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Merge branch 'develop' into collected-small-fixes

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This commit is contained in:
Axel Kohlmeyer
2023-05-02 20:47:33 -04:00
parent 81523b7ba3 8054923941
commit 89d59fad61
62 changed files with 2322 additions and 650 deletions
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2
cmake/CMakeLists.txt
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@ -440,7 +440,7 @@ if(BUILD_OMP)
target_link_libraries(lmp PRIVATE OpenMP::OpenMP_CXX)
endif()
if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_ELECTRODE)
if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_ELECTRODE OR BUILD_TOOLS)
enable_language(C)
if (NOT USE_INTERNAL_LINALG)
find_package(LAPACK)

2
cmake/Modules/Tools.cmake
View File

@ -33,6 +33,8 @@ if(BUILD_TOOLS)
endif()
install(TARGETS msi2lmp DESTINATION ${CMAKE_INSTALL_BINDIR})
install(FILES ${LAMMPS_DOC_DIR}/msi2lmp.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1)
add_subdirectory(${LAMMPS_TOOLS_DIR}/phonon ${CMAKE_BINARY_DIR}/phana_build)
endif()
if(BUILD_LAMMPS_SHELL)

1
doc/src/Commands_compute.rst
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@ -46,6 +46,7 @@ KOKKOS, o = OPENMP, t = OPT.
* :doc:`com/chunk <compute_com_chunk>`
* :doc:`contact/atom <compute_contact_atom>`
* :doc:`coord/atom (k) <compute_coord_atom>`
* :doc:`count/type <compute_count_type>`
* :doc:`damage/atom <compute_damage_atom>`
* :doc:`dihedral <compute_dihedral>`
* :doc:`dihedral/local <compute_dihedral_local>`

78
doc/src/Howto_broken_bonds.rst
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@ -1,48 +1,56 @@
Broken Bonds
============
Typically, bond interactions persist for the duration of a simulation in
LAMMPS. However, there are some exceptions that allow for bonds to
break, including the :doc:`quartic bond style <bond_quartic>` and the
bond styles in the :doc:`BPM package <Howto_bpm>` which contains the
:doc:`bpm/spring <bond_bpm_spring>` and :doc:`bpm/rotational
<bond_bpm_rotational>` bond styles. In these cases, a bond can be broken
if it is stretched beyond a user-defined threshold. LAMMPS accomplishes
this by setting the bond type to 0, such that the bond force is no
longer computed.
Typically, molecular bond interactions persist for the duration of a
simulation in LAMMPS. However, some commands break bonds dynamically,
including the following:
Users are normally able to weight the contribution of pair forces to atoms
that are bonded using the :doc:`special_bonds command <special_bonds>`.
When bonds break, this is not always the case. For the quartic bond style,
pair forces are always turned off between bonded particles. LAMMPS does
this via a computational sleight-of-hand. It subtracts the pairwise
interaction as part of the bond computation. When the bond breaks, the
subtraction stops. For this to work, the pairwise interaction must always
be computed by the :doc:`pair_style <pair_style>` command, whether the bond
is broken or not. This means that :doc:`special_bonds <special_bonds>` must
be set to 1,1,1. After the bond breaks, the pairwise interaction between the
two atoms is turned on, since they are no longer bonded.
* :doc:`bond_style quartic <bond_quartic>`
* :doc:`fix bond/break <fix_bond_break>`
* :doc:`fix bond/react <fix_bond_react>`
* :doc:`BPM package <Howto_bpm>` bond styles
In the BPM package, one can either turn off all pair interactions between
bonded particles or leave them on, overlaying pair forces on top of bond
forces. To remove pair forces, the special bond list is dynamically
updated. More details can be found on the :doc:`Howto BPM <Howto_bpm>`
page.
A bond can break if it is stretched beyond a user-defined threshold or
more generally if other criteria are met.
Bonds can also be broken by fixes which change bond topology, including
:doc:`fix bond/break <fix_bond_break>` and
:doc:`fix bond/react <fix_bond_react>`. These fixes will automatically
trigger a rebuild of the neighbor list and update special bond data structures
when bonds are broken.
For the quartic bond style, when a bond is broken its bond type is set
to 0 to effectively break it and pairwise forces between the two atoms
in the broken bond are "turned on". Angles, dihedrals, etc cannot be
defined for a system when :doc:`bond_style quartic <bond_quartic>` is
used.
Note that when bonds are dumped to a file via the :doc:`dump local <dump>` command, bonds with type 0 are not included. The
:doc:`delete_bonds <delete_bonds>` command can also be used to query the
status of broken bonds or permanently delete them, e.g.:
Similarly, bond styles in the BPM package are also incompatible with
angles, dihedrals, etc. and when a bond breaks its type is set to zero.
However, in the BPM package one can either turn off all pair interactions
between bonded particles or leave them on, overlaying pair forces on
top of bond forces. To remove pair forces, the special bond list is
dynamically updated. More details can be found on the :doc:`Howto BPM
<Howto_bpm>` page.
The :doc:`fix bond/break <fix_bond_break>` and :doc:`fix bond/react
<fix_bond_react>` commands allow breaking of bonds within a molecular
topology with may also define angles, dihedrals, etc. These commands
update internal topology data structures to remove broken bonds, as
well as the appropriate angle, dihederal, etc interactions which
include the bond. They also trigger a rebuild of the neighbor list
when this occurs, to turn on the appropriate pairwise forces.
Note that when bonds are dumped to a file via the :doc:`dump local
<dump>` command, bonds with type 0 are not included.
The :doc:`delete_bonds <delete_bonds>` command can be used to query
the status of broken bonds with type = 0 or permanently delete them,
e.g.:
.. code-block:: LAMMPS
delete_bonds all stats
delete_bonds all bond 0 remove
The compute :doc:`nbond/atom <compute_nbond_atom>` can also be used
to tally the current number of bonds per atom, excluding broken bonds.
The compute :doc:`count/type <compute_count_type>` command tallies the
current number of bonds (or angles, etc) for each bond (angle, etc)
type. It also tallies broken bonds with type = 0.
The compute :doc:`nbond/atom <compute_nbond_atom>` command tallies the
current number of bonds each atom is part of, excluding broken bonds
with type = 0.

6
doc/src/Tools.rst
View File

@ -883,9 +883,9 @@ dependencies and redirects the download to the local cache.
phonon tool
------------------------
The phonon subdirectory contains a post-processing tool useful for
analyzing the output of the :doc:`fix phonon <fix_phonon>` command in
the PHONON package.
The phonon subdirectory contains a post-processing tool, *phana*, useful
for analyzing the output of the :doc:`fix phonon <fix_phonon>` command
in the PHONON package.
See the README file for instruction on building the tool and what
library it needs. And see the examples/PACKAGES/phonon directory

14
doc/src/bond_style.rst
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@ -32,13 +32,13 @@ Set the formula(s) LAMMPS uses to compute bond interactions between
pairs of atoms. In LAMMPS, a bond differs from a pairwise
interaction, which are set via the :doc:`pair_style <pair_style>`
command. Bonds are defined between specified pairs of atoms and
remain in force for the duration of the simulation (unless the bond
breaks which is possible in some bond potentials). The list of bonded
atoms is read in by a :doc:`read_data <read_data>` or
:doc:`read_restart <read_restart>` command from a data or restart file.
By contrast, pair potentials are typically defined between all pairs
of atoms within a cutoff distance and the set of active interactions
changes over time.
remain in force for the duration of the simulation (unless new bonds
are created or existing bonds break, which is possible in some fixes
and bond potentials). The list of bonded atoms is read in by a
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
command from a data or restart file. By contrast, pair potentials are
typically defined between all pairs of atoms within a cutoff distance
and the set of active interactions changes over time.
Hybrid models where bonds are computed using different bond potentials
can be setup using the *hybrid* bond style.

1
doc/src/compute.rst
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@ -200,6 +200,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
* :doc:`com/chunk <compute_com_chunk>` - center of mass for each chunk
* :doc:`contact/atom <compute_contact_atom>` - contact count for each spherical particle
* :doc:`coord/atom <compute_coord_atom>` - coordination number for each atom
* :doc:`count/type <compute_count_type>` - count of atoms or bonds by type
* :doc:`damage/atom <compute_damage_atom>` - Peridynamic damage for each atom
* :doc:`dihedral <compute_dihedral>` - energy of each dihedral sub-style
* :doc:`dihedral/local <compute_dihedral_local>` - angle of each dihedral

130
doc/src/compute_count_type.rst Normal file
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@ -0,0 +1,130 @@
.. index:: compute count/type
compute count/type command
====================
Syntax
""""""
.. code-block:: LAMMPS
compute ID group-ID count/type mode
* ID, group-ID are documented in :doc:`compute <compute>` command
* count/type = style name of this compute command
* mode = {atom} or {bond} or {angle} or {dihedral} or {improper}
Examples
""""""""
.. code-block:: LAMMPS
compute 1 all count/type atom
compute 1 flowmols count/type bond
Description
"""""""""""
.. versionadded:: TBD
Define a computation that counts the current number of atoms for each
atom type. Or the number of bonds (angles, dihedrals, impropers) for
each bond (angle, dihedral, improper) type.
The former can be useful if atoms are added to or deleted from the
system in random ways, e.g. via the :doc:`fix deposit <fix_deposit>`,
:doc:`fix pour <fix_pour>`, or :doc:`fix evaporate <fix_evaporate>`
commands. The latter can be useful in reactive simulations where
molecular bonds are broken or created, as well as angles, dihedrals,
impropers.
Note that for this command, bonds (angles, etc) are the topological
kind enumerated in a data file, initially read by the :doc:`read_data
<read_data>` command or defined by the :doc:`molecule <molecule>`
command. They do not refer to implicit bonds defined on-the-fly by
bond-order or reactive pair styles based on the current conformation
of small clusters of atoms.
These commands can turn off topological bonds (angles, etc) by setting
their bond (angle, etc) types to negative values. This command
includes the turned-off bonds (angles, etc) in the count for each
type:
* :doc:`fix shake <fix_shake>`
* :doc:`delete_bonds <delete_bonds>`
These commands can create and/or break topological bonds (angles,
etc). In the case of breaking, they remove the bond (angle, etc) from
the system, so that they no longer exist (:doc:`bond_style quartic
<bond_quartic>` and :doc:`BPM bond styles <Howto_bpm>` are exceptions,
see the discussion below). Thus they are not included in the counts
for each type:
* :doc:`delete_bonds remove <delete_bonds>`
* :doc:`bond_style quartic <bond_quartic>`
* :doc:`fix bond/react <fix_bond_react>`
* :doc:`fix bond/create <fix_bond_create>`
* :doc:`fix bond/break <fix_bond_break>`
* :doc:`BPM package <Howto_bpm>` bond styles
----------
If the {mode} setting is {atom} then the count of atoms for each atom
type is tallied. Only atoms in the specified group are counted.
If the {mode} setting is {bond} then the count of bonds for each bond
type is tallied. Only bonds with both atoms in the specified group
are counted.
For {mode} = {bond}, broken bonds with a bond type of zero are also
counted. The :doc:`bond_style quartic <bond_quartic>` and :doc:`BPM
bond styles <Howto_bpm>` break bonds by doing this. See the :doc:`
Howto broken bonds <Howto_broken_bonds>` doc page for more details.
Note that the group setting is ignored for broken bonds; all broken
bonds in the system are counted.
If the {mode} setting is {angle} then the count of angles for each
angle type is tallied. Only angles with all 3 atoms in the specified
group are counted.
If the {mode} setting is {dihedral} then the count of dihedrals for
each dihedral type is tallied. Only dihedrals with all 4 atoms in the
specified group are counted.
If the {mode} setting is {improper} then the count of impropers for
each improper type is tallied. Only impropers with all 4 atoms in the
specified group are counted.
----------
Output info
"""""""""""
This compute calculates a global vector of counts. If the mode is
{atom} or {bond} or {angle} or {dihedral} or {improper}, then the
vector length is the number of atom types or bond types or angle types
or dihedral types or improper types, respectively.
If the mode is {bond} this compute also calculates a global scalar
which is the number of broken bonds with type = 0, as explained above.
These values can be used by any command that uses global scalar or
vector values from a compute as input. See the :doc:`Howto output
<Howto_output>` page for an overview of LAMMPS output options.
The scalar and vector values calculated by this compute are "extensive".
Restrictions
""""""""""""
none
Related commands
""""""""""""""""
none
Default
"""""""
none

