparam,ad->pdim);
if (ptr == nullptr)
error->all(FLERR,"Fix adapt pair style param not supported");
error->all(FLERR,"Fix adapt pair style {} param {} not supported", ad->pstyle, ad->pparam);
// for pair styles only parameters that are 2-d arrays in atom types or
// scalars are supported
if (ad->pdim != 2 && ad->pdim != 0)
error->all(FLERR,"Fix adapt pair style param is not compatible");
error->all(FLERR,"Pair style parameter {} is not compatible with fix adapt", ad->pparam);
if (ad->pdim == 2) ad->array = (double **) ptr;
if (ad->pdim == 0) ad->scalar = (double *) ptr;
@ -402,12 +394,12 @@ void FixAdapt::init()
if (ad->bond == nullptr) ad->bond = force->bond_match(bstyle);
if (ad->bond == nullptr )
error->all(FLERR,"Fix adapt bond style does not exist");
error->all(FLERR,"Fix adapt bond style {} does not exist", bstyle);
void *ptr = ad->bond->extract(ad->bparam,ad->bdim);
if (ptr == nullptr)
error->all(FLERR,"Fix adapt bond style param not supported");
error->all(FLERR,"Fix adapt bond style parameter {} not supported", ad->bparam);
// for bond styles, use a vector
@ -428,12 +420,12 @@ void FixAdapt::init()
if (ad->angle == nullptr) ad->angle = force->angle_match(astyle);
if (ad->angle == nullptr )
error->all(FLERR,"Fix adapt angle style does not exist");
error->all(FLERR,"Fix adapt angle style {} does not exist", astyle);
void *ptr = ad->angle->extract(ad->aparam,ad->adim);
if (ptr == nullptr)
error->all(FLERR,"Fix adapt angle style param not supported");
error->all(FLERR,"Fix adapt angle style parameter {} not supported", ad->aparam);
// for angle styles, use a vector
@ -446,7 +438,7 @@ void FixAdapt::init()
} else if (ad->which == KSPACE) {
if (force->kspace == nullptr)
error->all(FLERR,"Fix adapt kspace style does not exist");
error->all(FLERR,"Fix adapt expected a kspace style but none was defined");
kspace_scale = (double *) force->kspace->extract("scale");
} else if (ad->which == ATOM) {

2
src/fix_property_atom.cpp
View File

@ -25,8 +25,6 @@
using namespace LAMMPS_NS;
using namespace FixConst;
enum { MOLECULE, CHARGE, RMASS, TEMPERATURE, HEATFLOW, IVEC, DVEC, IARRAY, DARRAY };
/* ---------------------------------------------------------------------- */
FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :

11
src/fix_property_atom.h
View File

@ -27,11 +27,12 @@ namespace LAMMPS_NS {
class FixPropertyAtom : public Fix {
public:
FixPropertyAtom(class LAMMPS *, int, char **);
~FixPropertyAtom() override;
int setmask() override;
void init() override;
enum { MOLECULE, CHARGE, RMASS, TEMPERATURE, HEATFLOW, IVEC, DVEC, IARRAY, DARRAY };
void read_data_section(char *, int, char *, tagint) override;
bigint read_data_skip_lines(char *) override;
void write_data_section_size(int, int &, int &) override;
@ -55,10 +56,10 @@ class FixPropertyAtom : public Fix {
int nvalue, border;
int molecule_flag, q_flag, rmass_flag; // flags for specific fields
int temperature_flag, heatflow_flag;
int *styles; // style of each value, see enum
int *index; // indices into atom custom data structs
int *cols; // columns per value, for arrays
char *astyle; // atom style at instantiation
int *styles; // style of each value, see enum
int *index; // indices into atom custom data structs
int *cols; // columns per value, for arrays
char *astyle; // atom style at instantiation
int values_peratom; // # of values per atom, including multiple for arrays
int nmax_old; // length of peratom arrays the last time they grew

3
src/fix_update_special_bonds.cpp
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@ -72,6 +72,9 @@ void FixUpdateSpecialBonds::setup(int /*vflag*/)
force->special_coul[3] != 1.0)
error->all(FLERR, "Fix update/special/bonds requires special Coulomb weights = 1,1,1");
// Implies neighbor->special_flag = [X, 2, 1, 1]
if (utils::strmatch(force->pair_style, "^hybrid"))
error->all(FLERR, "Cannot use fix update/special/bonds with hybrid pair styles");
}
/* ----------------------------------------------------------------------