9
src/KOKKOS/fix_langevin_kokkos.cpp
View File

@ -44,6 +44,7 @@ FixLangevinKokkos<DeviceType>::FixLangevinKokkos(LAMMPS *lmp, int narg, char **a
FixLangevin(lmp, narg, arg),rand_pool(seed + comm->me)
{
kokkosable = 1;
fuse_integrate_flag = 1;
sort_device = 1;
atomKK = (AtomKokkos *) atom;
int ntypes = atomKK->ntypes;
@ -170,6 +171,14 @@ void FixLangevinKokkos<DeviceType>::initial_integrate_item(int i) const
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void FixLangevinKokkos<DeviceType>::fused_integrate(int vflag)
{
initial_integrate(vflag);
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void FixLangevinKokkos<DeviceType>::post_force(int /*vflag*/)
{

1
src/KOKKOS/fix_langevin_kokkos.h
View File

@ -70,6 +70,7 @@ namespace LAMMPS_NS {
void cleanup_copy();
void init() override;
void initial_integrate(int) override;
void fused_integrate(int) override;
void post_force(int) override;
void reset_dt() override;
void grow_arrays(int) override;

63
src/KOKKOS/fix_nve_kokkos.cpp
View File

@ -29,6 +29,7 @@ FixNVEKokkos<DeviceType>::FixNVEKokkos(LAMMPS *lmp, int narg, char **arg) :
FixNVE(lmp, narg, arg)
{
kokkosable = 1;
fuse_integrate_flag = 1;
atomKK = (AtomKokkos *) atom;
execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
@ -159,6 +160,66 @@ void FixNVEKokkos<DeviceType>::final_integrate_rmass_item(int i) const
}
}
/* ----------------------------------------------------------------------
allow for both per-type and per-atom mass
------------------------------------------------------------------------- */
template<class DeviceType>
void FixNVEKokkos<DeviceType>::fused_integrate(int /*vflag*/)
{
atomKK->sync(execution_space,datamask_read);
x = atomKK->k_x.view<DeviceType>();
v = atomKK->k_v.view<DeviceType>();
f = atomKK->k_f.view<DeviceType>();
rmass = atomKK->k_rmass.view<DeviceType>();
mass = atomKK->k_mass.view<DeviceType>();
type = atomKK->k_type.view<DeviceType>();
mask = atomKK->k_mask.view<DeviceType>();
int nlocal = atomKK->nlocal;
if (igroup == atomKK->firstgroup) nlocal = atomKK->nfirst;
if (rmass.data()) {
FixNVEKokkosFusedIntegrateFunctor<DeviceType,1> functor(this);
Kokkos::parallel_for(nlocal,functor);
} else {
FixNVEKokkosFusedIntegrateFunctor<DeviceType,0> functor(this);
Kokkos::parallel_for(nlocal,functor);
}
atomKK->modified(execution_space,datamask_modify);
}
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void FixNVEKokkos<DeviceType>::fused_integrate_item(int i) const
{
if (mask[i] & groupbit) {
const double dtfm = 2.0 * dtf / mass[type[i]];
v(i,0) += dtfm * f(i,0);
v(i,1) += dtfm * f(i,1);
v(i,2) += dtfm * f(i,2);
x(i,0) += dtv * v(i,0);
x(i,1) += dtv * v(i,1);
x(i,2) += dtv * v(i,2);
}
}
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void FixNVEKokkos<DeviceType>::fused_integrate_rmass_item(int i) const
{
if (mask[i] & groupbit) {
const double dtfm = 2.0 * dtf / rmass[i];
v(i,0) += dtfm * f(i,0);
v(i,1) += dtfm * f(i,1);
v(i,2) += dtfm * f(i,2);
x(i,0) += dtv * v(i,0);
x(i,1) += dtv * v(i,1);
x(i,2) += dtv * v(i,2);
}
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
@ -168,6 +229,8 @@ void FixNVEKokkos<DeviceType>::cleanup_copy()
vatom = nullptr;
}
/* ---------------------------------------------------------------------- */
namespace LAMMPS_NS {
template class FixNVEKokkos<LMPDeviceType>;
#ifdef LMP_KOKKOS_GPU

21
src/KOKKOS/fix_nve_kokkos.h
View File

@ -46,6 +46,7 @@ class FixNVEKokkos : public FixNVE {
void init() override;
void initial_integrate(int) override;
void final_integrate() override;
void fused_integrate(int) override;
KOKKOS_INLINE_FUNCTION
void initial_integrate_item(int) const;
@ -55,6 +56,10 @@ class FixNVEKokkos : public FixNVE {
void final_integrate_item(int) const;
KOKKOS_INLINE_FUNCTION
void final_integrate_rmass_item(int) const;
KOKKOS_INLINE_FUNCTION
void fused_integrate_item(int) const;
KOKKOS_INLINE_FUNCTION
void fused_integrate_rmass_item(int) const;
private:
@ -96,6 +101,22 @@ struct FixNVEKokkosFinalIntegrateFunctor {
}
};
template <class DeviceType, int RMass>
struct FixNVEKokkosFusedIntegrateFunctor {
typedef DeviceType device_type ;
FixNVEKokkos<DeviceType> c;
FixNVEKokkosFusedIntegrateFunctor(FixNVEKokkos<DeviceType>* c_ptr):
c(*c_ptr) {c.cleanup_copy();};
KOKKOS_INLINE_FUNCTION
void operator()(const int i) const {
if (RMass)
c.fused_integrate_rmass_item(i);
else
c.fused_integrate_item(i);
}
};
}
#endif

68
src/KOKKOS/fix_nve_sphere_kokkos.cpp
View File

@ -28,6 +28,7 @@ FixNVESphereKokkos<DeviceType>::FixNVESphereKokkos(LAMMPS *lmp, int narg, char *
FixNVESphere(lmp, narg, arg)
{
kokkosable = 1;
fuse_integrate_flag = 1;
atomKK = (AtomKokkos *)atom;
execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
@ -164,6 +165,73 @@ void FixNVESphereKokkos<DeviceType>::final_integrate_item(const int i) const
}
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void FixNVESphereKokkos<DeviceType>::fused_integrate(int /*vflag*/)
{
if (extra == DIPOLE)
atomKK->sync(execution_space, X_MASK | V_MASK | OMEGA_MASK| F_MASK | TORQUE_MASK | RMASS_MASK | RADIUS_MASK | MASK_MASK | MU_MASK);
else
atomKK->sync(execution_space, X_MASK | V_MASK | OMEGA_MASK| F_MASK | TORQUE_MASK | RMASS_MASK | RADIUS_MASK | MASK_MASK);
x = atomKK->k_x.view<DeviceType>();
v = atomKK->k_v.view<DeviceType>();
omega = atomKK->k_omega.view<DeviceType>();
f = atomKK->k_f.view<DeviceType>();
torque = atomKK->k_torque.view<DeviceType>();
mask = atomKK->k_mask.view<DeviceType>();
rmass = atomKK->k_rmass.view<DeviceType>();
radius = atomKK->k_radius.view<DeviceType>();
mu = atomKK->k_mu.view<DeviceType>();
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
FixNVESphereKokkosFusedIntegrateFunctor<DeviceType> f(this);
Kokkos::parallel_for(nlocal,f);
if (extra == DIPOLE)
atomKK->modified(execution_space, X_MASK | V_MASK | OMEGA_MASK | MU_MASK);
else
atomKK->modified(execution_space, X_MASK | V_MASK | OMEGA_MASK);
}
/* ---------------------------------------------------------------------- */
template <class DeviceType>
KOKKOS_INLINE_FUNCTION
void FixNVESphereKokkos<DeviceType>::fused_integrate_item(const int i) const
{
const double dtfrotate = dtf / inertia;
if (mask(i) & groupbit) {
const double dtfm = 2.0 * dtf / rmass(i);
v(i,0) += dtfm * f(i,0);
v(i,1) += dtfm * f(i,1);
v(i,2) += dtfm * f(i,2);
x(i,0) += dtv * v(i,0);
x(i,1) += dtv * v(i,1);
x(i,2) += dtv * v(i,2);
const double dtirotate = 2.0 * dtfrotate / (radius(i)*radius(i)*rmass(i));
omega(i,0) += dtirotate * torque(i,0);
omega(i,1) += dtirotate * torque(i,1);
omega(i,2) += dtirotate * torque(i,2);
if (extra == DIPOLE) {
const double g0 = mu(i,0) + dtv * (omega(i,1) * mu(i,2) - omega(i,2) * mu(i,1));
const double g1 = mu(i,1) + dtv * (omega(i,2) * mu(i,0) - omega(i,0) * mu(i,2));
const double g2 = mu(i,2) + dtv * (omega(i,0) * mu(i,1) - omega(i,1) * mu(i,0));
const double msq = g0*g0 + g1*g1 + g2*g2;
const double scale = mu(i,3)/sqrt(msq);
mu(i,0) = g0*scale;
mu(i,1) = g1*scale;
mu(i,2) = g2*scale;
}
}
}
namespace LAMMPS_NS {
template class FixNVESphereKokkos<LMPDeviceType>;
#ifdef LMP_KOKKOS_GPU

14
src/KOKKOS/fix_nve_sphere_kokkos.h
View File

@ -37,11 +37,14 @@ class FixNVESphereKokkos : public FixNVESphere {
void init() override;
void initial_integrate(int) override;
void final_integrate() override;
void fused_integrate(int) override;
KOKKOS_INLINE_FUNCTION
void initial_integrate_item(const int i) const;
KOKKOS_INLINE_FUNCTION
void final_integrate_item(const int i) const;
KOKKOS_INLINE_FUNCTION
void fused_integrate_item(int) const;
private:
typename ArrayTypes<DeviceType>::t_x_array x;
@ -77,6 +80,17 @@ struct FixNVESphereKokkosFinalIntegrateFunctor {
}
};
template <class DeviceType>
struct FixNVESphereKokkosFusedIntegrateFunctor {
typedef DeviceType device_type;
FixNVESphereKokkos<DeviceType> c;
FixNVESphereKokkosFusedIntegrateFunctor(FixNVESphereKokkos<DeviceType> *c_ptr): c(*c_ptr) { c.cleanup_copy(); }
KOKKOS_INLINE_FUNCTION
void operator()(const int i) const {
c.fused_integrate_item(i);
}
};
} // namespace LAMMPS_NS
#endif // LMP_FIX_NVE_SPHERE_KOKKOS_H

37
src/KOKKOS/modify_kokkos.cpp
View File

@ -392,6 +392,24 @@ void ModifyKokkos::final_integrate()
}
}
/* ----------------------------------------------------------------------
fused initial and final integrate call, only for relevant fixes
------------------------------------------------------------------------- */
void ModifyKokkos::fused_integrate(int vflag)
{
for (int i = 0; i < n_final_integrate; i++) {
atomKK->sync(fix[list_final_integrate[i]]->execution_space,
fix[list_final_integrate[i]]->datamask_read);
int prev_auto_sync = lmp->kokkos->auto_sync;
if (!fix[list_final_integrate[i]]->kokkosable) lmp->kokkos->auto_sync = 1;
fix[list_final_integrate[i]]->fused_integrate(vflag);
lmp->kokkos->auto_sync = prev_auto_sync;
atomKK->modified(fix[list_final_integrate[i]]->execution_space,
fix[list_final_integrate[i]]->datamask_modify);
}
}
/* ----------------------------------------------------------------------
end-of-timestep call, only for relevant fixes
only call fix->end_of_step() on timesteps that are multiples of nevery
@ -881,3 +899,22 @@ int ModifyKokkos::min_reset_ref()
}
return itmpall;
}
/* ----------------------------------------------------------------------
check if initial and final integrate can be fused
------------------------------------------------------------------------- */
int ModifyKokkos::check_fuse_integrate()
{
int fuse_integrate_flag = 1;
for (int i = 0; i < n_initial_integrate; i++)
if (!fix[list_initial_integrate[i]]->fuse_integrate_flag)
fuse_integrate_flag = 0;
for (int i = 0; i < n_final_integrate; i++)
if (!fix[list_final_integrate[i]]->fuse_integrate_flag)
fuse_integrate_flag = 0;
return fuse_integrate_flag;
}

3
src/KOKKOS/modify_kokkos.h
View File

@ -39,6 +39,7 @@ class ModifyKokkos : public Modify {
void pre_reverse(int,int) override;
void post_force(int) override;
void final_integrate() override;
void fused_integrate(int) override;
void end_of_step() override;
double energy_couple() override;
double energy_global() override;
@ -69,6 +70,8 @@ class ModifyKokkos : public Modify {
int min_dof() override;
int min_reset_ref() override;
int check_fuse_integrate();
protected:
};

26
src/KOKKOS/pair_kokkos.h
View File

@ -280,6 +280,12 @@ struct PairComputeFunctor {
const X_FLOAT ztmp = c.x(i,2);
const int itype = c.type(i);
Kokkos::single(Kokkos::PerThread(team), [&] (){
f(i,0) = 0.0;
f(i,1) = 0.0;
f(i,2) = 0.0;
});
const AtomNeighborsConst neighbors_i = list.get_neighbors_const(i);
const int jnum = list.d_numneigh[i];
@ -337,6 +343,12 @@ struct PairComputeFunctor {
const int itype = c.type(i);
const F_FLOAT qtmp = c.q(i);
Kokkos::single(Kokkos::PerThread(team), [&] (){
f(i,0) = 0.0;
f(i,1) = 0.0;
f(i,2) = 0.0;
});
const AtomNeighborsConst neighbors_i = list.get_neighbors_const(i);
const int jnum = list.d_numneigh[i];
@ -399,6 +411,12 @@ struct PairComputeFunctor {
const X_FLOAT ztmp = c.x(i,2);
const int itype = c.type(i);
Kokkos::single(Kokkos::PerThread(team), [&] (){
f(i,0) = 0.0;
f(i,1) = 0.0;
f(i,2) = 0.0;
});
const AtomNeighborsConst neighbors_i = list.get_neighbors_const(i);
const int jnum = list.d_numneigh[i];
@ -495,6 +513,12 @@ struct PairComputeFunctor {
const int itype = c.type(i);
const F_FLOAT qtmp = c.q(i);
Kokkos::single(Kokkos::PerThread(team), [&] (){
f(i,0) = 0.0;
f(i,1) = 0.0;
f(i,2) = 0.0;
});
const AtomNeighborsConst neighbors_i = list.get_neighbors_const(i);
const int jnum = list.d_numneigh[i];
@ -743,6 +767,8 @@ EV_FLOAT pair_compute_neighlist (PairStyle* fpair, typename std::enable_if<(NEIG
fpair->lmp->kokkos->neigh_thread = 1;
if (fpair->lmp->kokkos->neigh_thread) {
fpair->fuse_force_clear_flag = 1;
int vector_length = 8;
int atoms_per_team = 32;

52
src/KOKKOS/verlet_kokkos.cpp
View File

@ -27,7 +27,7 @@
#include "kspace.h"
#include "output.h"
#include "update.h"
#include "modify.h"
#include "modify_kokkos.h"
#include "timer.h"
#include "memory_kokkos.h"
#include "kokkos.h"
@ -276,6 +276,9 @@ void VerletKokkos::run(int n)
lmp->kokkos->auto_sync = 0;
fuse_integrate = 0;
fuse_force_clear = 0;
if (atomKK->sortfreq > 0) sortflag = 1;
else sortflag = 0;
@ -296,7 +299,8 @@ void VerletKokkos::run(int n)
// initial time integration
timer->stamp();
modify->initial_integrate(vflag);
if (!fuse_integrate)
modify->initial_integrate(vflag);
if (n_post_integrate) modify->post_integrate();
timer->stamp(Timer::MODIFY);
@ -357,12 +361,17 @@ void VerletKokkos::run(int n)
}
}
// check if kernels can be fused, must come after initial_integrate
fuse_check(i,n);
// force computations
// important for pair to come before bonded contributions
// since some bonded potentials tally pairwise energy/virial
// and Pair:ev_tally() needs to be called before any tallying
force_clear();
if (!fuse_force_clear)
force_clear();
timer->stamp();
@ -494,7 +503,10 @@ void VerletKokkos::run(int n)
// force modifications, final time integration, diagnostics
if (n_post_force) modify->post_force(vflag);
modify->final_integrate();
if (fuse_integrate) modify->fused_integrate(vflag);
else modify->final_integrate();
if (n_end_of_step) modify->end_of_step();
timer->stamp(Timer::MODIFY);
@ -593,3 +605,35 @@ void VerletKokkos::force_clear()
}
}
}
/* ----------------------------------------------------------------------
check if can fuse force_clear() with pair compute()
Requirements:
- no pre_force fixes
- no torques, SPIN forces, or includegroup set
- pair compute() must be called
- pair_style must support fusing
check if can fuse initial_integrate() with final_integrate()
Requirements:
- no end_of_step fixes
- not on last or output step
- no timers to break out of loop
- integrate fix style must support fusing
------------------------------------------------------------------------- */
void VerletKokkos::fuse_check(int i, int n)
{
fuse_force_clear = 1;
if (modify->n_pre_force) fuse_force_clear = 0;
else if (torqueflag || extraflag || neighbor->includegroup) fuse_force_clear = 0;
else if (!force->pair || !pair_compute_flag) fuse_force_clear = 0;
else if (!force->pair->fuse_force_clear_flag) fuse_force_clear = 0;
fuse_integrate = 1;
if (modify->n_end_of_step) fuse_integrate = 0;
else if (i == n-1) fuse_integrate = 0;
else if (update->ntimestep == output->next) fuse_integrate = 0;
else if (timer->has_timeout()) fuse_integrate = 0;
else if (!((ModifyKokkos*)modify)->check_fuse_integrate()) fuse_integrate = 0;
}

3
src/KOKKOS/verlet_kokkos.h
View File

@ -46,6 +46,9 @@ class VerletKokkos : public Verlet {
protected:
DAT::t_f_array f_merge_copy,f;
int fuse_force_clear,fuse_integrate;
void fuse_check(int, int);
};
}