10
src/neighbor.cpp
View File

@ -95,6 +95,16 @@ static const char cite_neigh_multi[] =
" Detection Applied to Investigate the Quasi-Static Limit},\n"
" journal = {Computational Particle Mechanics},\n"
" year = {2020}\n"
"@article{Monti2022,\n"
" author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava, \n"
" Ishan and Silbert, Leonardo E. and Grest, Gary S. \n"
" and Lechman, Jeremy B.},\n"
" title = {Large-scale frictionless jamming with power-law particle \n"
" size distributions},\n"
" journal = {Phys. Rev. E},\n"
" volume = {106}\n"
" issue = {3}\n"
" year = {2022}\n"
"}\n\n";
// template for factory functions:

4
tools/fep/fdti.py
View File

@ -10,7 +10,7 @@ if len(sys.argv) < 3:
print("usage: fdti.py temperature hderiv < out.fep")
sys.exit()
rt = 0.008314 / 4.184 * float(sys.argv[1])
rt = 0.008314 / 4.184 * float(sys.argv[1]) # in kcal/mol
hderiv = float(sys.argv[2])
line = sys.stdin.readline()
@ -23,7 +23,7 @@ if len(tok) == 4:
v = float(tok[3])
lo = -rt * math.log(float(tok[2]) / v)
i = 0
i = 1
sum = 0.0
for line in sys.stdin:
tok = line.split()

2
tools/fep/fep.py
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@ -9,7 +9,7 @@ if len(sys.argv) < 2:
print("usage: fep.py temperature < out.fep")
sys.exit()
rt = 0.008314 / 4.184 * float(sys.argv[1])
rt = 0.008314 / 4.184 * float(sys.argv[1]) # in kcal/mol
v = 1.0
sum = 0.0

2
tools/fep/nti.py
View File

@ -19,7 +19,7 @@ while line.startswith("#"):
tok = line.split()
lo = float(tok[1])
i = 0
i = 1
sum = 0.0
for line in sys.stdin:
tok = line.split()

5
tools/python/pizza/dump.py
View File

@ -657,11 +657,14 @@ class dump:
atoms = snap.atoms
nvalues = len(atoms[0])
keys = dict()
for pair in self.names.items():
keys[pair[1]] = pair[0]
for i in range(snap.natoms):
if not snap.aselect[i]: continue
line = ""
for j in range(nvalues):
if (j < 2):
if keys[j] == 'id' or keys[j] == 'type' or keys[j] == 'mol':
line += str(int(atoms[i][j])) + " "
else:
line += str(atoms[i][j]) + " "

16
unittest/commands/test_kim_commands.cpp
View File

@ -92,14 +92,14 @@ TEST_F(KimCommandsTest, kim_interactions)
{
if (!LAMMPS::is_installed_pkg("KIM")) GTEST_SKIP();
TEST_FAILURE(".*ERROR: Illegal 'kim interactions' command.*", command("kim interactions"););
TEST_FAILURE(".*ERROR: Illegal kim interactions command: missing argument.*",
command("kim interactions"););
BEGIN_HIDE_OUTPUT();
command("kim init LennardJones_Ar real");
END_HIDE_OUTPUT();
TEST_FAILURE(".*ERROR: Must use 'kim interactions' command "
"after simulation box is defined.*",
TEST_FAILURE(".*ERROR: Use of 'kim interactions' before simulation box is defined.*",
command("kim interactions Ar"););
BEGIN_HIDE_OUTPUT();
@ -410,11 +410,11 @@ TEST_F(KimCommandsTest, kim_property)
"3 >= 3.6 support.*",
command("kim property"););
} else {
TEST_FAILURE(".*ERROR: Invalid 'kim property' command.*", command("kim property"););
TEST_FAILURE(".*ERROR: Invalid 'kim property' command.*", command("kim property create"););
TEST_FAILURE(".*ERROR: Incorrect arguments in 'kim property' command."
"\n'kim property create/destroy/modify/remove/dump' "
"is mandatory.*",
TEST_FAILURE(".*ERROR: Illegal kim property command: missing argument.*",
command("kim property"););
TEST_FAILURE(".*ERROR: Illegal kim property command: missing argument.*",
command("kim property create"););
TEST_FAILURE(".*ERROR: Incorrect first argument unknown to 'kim property' command.*",
command("kim property unknown 1 atomic-mass"););
}
#if defined(KIM_EXTRA_UNITTESTS)