400
src/compute_count_type.cpp Normal file
View File

@ -0,0 +1,400 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "compute_count_type.h"
#include "atom.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "group.h"
#include "update.h"
using namespace LAMMPS_NS;
enum { ATOM, BOND, ANGLE, DIHEDRAL, IMPROPER };
/* ---------------------------------------------------------------------- */
ComputeCountType::ComputeCountType(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg), count(nullptr), bcount_me(nullptr), bcount(nullptr)
{
if (narg != 4) error->all(FLERR, "Incorrect number of args for compute count/type command");
// process args
if (strcmp(arg[3], "atom") == 0)
mode = ATOM;
else if (strcmp(arg[3], "bond") == 0)
mode = BOND;
else if (strcmp(arg[3], "angle") == 0)
mode = ANGLE;
else if (strcmp(arg[3], "dihedral") == 0)
mode = DIHEDRAL;
else if (strcmp(arg[3], "improper") == 0)
mode = IMPROPER;
else
error->all(FLERR, "Invalid compute count/type keyword {}", arg[3]);
// error check
if (mode == BOND && !atom->nbondtypes)
error->all(FLERR, "Compute count/type bond command with no bonds defined");
if (mode == ANGLE && !atom->nangletypes)
error->all(FLERR, "Compute count/type bond command with no angles defined");
if (mode == DIHEDRAL && !atom->ndihedraltypes)
error->all(FLERR, "Compute count/type dihedral command with no dihedrals defined");
if (mode == IMPROPER && !atom->nimpropertypes)
error->all(FLERR, "Compute count/type improper command with no impropers defined");
// set vector lengths
if (mode == ATOM) {
vector_flag = 1;
size_vector = atom->ntypes;
extvector = 1;
} else if (mode == BOND) {
scalar_flag = vector_flag = 1;
size_vector = atom->nbondtypes;
extscalar = 1;
extvector = 1;
} else if (mode == ANGLE) {
vector_flag = 1;
size_vector = atom->nangletypes;
extvector = 1;
} else if (mode == DIHEDRAL) {
vector_flag = 1;
size_vector = atom->ndihedraltypes;
extvector = 1;
} else if (mode == IMPROPER) {
vector_flag = 1;
size_vector = atom->nimpropertypes;
extvector = 1;
}
// output vector
vector = new double[size_vector];
// work vectors
count = new int[size_vector];
bcount_me = new bigint[size_vector];
bcount = new bigint[size_vector];
}
/* ---------------------------------------------------------------------- */
ComputeCountType::~ComputeCountType()
{
delete[] vector;
delete[] count;
delete[] bcount_me;
delete[] bcount;
}
/* ----------------------------------------------------------------------
only invoked for mode = BOND to count broken bonds
broken bonds have bond_type = 0
---------------------------------------------------------------------- */
double ComputeCountType::compute_scalar()
{
invoked_scalar = update->ntimestep;
int *num_bond = atom->num_bond;
int **bond_type = atom->bond_type;
int nlocal = atom->nlocal;
// count broken bonds with bond_type = 0
// ignore group setting since 2 atoms in a broken bond
// can be arbitrarily far apart
int count = 0;
for (int i = 0; i < nlocal; i++) {
int nbond = num_bond[i];
for (int m = 0; m < nbond; m++)
if (bond_type[i][m] == 0) count++;
}
// sum across procs as bigint, then convert to double
// correct for double counting if newton_bond off
bigint bcount = 0;
bigint bcount_me = count;
MPI_Allreduce(&bcount_me, &bcount, 1, MPI_LMP_BIGINT, MPI_SUM, world);
if (force->newton_bond == 0) bcount /= 2;
if (bcount > MAXDOUBLEINT) error->all(FLERR, "Compute count/type overflow");
scalar = bcount;
return scalar;
}
/* ---------------------------------------------------------------------- */
void ComputeCountType::compute_vector()
{
invoked_vector = update->ntimestep;
int nvec;
if (mode == ATOM)
nvec = count_atoms();
else if (mode == BOND)
nvec = count_bonds();
else if (mode == ANGLE)
nvec = count_angles();
else if (mode == DIHEDRAL)
nvec = count_dihedrals();
else if (mode == IMPROPER)
nvec = count_impropers();
// sum across procs as bigint, then convert to double
// correct for multiple counting if newton_bond off
for (int m = 0; m < nvec; m++) bcount_me[m] = count[m];
MPI_Allreduce(bcount_me, bcount, nvec, MPI_LMP_BIGINT, MPI_SUM, world);
if (force->newton_bond == 0) {
if (mode == BOND)
for (int m = 0; m < nvec; m++) bcount[m] /= 2;
else if (mode == ANGLE)
for (int m = 0; m < nvec; m++) bcount[m] /= 3;
if (mode == DIHEDRAL || mode == IMPROPER)
for (int m = 0; m < nvec; m++) bcount[m] /= 4;
}
for (int m = 0; m < nvec; m++)
if (bcount[m] > MAXDOUBLEINT) error->all(FLERR, "Compute count/type overflow");
for (int m = 0; m < nvec; m++) vector[m] = bcount[m];
}
/* ----------------------------------------------------------------------
count atoms by type
atom must be in group to be counted
---------------------------------------------------------------------- */
int ComputeCountType::count_atoms()
{
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int ntypes = atom->ntypes;
for (int m = 0; m < ntypes; m++) count[m] = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) count[type[i] - 1]++;
return ntypes;
}
/* ----------------------------------------------------------------------
count bonds by type
both atoms in bond must be in group to be counted
skip type = 0 bonds, they are counted by compute_scalar()
bond types can be negative, count them as if positive
---------------------------------------------------------------------- */
int ComputeCountType::count_bonds()
{
tagint **bond_atom = atom->bond_atom;
int **bond_type = atom->bond_type;
int *num_bond = atom->num_bond;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int nbondtypes = atom->nbondtypes;
int flag = 0;
for (int m = 0; m < nbondtypes; m++) count[m] = 0;
for (int i = 0; i < nlocal; i++) {
int nbond = num_bond[i];
for (int m = 0; m < nbond; m++) {
int itype = bond_type[i][m];
if (itype == 0) continue;
int j = atom->map(bond_atom[i][m]);
if (j < 0) {
flag = 1;
continue;
}
if ((mask[i] & groupbit) && (mask[j] & groupbit)) {
if (itype > 0)
count[itype - 1]++;
else
count[-itype - 1]++;
}
}
}
int flagany;
MPI_Allreduce(&flag, &flagany, 1, MPI_INT, MPI_SUM, world);
if (flagany) error->all(FLERR, "Missing bond atom in compute count/type");
return nbondtypes;
}
/* ----------------------------------------------------------------------
count angles by type
all 3 atoms in angle must be in group to be counted
angle types can be negative, count them as if positive
---------------------------------------------------------------------- */
int ComputeCountType::count_angles()
{
tagint **angle_atom1 = atom->angle_atom1;
tagint **angle_atom2 = atom->angle_atom2;
tagint **angle_atom3 = atom->angle_atom3;
int **angle_type = atom->angle_type;
int *num_angle = atom->num_angle;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int nangletypes = atom->nangletypes;
int flag = 0;
for (int m = 0; m < nangletypes; m++) count[m] = 0;
for (int i = 0; i < nlocal; i++) {
int nangle = num_angle[i];
for (int m = 0; m < nangle; m++) {
int itype = angle_type[i][m];
int j1 = atom->map(angle_atom1[i][m]);
int j2 = atom->map(angle_atom2[i][m]);
int j3 = atom->map(angle_atom3[i][m]);
if (j1 < 0 || j2 < 0 || j3 < 0) {
flag = 1;
continue;
}
if ((mask[j1] & groupbit) && (mask[j2] & groupbit) && (mask[j3] & groupbit)) {
if (itype > 0)
count[itype - 1]++;
else if (itype < 0)
count[-itype - 1]++;
}
}
}
int flagany;
MPI_Allreduce(&flag, &flagany, 1, MPI_INT, MPI_SUM, world);
if (flagany) error->all(FLERR, "Missing angle atom in compute count/type");
return nangletypes;
}
/* ----------------------------------------------------------------------
count dihedrals by type
all 4 atoms in dihedral must be in group to be counted
dihedral types can be negative, count them as if positive
---------------------------------------------------------------------- */
int ComputeCountType::count_dihedrals()
{
tagint **dihedral_atom1 = atom->dihedral_atom1;
tagint **dihedral_atom2 = atom->dihedral_atom2;
tagint **dihedral_atom3 = atom->dihedral_atom3;
tagint **dihedral_atom4 = atom->dihedral_atom4;
int **dihedral_type = atom->dihedral_type;
int *num_dihedral = atom->num_dihedral;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int ndihedraltypes = atom->ndihedraltypes;
int flag = 0;
for (int m = 0; m < ndihedraltypes; m++) count[m] = 0;
for (int i = 0; i < nlocal; i++) {
int ndihedral = num_dihedral[i];
for (int m = 0; m < ndihedral; m++) {
int itype = dihedral_type[i][m];
int j1 = atom->map(dihedral_atom1[i][m]);
int j2 = atom->map(dihedral_atom2[i][m]);
int j3 = atom->map(dihedral_atom3[i][m]);
int j4 = atom->map(dihedral_atom4[i][m]);
if (j1 < 0 || j2 < 0 || j3 < 0 || j4 < 0) {
flag = 1;
continue;
}
if ((mask[j1] & groupbit) && (mask[j2] & groupbit) && (mask[j3] & groupbit) &&
(mask[j4] & groupbit)) {
if (itype > 0)
count[itype - 1]++;
else if (itype < 0)
count[-itype - 1]++;
}
}
}
int flagany;
MPI_Allreduce(&flag, &flagany, 1, MPI_INT, MPI_SUM, world);
if (flagany) error->all(FLERR, "Missing dihedral atom in compute count/type");
return ndihedraltypes;
}
/* ----------------------------------------------------------------------
count impropers by type
all 4 atoms in improper must be in group to be counted
improper types can be negative, count them as if positive
---------------------------------------------------------------------- */
int ComputeCountType::count_impropers()
{
tagint **improper_atom1 = atom->improper_atom1;
tagint **improper_atom2 = atom->improper_atom2;
tagint **improper_atom3 = atom->improper_atom3;
tagint **improper_atom4 = atom->improper_atom4;
int **improper_type = atom->improper_type;
int *num_improper = atom->num_improper;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int nimpropertypes = atom->nimpropertypes;
int flag = 0;
for (int m = 0; m < nimpropertypes; m++) count[m] = 0;
for (int i = 0; i < nlocal; i++) {
int nimproper = num_improper[i];
for (int m = 0; m < nimproper; m++) {
int itype = improper_type[i][m];
int j1 = atom->map(improper_atom1[i][m]);
int j2 = atom->map(improper_atom2[i][m]);
int j3 = atom->map(improper_atom3[i][m]);
int j4 = atom->map(improper_atom4[i][m]);
if (j1 < 0 || j2 < 0 || j3 < 0 || j4 < 0) {
flag = 1;
continue;
}
if ((mask[j1] & groupbit) && (mask[j2] & groupbit) && (mask[j3] & groupbit) &&
(mask[j4] & groupbit)) {
if (itype > 0)
count[itype - 1]++;
else if (itype < 0)
count[-itype - 1]++;
}
}
}
int flagany;
MPI_Allreduce(&flag, &flagany, 1, MPI_INT, MPI_SUM, world);
if (flagany) error->all(FLERR, "Missing improper atom in compute count/type");
return nimpropertypes;
}

52
src/compute_count_type.h Normal file
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@ -0,0 +1,52 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef COMPUTE_CLASS
// clang-format off
ComputeStyle(count/type,ComputeCountType);
// clang-format on
#else
#ifndef LMP_COMPUTE_COMPUTE_TYPE_H
#define LMP_COMPUTE_COMPUTE_TYPE_H
#include "compute.h"
namespace LAMMPS_NS {
class ComputeCountType : public Compute {
public:
ComputeCountType(class LAMMPS *, int, char **);
~ComputeCountType() override;
void init() override {}
double compute_scalar() override;
void compute_vector() override;
protected:
int mode;
int *count;
bigint *bcount_me;
bigint *bcount;
int count_atoms();
int count_bonds();
int count_angles();
int count_dihedrals();
int count_impropers();
};
} // namespace LAMMPS_NS
#endif
#endif

6
src/fix.cpp
View File

@ -102,15 +102,15 @@ Fix::Fix(LAMMPS *lmp, int /*narg*/, char **arg) :
vflag_atom = cvflag_atom = 0;
centroidstressflag = CENTROID_SAME;
// KOKKOS per-fix data masks
// KOKKOS package
execution_space = Host;
datamask_read = ALL_MASK;
datamask_modify = ALL_MASK;
kokkosable = 0;
kokkosable = copymode = 0;
forward_comm_device = exchange_comm_device = sort_device = 0;
copymode = 0;
fuse_integrate_flag = 0;
}
/* ---------------------------------------------------------------------- */

4
src/fix.h
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@ -127,11 +127,12 @@ class Fix : protected Pointers {
int restart_reset; // 1 if restart just re-initialized fix
// KOKKOS host/device flag and data masks
// KOKKOS flags and variables
int kokkosable; // 1 if Kokkos fix
int forward_comm_device; // 1 if forward comm on Device
int exchange_comm_device; // 1 if exchange comm on Device
int fuse_integrate_flag; // 1 if can fuse initial integrate with final integrate
int sort_device; // 1 if sort on Device
ExecutionSpace execution_space;
unsigned int datamask_read, datamask_modify;
@ -161,6 +162,7 @@ class Fix : protected Pointers {
virtual void pre_reverse(int, int) {}
virtual void post_force(int) {}
virtual void final_integrate() {}
virtual void fused_integrate(int) {}
virtual void end_of_step() {}
virtual void post_run() {}
virtual void write_restart(FILE *) {}

3
src/lmptype.h
View File

@ -95,6 +95,7 @@ typedef int64_t bigint;
#define MAXSMALLINT INT_MAX
#define MAXTAGINT INT_MAX
#define MAXBIGINT INT64_MAX
#define MAXDOUBLEINT 9007199254740992 // 2^53
#define MPI_LMP_TAGINT MPI_INT
#define MPI_LMP_IMAGEINT MPI_INT
@ -132,6 +133,7 @@ typedef int64_t bigint;
#define MAXSMALLINT INT_MAX
#define MAXTAGINT INT64_MAX
#define MAXBIGINT INT64_MAX
#define MAXDOUBLEINT 9007199254740992 // 2^53
#define MPI_LMP_TAGINT MPI_LL
#define MPI_LMP_IMAGEINT MPI_LL
@ -168,6 +170,7 @@ typedef int bigint;
#define MAXSMALLINT INT_MAX
#define MAXTAGINT INT_MAX
#define MAXBIGINT INT_MAX
#define MAXDOUBLEINT INT_MAX
#define MPI_LMP_TAGINT MPI_INT
#define MPI_LMP_IMAGEINT MPI_INT

1
src/modify.h
View File

@ -69,6 +69,7 @@ class Modify : protected Pointers {
virtual void pre_reverse(int, int);
virtual void post_force(int);
virtual void final_integrate();
virtual void fused_integrate(int) {}
virtual void end_of_step();
virtual double energy_couple();
virtual double energy_global();

7
src/pair.cpp
View File

@ -116,15 +116,14 @@ Pair::Pair(LAMMPS *lmp) :
nondefault_history_transfer = 0;
beyond_contact = 0;
// KOKKOS per-fix data masks
// KOKKOS package
execution_space = Host;
datamask_read = ALL_MASK;
datamask_modify = ALL_MASK;
kokkosable = 0;
reverse_comm_device = 0;
copymode = 0;
kokkosable = copymode = 0;
reverse_comm_device = fuse_force_clear_flag = 0;
}
/* ---------------------------------------------------------------------- */

3
src/pair.h
View File

@ -119,12 +119,13 @@ class Pair : protected Pointers {
int beyond_contact, nondefault_history_transfer; // for granular styles
// KOKKOS host/device flag and data masks
// KOKKOS flags and variables
ExecutionSpace execution_space;
unsigned int datamask_read, datamask_modify;
int kokkosable; // 1 if Kokkos pair
int reverse_comm_device; // 1 if reverse comm on Device
int fuse_force_clear_flag; // 1 if can fuse force clear with force compute
Pair(class LAMMPS *);
~Pair() override;

1
src/timer.h
View File

@ -63,6 +63,7 @@ class Timer : protected Pointers {
bool has_normal() const { return (_level >= NORMAL); }
bool has_full() const { return (_level >= FULL); }
bool has_sync() const { return (_sync != OFF); }
bool has_timeout() const { return (_timeout >= 0.0); }
// flag if wallclock time is expired
bool is_timeout() const { return (_timeout == 0.0); }

54
tools/phonon/CMakeLists.spglib Normal file
View File

@ -0,0 +1,54 @@
cmake_minimum_required(VERSION 3.10)
project(spglib C)
set(CMAKE_MACOSX_RPATH 1)
set(CMAKE_C_FLAGS_RELEASE "-Wall -O2")
set(CMAKE_C_FLAGS_DEBUG "-g -DSPGDEBUG -DSPGWARNING")
if(NOT CMAKE_BUILD_TYPE)
set(CMAKE_BUILD_TYPE Release)
endif(NOT CMAKE_BUILD_TYPE)
message(STATUS "Build type: ${CMAKE_BUILD_TYPE}")
set(CMAKE_POSITION_INDEPENDENT_CODE ON)
# Version numbers
file(READ ${PROJECT_SOURCE_DIR}/src/version.h version_file)
string(REGEX MATCH "SPGLIB_MAJOR_VERSION ([0-9]+)" spglib_major_version ${version_file})
set(spglib_major_version ${CMAKE_MATCH_1})
string(REGEX MATCH "SPGLIB_MINOR_VERSION ([0-9]+)" spglib_minor_version ${version_file})
set(spglib_minor_version ${CMAKE_MATCH_1})
string(REGEX MATCH "SPGLIB_MICRO_VERSION ([0-9]+)" spglib_micro_version ${version_file})
set(spglib_micro_version ${CMAKE_MATCH_1})
set(serial "${spglib_major_version}.${spglib_minor_version}.${spglib_micro_version}")
set(soserial "1")
# Source code
include_directories("${PROJECT_SOURCE_DIR}/src")
set(SOURCES ${PROJECT_SOURCE_DIR}/src/arithmetic.c
${PROJECT_SOURCE_DIR}/src/cell.c
${PROJECT_SOURCE_DIR}/src/debug.c
${PROJECT_SOURCE_DIR}/src/delaunay.c
${PROJECT_SOURCE_DIR}/src/determination.c
${PROJECT_SOURCE_DIR}/src/hall_symbol.c
${PROJECT_SOURCE_DIR}/src/kgrid.c
${PROJECT_SOURCE_DIR}/src/kpoint.c
${PROJECT_SOURCE_DIR}/src/mathfunc.c
${PROJECT_SOURCE_DIR}/src/niggli.c
${PROJECT_SOURCE_DIR}/src/overlap.c
${PROJECT_SOURCE_DIR}/src/pointgroup.c
${PROJECT_SOURCE_DIR}/src/primitive.c
${PROJECT_SOURCE_DIR}/src/refinement.c
${PROJECT_SOURCE_DIR}/src/site_symmetry.c
${PROJECT_SOURCE_DIR}/src/sitesym_database.c
${PROJECT_SOURCE_DIR}/src/spacegroup.c
${PROJECT_SOURCE_DIR}/src/spg_database.c
${PROJECT_SOURCE_DIR}/src/spglib.c
${PROJECT_SOURCE_DIR}/src/spin.c
${PROJECT_SOURCE_DIR}/src/symmetry.c)
add_library(symspg STATIC ${SOURCES})
install(TARGETS symspg ARCHIVE DESTINATION ${CMAKE_INSTALL_PREFIX}/lib)
# Header file
install(FILES ${PROJECT_SOURCE_DIR}/src/spglib.h DESTINATION ${CMAKE_INSTALL_PREFIX}/include)

120
tools/phonon/CMakeLists.txt Normal file
View File

@ -0,0 +1,120 @@
# Support Linux from Ubuntu 20.04LTS onward, CentOS 7.x (with EPEL),
# macOS, MSVC 2019 (=Version 16)
cmake_minimum_required(VERSION 3.10)
# set timestamp of downloaded files to that of archive
if(POLICY CMP0135)
cmake_policy(SET CMP0135 NEW)
endif()
# set up project
set(PHANA_MINOR_VERSION 48)
project(phonon VERSION ${PHANA_MINOR_VERSION}
DESCRIPTION "Fix phonon post-processor"
LANGUAGES CXX C)
set(CMAKE_POSITION_INDEPENDENT_CODE ON)
if(NOT CMAKE_BUILD_TYPE)
set(CMAKE_BUILD_TYPE RelWithDebInfo)
endif()
# hacks for MSVC to prevent lots of pointless warnings about "unsafe" functions,
# padding and Spectre mitigation
if(MSVC)
add_compile_options(/wd4244)
add_compile_options(/wd4267)
add_compile_options(/wd4711)
add_compile_options(/wd4820)
add_compile_options(/wd5045)
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
endif()
set(CMAKE_PROJECT_VERSION ${PHANA_MINOR_VERSION})
configure_file(version.h.in version.h @ONLY)
add_executable(phana
main.cpp
disp.cpp
dynmat.cpp
green.cpp
input.cpp
interpolate.cpp
kpath.cpp
memory.cpp
phonon.cpp
phonopy.cpp
qnodes.cpp
timer.cpp
)
target_include_directories(phana PUBLIC $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}>)
if(NOT LAMMPS_DIR)
set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/../../cmake/Modules)
set(LAMMPS_THIRDPARTY_URL "https://download.lammps.org/thirdparty")
endif()
find_package(FFTW3)
if(FFTW3_FOUND)
target_compile_definitions(phana PRIVATE FFTW3)
target_link_libraries(phana PRIVATE FFTW3::FFTW3)
endif()
# build bundeled libraries
add_subdirectory(tricubic)
# standalone build must build our own version of linalg
if(NOT LAMMPS_DIR)
if(NOT USE_INTERNAL_LINALG)
find_package(LAPACK)
find_package(BLAS)
endif()
if(NOT LAPACK_FOUND OR NOT BLAS_FOUND OR USE_INTERNAL_LINALG)
file(GLOB LINALG_SOURCES CONFIGURE_DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/../../lib/linalg/[^.]*.cpp)
add_library(linalg STATIC ${LINALG_SOURCES})
set(BLAS_LIBRARIES "$<TARGET_FILE:linalg>")
set(LAPACK_LIBRARIES "$<TARGET_FILE:linalg>")
else()
list(APPEND LAPACK_LIBRARIES ${BLAS_LIBRARIES})
endif()
endif()
option(USE_SPGLIB "Download and use spglib for phonon DOS and other optional properties" ON)
if(USE_SPGLIB)
set(SPGLIB_URL "https://github.com/spglib/spglib/archive/refs/tags/v1.11.2.1.tar.gz" CACHE STRING "URL for spglib v1.x tarball")
set(SPGLIB_MD5 "3089782bc85b5034dd4765a18ee70bc7" CACHE STRING "MD5 checksum for spglib tarball")
mark_as_advanced(SPGLIB_URL)
mark_as_advanced(SPGLIB_MD5)
include(LAMMPSUtils)
GetFallbackURL(SPGLIB_URL SPGLIB_FALLBACK)
include(ExternalProject)
ExternalProject_Add(spglib_build
URL ${SPGLIB_URL} ${SPGLIB_FALLBACK}
URL_MD5 ${SPGLIB_MD5}
PREFIX ${CMAKE_CURRENT_BINARY_DIR}/spglib_build_ext
CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${CMAKE_CURRENT_BINARY_DIR}/spglib_build_ext
-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
-DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
-DCMAKE_POSITION_INDEPENDENT_CODE=ON
UPDATE_COMMAND ${CMAKE_COMMAND} -E copy_if_different ${CMAKE_CURRENT_SOURCE_DIR}/CMakeLists.spglib ${CMAKE_CURRENT_BINARY_DIR}/spglib_build_ext/src/spglib_build/CMakeLists.txt
INSTALL_COMMAND ${CMAKE_COMMAND} --build ${CMAKE_CURRENT_BINARY_DIR}/spglib_build_ext/src/spglib_build-build --target install
BUILD_BYPRODUCTS "${CMAKE_CURRENT_BINARY_DIR}/spglib_build_ext/lib/${CMAKE_STATIC_LIBRARY_PREFIX}symspg${CMAKE_STATIC_LIBRARY_SUFFIX}"
)
# workaround for older CMake versions
file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/spglib_build_ext/lib)
file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/spglib_build_ext/include)
add_library(SPGLIB::SYMSPG UNKNOWN IMPORTED)
add_dependencies(SPGLIB::SYMSPG spglib_build)
set_target_properties(SPGLIB::SYMSPG PROPERTIES
IMPORTED_LOCATION "${CMAKE_CURRENT_BINARY_DIR}/spglib_build_ext/lib/${CMAKE_STATIC_LIBRARY_PREFIX}symspg${CMAKE_STATIC_LIBRARY_SUFFIX}"
INTERFACE_INCLUDE_DIRECTORIES ${CMAKE_CURRENT_BINARY_DIR}/spglib_build_ext/include
)
target_compile_definitions(phana PRIVATE UseSPG)
target_link_libraries(phana PRIVATE SPGLIB::SYMSPG)
endif()
target_link_libraries(phana PRIVATE tricubic ${LAPACK_LIBRARIES})
install(TARGETS phana EXPORT LAMMPS_Targets DESTINATION ${CMAKE_INSTALL_BINDIR})

67
tools/phonon/Makefile
View File

@ -1,67 +0,0 @@
.SUFFIXES : .o .cpp
# compiler and flags
CC = g++ -Wno-unused-result
LINK = $(CC) -static
CFLAGS = -O3 $(DEBUG) $(UFLAG)
OFLAGS = -O3 $(DEBUG)
INC = $(LPKINC) $(TCINC) $(SPGINC) $(FFTINC)
LIB = $(LPKLIB) $(TCLIB) $(SPGLIB) $(FFTLIB)
# cLapack library needed
LPKINC = -I/opt/clapack/3.2.1/include
LPKLIB = -L/opt/clapack/3.2.1/lib -lclapack -lblas -lf2c -lm
# Tricubic library needed
TCINC = -I/opt/tricubic/1.0/include
TCLIB = -L/opt/tricubic/1.0/lib -ltricubic
# spglib, used to get the irreducible q-points
# if SFLAG is not set, spglib won't be used.
SFLAG = -DUseSPG
SPGINC = -I/opt/spglib/1.9.7/include/spglib
SPGLIB = -L/opt/spglib/1.9.7/lib -lsymspg
# FFTW 3， used to deduce the force constants in real space
# if FFLAG is not set, fftw won't be used.
FFLAG = -DFFTW3
FFTINC = -I/opt/fftw/3.3.7/include
FFTLIB = -L/opt/fftw/3.3.7/lib -lfftw3
# Debug flags
# DEBUG = -g -DDEBUG
UFLAG = $(SFLAG) $(FFLAG)
#====================================================================
ROOT = phana
# executable name
EXE = $(ROOT)
#====================================================================
# source and rules
SRC = $(wildcard *.cpp)
OBJ = $(SRC:.cpp=.o)
#====================================================================
all: ${EXE}
${EXE}: $(OBJ)
$(LINK) $(OFLAGS) $(OBJ) $(LIB) -o $@
clean:
rm -f *.o *~ *.mod ${EXE}
tar:
rm -f ${ROOT}.tar.gz; tar -czvf ${ROOT}.tar.gz *.cpp *.h Makefile README
ver:
@echo "#define VERSION `git log|grep '^commit'|wc -l`" > version.h
#====================================================================
.f.o:
$(FC) $(FFLAGS) $(FREE) $(MPI) ${INC} -c $<
.f90.o:
$(FC) $(FFLAGS) $(FREE) $(MPI) ${INC} -c $<
.c.o:
$(CC) $(CFLAGS) -c $<
.cpp.o:
$(CC) $(CFLAGS) $(INC) -c $<

56
tools/phonon/README
View File

@ -5,34 +5,38 @@
analyse the phonon related information.
#-------------------------------------------------------------------------------
1. Dependencies
The clapack library is needed to solve the eigen problems,
which could be downloaded from:
http://www.netlib.org/clapack/
The tricubic library is also needed to do tricubic interpolations,
which could now be obtained from:
https://github.com/nbigaouette/libtricubic/
The ZHEEVD LAPACK function is needed to solve the eigen problems.
A C++ compilable version based on CLAPACK is included in the linalg folder
and will be automatically built.
The tricubic library is also needed to do tricubic interpolations.
A copy is included and will be automatically built.
The spglib is optionally needed, enabling one to evaluate the
phonon density of states or vibrational thermal properties
using only the irreducible q-points in the first Brillouin zone,
as well as to evaluate the phonon dispersion curvers with the
automatic mode. Currently, the 1.8.3 version of spglib is used.
It can be obtained from:
http://spglib.sourceforge.net/
automatic mode. Currently, version 1.11.2.1 of spglib is used.
It is automatically downloaded and compiled unless the -DUSE_SPGLIB=off
variable is set during CMake configuration.
FFTW 3 might also be needed if you would like to interface with
phonopy: necessary input files for phonopy will be prepared so
that you can make use of the functions provided by phonopy.
FFTW 3 can be downloaded from:
http://www.fftw.org
It is autodetected and used if available.
FFTW 3 can be downloaded from: http://www.fftw.org
2. Compilation
To compile the code, one needs therefore to install the above
libraries and set the paths correctly in the Makefile.
Once this is done, by typing
make
will yield the executable "phana".
To compile the code, one needs to have CMake version 3.16
or later installed.
The CMake configuration is done with:
cmake -S . -B build
And compilation then performed with:
cmake --build build
The phana (or phana.exe) executable is then available in
the "build" folder
3. Unit system
The units of the output frequencies by this code is THz for
@ -46,6 +50,18 @@
5. Bug report
If any bug found, please drop a line to: konglt(at)sjtu.edu.cn
6. Precompiled executable
The "precompiled" folder contains a precompiled and statically
linked Linux executable for x86_64 CPUs. It should work on *any*
Linux machine with using the x86_64 architecture. It includes
spglib support but not fftw3.
7. Portability
Build and use of phana has been successfully tested on:
- Fedora Linux 38 using GCC, Clang, and MinGW Linux2Windows cross-compiler
- macOS 12 (Monterey) using Xcode
- Windows 11 using Visual Studio 2022 with MSVC and Clang
#-------------------------------------------------------------------------------
Author: Ling-Ti Kong, konglt(at)sjtu.edu.cn
May 2020
Aug 2021

43
tools/phonon/disp.cpp
View File

@ -1,10 +1,18 @@
#include "string.h"
#include "qnodes.h"
#include "global.h"
#include "phonon.h"
#include "green.h"
#include "timer.h"
#include "dynmat.h"
#include "global.h"
#include "input.h"
#include "kpath.h"
#include "qnodes.h"
#include <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include <string>
#include <vector>
/*------------------------------------------------------------------------------
* Private method to evaluate the phonon dispersion curves
@ -13,19 +21,22 @@ void Phonon::pdisp()
{
// ask the output file name and write the header.
char str[MAXLINE];
for (int ii = 0; ii < 80; ++ii) printf("="); printf("\n");
puts("================================================================================");
#ifdef UseSPG
// ask method to generate q-lines
int method = 2;
printf("Please select your method to generate the phonon dispersion:\n");
printf(" 1. Manual, should always work;\n");
printf(" 2. Automatic, works only for 3D crystals (CMS49-299).\nYour choice [2]: ");
if (count_words(fgets(str,MAXLINE,stdin)) > 0) method = atoi(strtok(str," \t\n\r\f"));
input->read_stdin(str);
if (count_words(str) > 0) method = atoi(strtok(str," \t\n\r\f"));
method = 2 - method%2;
printf("Your selection: %d\n", method);
#endif
printf("\nPlease input the filename to output the dispersion data [pdisp.dat]:");
if (count_words(fgets(str,MAXLINE,stdin)) < 1) strcpy(str, "pdisp.dat");
input->read_stdin(str);
if (count_words(str) < 1) strcpy(str, "pdisp.dat");
char *ptr = strtok(str," \t\n\r\f");
char *fname = new char[strlen(ptr)+1];
strcpy(fname,ptr);
@ -45,9 +56,9 @@ void Phonon::pdisp()
while (1){
for (int i = 0; i < 3; ++i) qstr[i] = qend[i];
int quit = 0;
printf("\nPlease input the start q-point in unit of B1->B3, q to exit [%g %g %g]: ", qstr[0], qstr[1], qstr[2]);
int n = count_words(fgets(str, MAXLINE, stdin));
input->read_stdin(str);
int n = count_words(str);
ptr = strtok(str, " \t\n\r\f");
if ((n == 1) && (strcmp(ptr,"q") == 0)) break;
else if (n >= 3){
@ -56,14 +67,18 @@ void Phonon::pdisp()
qstr[2] = atof(strtok(NULL, " \t\n\r\f"));
}
do printf("Please input the end q-point in unit of B1->B3: ");
while (count_words(fgets(str, MAXLINE, stdin)) < 3);
while ( 1 ){
printf("Please input the end q-point in unit of B1->B3: ");
input->read_stdin(str);
if (count_words(str) >= 3) break;
}
qend[0] = atof(strtok(str, " \t\n\r\f"));
qend[1] = atof(strtok(NULL, " \t\n\r\f"));
qend[2] = atof(strtok(NULL, " \t\n\r\f"));
printf("Please input the # of points along the line [%d]: ", nq);
if (count_words(fgets(str, MAXLINE, stdin)) > 0) nq = atoi(strtok(str," \t\n\r\f"));
input->read_stdin(str);
if (count_words(str) > 0) nq = atoi(strtok(str," \t\n\r\f"));
nq = MAX(nq,2);
double *qtmp = new double [3];
@ -147,7 +162,7 @@ void Phonon::pdisp()
printf("\nPhonon dispersion data are written to: %s, you can visualize the results\n", fname);
printf("by invoking: `gnuplot pdisp.gnuplot; gv pdisp.eps`\n");
}
for (int ii = 0; ii < 80; ++ii) printf("="); printf("\n");
puts("================================================================================");
delete []fname;
delete qnodes;

72
tools/phonon/dynmat.cpp
View File

@ -1,7 +1,16 @@
#include "dynmat.h"
#include "math.h"
#include "version.h"
#include "global.h"
#include "input.h"
#include "interpolate.h"
#include "memory.h"
#include "version.h"
#include "zheevd.h"
#include <cmath>
#include <cstdlib>
#include <cstring>
/* ----------------------------------------------------------------------------
* Class DynMat stores the Dynamic Matrix read from the binary file from
@ -9,6 +18,7 @@
* ---------------------------------------------------------------------------- */
DynMat::DynMat(int narg, char **arg)
{
input = NULL;
attyp = NULL;
memory = NULL;
M_inv_sqrt = NULL;
@ -19,6 +29,8 @@ DynMat::DynMat(int narg, char **arg)
attyp = NULL;
basis = NULL;
flag_reset_gamma = flag_skip = 0;
symprec = -1.;
int flag_save = 0;
// analyze the command line options
int iarg = 1;
@ -29,9 +41,16 @@ DynMat::DynMat(int narg, char **arg)
} else if (strcmp(arg[iarg], "-r") == 0){
flag_reset_gamma = 1;
} else if (strcmp(arg[iarg], "-p") == 0){
if (++iarg >= narg) help();
else symprec = fabs(atof(arg[iarg]));
} else if (strcmp(arg[iarg], "-h") == 0){
help();
} else if (strcmp(arg[iarg], "-save") == 0){
flag_save = 1;
} else {
if (binfile) delete []binfile;
int n = strlen(arg[iarg]) + 1;
@ -43,6 +62,8 @@ DynMat::DynMat(int narg, char **arg)
}
ShowVersion();
input = new UserInput(flag_save);
// get the binary file name from user input if not found in command line
char str[MAXLINE];
if (binfile == NULL) {
@ -50,7 +71,7 @@ DynMat::DynMat(int narg, char **arg)
printf("\n");
do {
printf("Please input the binary file name from fix_phonon: ");
fgets(str,MAXLINE,stdin);
input->read_stdin(str);
ptr = strtok(str, " \n\t\r\f");
} while (ptr == NULL);
@ -137,17 +158,17 @@ DynMat::DynMat(int narg, char **arg)
fclose(fp);
exit(3);
}
if (fread(basis[0], sizeof(double), fftdim, fp) != fftdim){
if (fread(basis[0], sizeof(double), fftdim, fp) != (size_t)fftdim){
printf("\nError while reading basis info from file: %s\n", binfile);
fclose(fp);
exit(3);
}
if (fread(&attyp[0], sizeof(int), nucell, fp) != nucell){
if (fread(&attyp[0], sizeof(int), nucell, fp) != (size_t)nucell){
printf("\nError while reading atom types from file: %s\n", binfile);
fclose(fp);
exit(3);
}
if (fread(&M_inv_sqrt[0], sizeof(double), nucell, fp) != nucell){
if (fread(&M_inv_sqrt[0], sizeof(double), nucell, fp) != (size_t)nucell){
printf("\nError while reading atomic masses from file: %s\n", binfile);
fclose(fp);
exit(3);
@ -159,6 +180,7 @@ DynMat::DynMat(int narg, char **arg)
// initialize interpolation
interpolate = new Interpolate(nx,ny,nz,fftdim2,DM_all);
interpolate->input = input;
if (flag_reset_gamma) interpolate->reset_gamma();
// Enforcing Austic Sum Rule
@ -217,7 +239,7 @@ void DynMat::writeDMq(double *q)
printf("\n");
while ( 1 ){
printf("Please input the filename to output the DM at selected q: ");
fgets(str,MAXLINE,stdin);
input->read_stdin(str);
ptr = strtok(str, " \r\t\n\f");
if (ptr) break;
}
@ -264,9 +286,9 @@ void DynMat::writeDMq(double *q, const double qr, FILE *fp)
int DynMat::geteigen(double *egv, int flag)
{
char jobz, uplo;
integer n, lda, lwork, lrwork, *iwork, liwork, info;
int n, lda, lwork, lrwork, *iwork, liwork, info;
doublecomplex *work;
doublereal *w = &egv[0], *rwork;
double *w = &egv[0], *rwork;
n = fftdim;
if (flag) jobz = 'V';
@ -348,7 +370,7 @@ void DynMat::EnforceASR()
char str[MAXLINE];
int nasr = 20;
if (nucell <= 1) nasr = 1;
printf("\n"); for (int i = 0; i < 80; ++i) printf("=");
printf("\n================================================================================");
// compute and display eigenvalues of Phi at gamma before ASR
if (nucell > 100){
@ -356,7 +378,7 @@ void DynMat::EnforceASR()
fflush(stdout);
}
double egvs[fftdim];
double *egvs = new double[fftdim];
for (int i = 0; i < fftdim; ++i)
for (int j = 0; j < fftdim; ++j) DM_q[i][j] = DM_all[0][i*fftdim+j];
geteigen(egvs, 0);
@ -370,11 +392,11 @@ void DynMat::EnforceASR()
// ask for iterations to enforce ASR
printf("Please input the # of iterations to enforce ASR [%d]: ", nasr);
fgets(str,MAXLINE,stdin);
input->read_stdin(str);
char *ptr = strtok(str," \t\n\r\f");
if (ptr) nasr = atoi(ptr);
if (nasr < 1){
for (int i=0; i<80; i++) printf("="); printf("\n");
puts("================================================================================");
return;
}
@ -439,9 +461,8 @@ void DynMat::EnforceASR()
if (i%10 == 9) printf("\n");
if (i == 99){ printf("...... (%d more skiped)", fftdim-100); break;}
}
printf("\n");
for (int i = 0; i < 80; ++i) printf("="); printf("\n\n");
delete[] egvs;
puts("\n================================================================================\n");
return;
}
@ -468,7 +489,7 @@ void DynMat::real2rec()
for (int i = 0; i < 9; ++i) ibasevec[i] *= vol;
printf("\n"); for (int i = 0; i < 80; ++i) printf("=");
printf("\n================================================================================");
printf("\nBasis vectors of the unit cell in real space:");
for (int i = 0; i < sysdim; ++i){
printf("\n A%d: ", i+1);
@ -479,8 +500,7 @@ void DynMat::real2rec()
printf("\n B%d: ", i+1);
for (int j = 0; j < sysdim; ++j) printf("%8.4f ", ibasevec[i*3+j]);
}
printf("\n"); for (int i = 0; i < 80; ++i) printf("="); printf("\n");
puts("\n================================================================================");
return;
}
@ -500,16 +520,17 @@ void DynMat::GaussJordan(int n, double *Mat)
indxc = new int[n];
indxr = new int[n];
ipiv = new int[n];
irow = icol = -1;
for (i = 0; i < n; ++i) ipiv[i] = 0;
for (i = 0; i < n; ++i){
big = 0.;
big = 0.0;
for (j = 0; j < n; ++j){
if (ipiv[j] != 1){
for (k = 0; k < n; ++k){
if (ipiv[k] == 0){
idr = j * n + k;
nmjk = abs(Mat[idr]);
nmjk = fabs(Mat[idr]);
if (nmjk >= big){
big = nmjk;
irow = j;
@ -602,6 +623,9 @@ void DynMat::help()
printf(" will also inform the code to skip all q-points that is in the vicinity\n");
printf(" of the gamma point when evaluating phonon DOS and/or phonon dispersion.\n\n");
printf(" By default, this is not set; and not expected for uncharged systems.\n\n");
printf(" -p prec To define the precision for symmetry identification with spglib.\n");
printf(" By default, 1.e-3.\n\n");
printf(" -save To record user input in `script.inp`, facilitating scripting.\n\n");
printf(" -h To print out this help info.\n\n");
printf(" file To define the filename that carries the binary dynamical matrice generated\n");
printf(" by fix-phonon. If not provided, the code will ask for it.\n");
@ -680,13 +704,13 @@ void DynMat::Define_Conversion_Factor()
* ---------------------------------------------------------------------------- */
void DynMat::ShowInfo()
{
printf("\n"); for (int i = 0; i < 80; ++i) printf("="); printf("\n");
puts("\n================================================================================");
printf("Dynamical matrix is read from file: %s\n", binfile);
printf("The system size in three dimension: %d x %d x %d\n", nx, ny, nz);
printf("Number of atoms per unit cell : %d\n", nucell);
printf("System dimension : %d\n", sysdim);
printf("Boltzmann constant in used units : %g\n", boltz);
for (int i = 0; i < 80; ++i) printf("="); printf("\n");
puts("================================================================================");
return;
}
/* --------------------------------------------------------------------*/

20
tools/phonon/dynmat.h
View File

@ -1,11 +1,9 @@
#ifndef DYNMAT_H
#define DYNMAT_H
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "memory.h"
#include "interpolate.h"
#include "zheevd.h"
#include <cstdio>
class DynMat {
public:
@ -15,7 +13,7 @@ public:
int nx, ny, nz, nucell;
int sysdim, fftdim;
double eml2f, eml2fc;
double eml2f, eml2fc, symprec;
char *funit;
void getDMq(double *);
@ -34,18 +32,18 @@ public:
double **basis;
int *attyp;
class UserInput *input;
private:
int flag_skip, flag_reset_gamma;
Interpolate *interpolate;
Memory *memory;
class Interpolate *interpolate;
class Memory *memory;
int nasr;
void EnforceASR();
char *binfile, *dmfile;
double boltz, q[3];
double boltz;
doublecomplex **DM_all;

2
tools/phonon/global.h
View File

@ -1,7 +1,7 @@
#ifndef GLOBAL_H
#define GLOBAL_H
#define ZERO 1.e-8
#define ZERO 1.0e-8
#define MAXLINE 512
#define MIN(a,b) ((a)>(b)?(b):(a))

13
tools/phonon/green.cpp
View File

@ -1,10 +1,10 @@
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include "green.h"
#include "memory.h"
#include <complex>
#include "global.h"
#include <cmath>
#include <cstdio>
/*******************************************************************************
* The class of Green is designed to evaluate the LDOS via the Green's Function
@ -59,7 +59,6 @@ Green::Green(const int ntm, const int sdim, const int niter, const double min, c
dw = (wmax - wmin)/double(nw-1);
memory->create(alpha, sysdim,nit, "Green_Green:alpha");
memory->create(beta, sysdim,nit+1,"Green_Green:beta");
//memory->create(ldos, nw,sysdim, "Green_Green:ldos");
// use Lanczos algorithm to diagonalize the Hessian
Lanczos();
@ -224,8 +223,6 @@ void Green::recursion()
{
// local variables
std::complex<double> Z, rec_x, rec_x_inv;
std::complex<double> cunit = std::complex<double>(0.,1.);
double w = wmin;
for (int i = 0; i < nw; ++i){

5
tools/phonon/green.h
View File

@ -1,8 +1,6 @@
#ifndef GREEN_H
#define GREEN_H
#include "memory.h"
class Green{
public:
Green(const int, const int, const int, const double, const double,
@ -14,12 +12,11 @@ private:
void Recursion();
void recursion();
int ndos;
double **ldos;
int natom, iatom, sysdim, nit, nw, ndim;
double dw, wmin, wmax, epson;
double **alpha, **beta, **H;
Memory *memory;
class Memory *memory;
};
#endif

35
tools/phonon/input.cpp Normal file
View File

@ -0,0 +1,35 @@
#include "input.h"
#include "global.h"
/* -------------------------------------------------------------------
* Constructor. If flag = 1, output user inputs as script.inp
* ---------------------------------------------------------------- */
UserInput::UserInput(int flag)
{
fp = NULL;
if (flag) fp = fopen("script.inp", "w");
return;
}
/* -------------------------------------------------------------------
* Deconstructor. Output user inputs as required and clear workspace.
* ---------------------------------------------------------------- */
UserInput::~UserInput()
{
if (fp) fclose(fp);
fp = NULL;
}
/* -------------------------------------------------------------------
* Read stdin and keep a record of it.
* ---------------------------------------------------------------- */
void UserInput::read_stdin(char *str)
{
fgets(str, MAXLINE, stdin);
if (fp) fprintf(fp, "%s", str);
return;
}
/* ---------------------------------------------------------------- */

17
tools/phonon/input.h Normal file
View File

@ -0,0 +1,17 @@
#ifndef INPUT_H
#define INPUT_H
#include <cstdio>
class UserInput {
public:
UserInput(int);
~UserInput();
void read_stdin(char *);
private:
FILE *fp;
};
#endif

21
tools/phonon/interpolate.cpp
View File

@ -1,6 +1,14 @@
#include "interpolate.h"
#include "math.h"
#include "global.h"
#include "input.h"
#include "memory.h"
#include "tricubic.h"
#include <cstdio>
#include <cstdlib>
#include <cstring>
/* ----------------------------------------------------------------------------
* Constructor used to get info from caller, and prepare other necessary data
@ -19,6 +27,7 @@ Interpolate::Interpolate(int nx, int ny, int nz, int ndm, doublecomplex **DM)
data = DM;
Dfdx = Dfdy = Dfdz = D2fdxdy = D2fdxdz = D2fdydz = D3fdxdydz = NULL;
flag_reset_gamma = flag_allocated_dfs = 0;
input = NULL;
return;
}
@ -265,17 +274,19 @@ void Interpolate::set_method()
{
char str[MAXLINE];
int im = 1;
printf("\n");for(int i=0; i<80; i++) printf("=");
printf("\nWhich interpolation method would you like to use?\n");
if (input == NULL) input = new UserInput(0);
puts("\n================================================================================");
printf("Which interpolation method would you like to use?\n");
printf(" 1. Tricubic;\n 2. Trilinear;\n");
printf("Your choice [1]: ");
fgets(str,MAXLINE,stdin);
input->read_stdin(str);
char *ptr = strtok(str," \t\n\r\f");
if (ptr) im = atoi(ptr);
which =2-im%2;
printf("Your selection: %d\n", which);
for(int i=0; i<80; i++) printf("="); printf("\n\n");
puts("================================================================================\n");
if (which == 1) tricubic_init();

15
tools/phonon/interpolate.h
View File

@ -1,16 +1,7 @@
#ifndef INTERPOLATION_H
#define INTERPOLATION_H
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "memory.h"
#include "tricubic.h"
extern "C"{
#include "f2c.h"
#include "clapack.h"
}
#include "zheevd.h"
class Interpolate{
public:
@ -23,11 +14,13 @@ public:
int UseGamma;
class UserInput *input;
private:
void tricubic_init();
void tricubic(double *, doublecomplex *);
void trilinear(double *, doublecomplex *);
Memory *memory;
class Memory *memory;
int which;
int Nx, Ny, Nz, Npt, ndim;

39
tools/phonon/kpath.cpp
View File

@ -1,11 +1,19 @@
#include "global.h"
#include "kpath.h"
#include "global.h"
#include "dynmat.h"
#include "memory.h"
#include "qnodes.h"
#ifdef UseSPG
extern "C"{
#include "spglib.h"
}
#include "math.h"
#include <cmath>
#include <cstdio>
#include <string>
#include <vector>
/* ----------------------------------------------------------------------------
* Class kPath will help to find the high symmetry k-path for a given lattice.
@ -47,11 +55,15 @@ kPath::kPath(DynMat *dm, QNodes *qn)
for (int idim = 0; idim < sysdim; ++idim) atpos[i][idim] = dynmat->basis[i][idim];
// get the space group number
double symprec = 1.e-4, pos[num_atom][3];
double symprec = 1.0e-3;
double **pos;
memory->create(pos,num_atom,3,"kpath:pos");
if (dynmat->symprec > 0.0) symprec = dynmat->symprec;
for (int i = 0; i < num_atom; ++i)
for (int j = 0; j < 3; ++j) pos[i][j] = atpos[i][j];
spgnum = spg_get_international(symbol, latvec, pos, attyp, num_atom, symprec);
spgnum = spg_get_international(symbol, latvec, (double (*)[3])pos, attyp, num_atom, symprec);
memory->destroy(pos);
return;
}
@ -61,7 +73,7 @@ kPath::kPath(DynMat *dm, QNodes *qn)
void kPath::show_info()
{
// display the unit cell info read
for (int ii = 0; ii < 80; ++ii) printf("-"); printf("\n");
puts("--------------------------------------------------------------------------------");
printf("The basis vectors of the unit cell:\n");
for (int idim = 0; idim < 3; ++idim){
printf(" A%d =", idim+1);
@ -76,12 +88,10 @@ void kPath::show_info()
if (num_atom > NUMATOM) printf(" ... (%d atoms omitted.)\n", num_atom-NUMATOM);
printf("The space group number of your unit cell is: %d => %s\n", spgnum, symbol);
for (int ii = 0; ii < 80; ++ii) printf("-"); printf("\n");
puts("--------------------------------------------------------------------------------");
return;
}
/* ----------------------------------------------------------------------------
* Free the memeory used by kPath.
* ---------------------------------------------------------------------------- */
@ -2765,9 +2775,16 @@ void kPath::show_path()
if (q == NULL) return;
int nbin = q->ndstr.size();
if (nbin > 0){
printf("\nk-path for the current lattice will be:\n\t%s", q->ndstr[0].c_str());
puts("\n--------------------------------------------------------------------------------");
printf("k-path for the current lattice will be:\n %s", q->ndstr[0].c_str());
for (int is = 1; is < nbin; ++is) printf("-%s", q->ndstr[is].c_str());
printf("\n");
printf("\n\nThe fractional coordinates of these paths are:\n");
for (int is = 0; is < nbin-1; ++is)
printf(" [%6.4f %6.4f %6.4f] --> [%6.4f %6.4f %6.4f] (%s - %s)\n", q->qs[is][0],
q->qs[is][1], q->qs[is][2], q->qe[is][0], q->qe[is][1], q->qe[is][2],
q->ndstr[is].c_str(), q->ndstr[is+1].c_str() );
puts("--------------------------------------------------------------------------------");
}
return;

17
tools/phonon/kpath.h
View File

@ -4,14 +4,9 @@
#ifndef KPATH_H
#define KPATH_H
#include "qnodes.h"
#include "dynmat.h"
#include "memory.h"
class kPath{
public:
kPath(DynMat *, QNodes *);
kPath(class DynMat *, class QNodes *);
~kPath();
void kpath();
@ -19,13 +14,11 @@ public:
void show_info();
private:
Memory *memory;
DynMat *dynmat;
QNodes *q;
class Memory *memory;
class DynMat *dynmat;
class QNodes *q;
char symbol[11];
int spgnum, sysdim, fftdim, num_atom, *attyp;
int spgnum, sysdim, num_atom, *attyp;
double latvec[3][3], **atpos;
};

4
tools/phonon/main.cpp
View File

@ -1,10 +1,6 @@
#include "stdio.h"
#include "stdlib.h"
#include "dynmat.h"
#include "phonon.h"
using namespace std;
int main(int argc, char** argv)
{

6
tools/phonon/memory.cpp
View File

@ -1,8 +1,8 @@
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "memory.h"
#include <cstdio>
#include <cstdlib>
/* ----------------------------------------------------------------------
safe malloc
------------------------------------------------------------------------- */

308
tools/phonon/memory.h
View File

@ -4,18 +4,16 @@
#define __STDC_LIMIT_MACROS
#define __STDC_FORMAT_MACROS
#include "stdio.h"
#include "stdlib.h"
#include "limits.h"
#include "stdint.h"
#include "inttypes.h"
#include <cstdlib>
#include <stdint.h>
#include <inttypes.h>
typedef int64_t bigint;
#define BIGINT_FORMAT "%" PRId64
#define ATOBIGINT atoll
class Memory {
public:
public:
Memory(){};
void *smalloc(bigint n, const char *);
@ -24,11 +22,11 @@ class Memory {
void fail(const char *);
/* ----------------------------------------------------------------------
create a 1d array
------------------------------------------------------------------------- */
create a 1d array
------------------------------------------------------------------------- */
template <typename TYPE>
TYPE *create(TYPE *&array, int n, const char *name)
TYPE *create(TYPE *&array, int n, const char *name)
{
bigint nbytes = sizeof(TYPE) * n;
array = (TYPE *) smalloc(nbytes,name);
@ -36,42 +34,42 @@ class Memory {
};
template <typename TYPE>
TYPE **create(TYPE **&array, int n, const char *name) {fail(name);}
TYPE **create(TYPE **&, int, const char *name) {fail(name);}
/* ----------------------------------------------------------------------
grow or shrink 1d array
------------------------------------------------------------------------- */
------------------------------------------------------------------------- */
template <typename TYPE>
TYPE *grow(TYPE *&array, int n, const char *name)
TYPE *grow(TYPE *&array, int n, const char *name)
{
if (array == NULL) return create(array,n,name);
bigint nbytes = sizeof(TYPE) * n;
array = (TYPE *) srealloc(array,nbytes,name);
return array;
};
template <typename TYPE>
TYPE **grow(TYPE **&array, int n, const char *name) {fail(name);}
TYPE **grow(TYPE **&, int, const char *name) {fail(name);}
/* ----------------------------------------------------------------------
destroy a 1d array
------------------------------------------------------------------------- */
destroy a 1d array
------------------------------------------------------------------------- */
template <typename TYPE>
void destroy(TYPE *array)
void destroy(TYPE *array)
{
sfree(array);
};
/* ----------------------------------------------------------------------
create a 1d array with index from nlo to nhi inclusive
create a 1d array with index from nlo to nhi inclusive
cannot grow it
------------------------------------------------------------------------- */
------------------------------------------------------------------------- */
template <typename TYPE>
TYPE *create1d_offset(TYPE *&array, int nlo, int nhi, const char *name)
TYPE *create1d_offset(TYPE *&array, int nlo, int nhi, const char *name)
{
bigint nbytes = sizeof(TYPE) * (nhi-nlo+1);
array = (TYPE *) smalloc(nbytes,name);
@ -80,76 +78,76 @@ class Memory {
}
template <typename TYPE>
TYPE **create1d_offset(TYPE **&array, int nlo, int nhi, const char *name)
TYPE **create1d_offset(TYPE **&, int, int, const char *name)
{fail(name);}
/* ----------------------------------------------------------------------
destroy a 1d array with index offset
------------------------------------------------------------------------- */
destroy a 1d array with index offset
------------------------------------------------------------------------- */
template <typename TYPE>
void destroy1d_offset(TYPE *array, int offset)
void destroy1d_offset(TYPE *array, int offset)
{
if (array) sfree(&array[offset]);
}
/* ----------------------------------------------------------------------
create a 2d array
------------------------------------------------------------------------- */
create a 2d array
------------------------------------------------------------------------- */
template <typename TYPE>
TYPE **create(TYPE **&array, int n1, int n2, const char *name)
TYPE **create(TYPE **&array, int n1, int n2, const char *name)
{
bigint nbytes = sizeof(TYPE) * n1*n2;
TYPE *data = (TYPE *) smalloc(nbytes,name);
nbytes = sizeof(TYPE *) * n1;
array = (TYPE **) smalloc(nbytes,name);
int n = 0;
for (int i = 0; i < n1; i++) {
array[i] = &data[n];
n += n2;
array[i] = &data[n];
n += n2;
}
return array;
}
template <typename TYPE>
TYPE ***create(TYPE ***&array, int n1, int n2, const char *name)
TYPE ***create(TYPE ***&, int, int, const char *name)
{fail(name);}
/* ----------------------------------------------------------------------
grow or shrink 1st dim of a 2d array
last dim must stay the same
------------------------------------------------------------------------- */
------------------------------------------------------------------------- */
template <typename TYPE>
TYPE **grow(TYPE **&array, int n1, int n2, const char *name)
TYPE **grow(TYPE **&array, int n1, int n2, const char *name)
{
if (array == NULL) return create(array,n1,n2,name);
bigint nbytes = sizeof(TYPE) * n1*n2;
TYPE *data = (TYPE *) srealloc(array[0],nbytes,name);
nbytes = sizeof(TYPE *) * n1;
array = (TYPE **) srealloc(array,nbytes,name);
int n = 0;
for (int i = 0; i < n1; i++) {
array[i] = &data[n];
n += n2;
array[i] = &data[n];
n += n2;
}
return array;
}
template <typename TYPE>
TYPE ***grow(TYPE ***&array, int n1, int n2, const char *name)
TYPE ***grow(TYPE ***&, int, int, const char *name)
{fail(name);}
/* ----------------------------------------------------------------------
destroy a 2d array
------------------------------------------------------------------------- */
destroy a 2d array
------------------------------------------------------------------------- */
template <typename TYPE>
void destroy(TYPE **array)
void destroy(TYPE **array)
{
if (array == NULL) return;
sfree(array[0]);
@ -157,42 +155,11 @@ class Memory {
}
/* ----------------------------------------------------------------------
create a 2d array with 2nd index from n2lo to n2hi inclusive
cannot grow it
------------------------------------------------------------------------- */
create a 3d array
------------------------------------------------------------------------- */
template <typename TYPE>
TYPE **create2d_offset(TYPE **&array, int n1, int n2lo, int n2hi,
const char *name)
{
int n2 = n2hi - n2lo + 1;
create(array,n1,n2,name);
for (int i = 0; i < n1; i++) array[i] -= n2lo;
return array;
}
template <typename TYPE>
TYPE ***create2d_offset(TYPE ***&array, int n1, int n2lo, int n2hi,
const char *name) {fail(name);}
/* ----------------------------------------------------------------------
destroy a 2d array with 2nd index offset
------------------------------------------------------------------------- */
template <typename TYPE>
void destroy2d_offset(TYPE **array, int offset)
{
if (array == NULL) return;
sfree(&array[0][offset]);
sfree(array);
}
/* ----------------------------------------------------------------------
create a 3d array
------------------------------------------------------------------------- */
template <typename TYPE>
TYPE ***create(TYPE ***&array, int n1, int n2, int n3, const char *name)
TYPE ***create(TYPE ***&array, int n1, int n2, int n3, const char *name)
{
bigint nbytes = sizeof(TYPE) * n1*n2*n3;
TYPE *data = (TYPE *) smalloc(nbytes,name);
@ -200,62 +167,62 @@ class Memory {
TYPE **plane = (TYPE **) smalloc(nbytes,name);
nbytes = sizeof(TYPE **) * n1;
array = (TYPE ***) smalloc(nbytes,name);
int i,j;
int n = 0;
for (i = 0; i < n1; i++) {
array[i] = &plane[i*n2];
for (j = 0; j < n2; j++) {
plane[i*n2+j] = &data[n];
n += n3;
}
array[i] = &plane[i*n2];
for (j = 0; j < n2; j++) {
plane[i*n2+j] = &data[n];
n += n3;
}
}
return array;
}
template <typename TYPE>
TYPE ****create(TYPE ****&array, int n1, int n2, int n3, const char *name)
TYPE ****create(TYPE ****&, int, int, int, const char *name)
{fail(name);}
/* ----------------------------------------------------------------------
grow or shrink 1st dim of a 3d array
last 2 dims must stay the same
------------------------------------------------------------------------- */
------------------------------------------------------------------------- */
template <typename TYPE>
TYPE ***grow(TYPE ***&array, int n1, int n2, int n3, const char *name)
TYPE ***grow(TYPE ***&array, int n1, int n2, int n3, const char *name)
{
if (array == NULL) return create(array,n1,n2,n3,name);
bigint nbytes = sizeof(TYPE) * n1*n2*n3;
TYPE *data = (TYPE *) srealloc(array[0][0],nbytes,name);
nbytes = sizeof(TYPE *) * n1*n2;
TYPE **plane = (TYPE **) srealloc(array[0],nbytes,name);
nbytes = sizeof(TYPE **) * n1;
array = (TYPE ***) srealloc(array,nbytes,name);
int i,j;
int n = 0;
for (i = 0; i < n1; i++) {
array[i] = &plane[i*n2];
for (j = 0; j < n2; j++) {
plane[i*n2+j] = &data[n];
n += n3;
}
array[i] = &plane[i*n2];
for (j = 0; j < n2; j++) {
plane[i*n2+j] = &data[n];
n += n3;
}
}
return array;
}
template <typename TYPE>
TYPE ****grow(TYPE ****&array, int n1, int n2, int n3, const char *name)
TYPE ****grow(TYPE ****&, int, int, int, const char *name)
{fail(name);}
/* ----------------------------------------------------------------------
destroy a 3d array
------------------------------------------------------------------------- */
destroy a 3d array
------------------------------------------------------------------------- */
template <typename TYPE>
void destroy(TYPE ***array)
void destroy(TYPE ***array)
{
if (array == NULL) return;
sfree(array[0][0]);
@ -263,168 +230,23 @@ class Memory {
sfree(array);
}
/* ----------------------------------------------------------------------
create a 3d array with 1st index from n1lo to n1hi inclusive
cannot grow it
------------------------------------------------------------------------- */
template <typename TYPE>
TYPE ***create3d_offset(TYPE ***&array, int n1lo, int n1hi,
int n2, int n3, const char *name)
{
int n1 = n1hi - n1lo + 1;
create(array,n1,n2,n3,name);
array -= n1lo;
return array;
}
template <typename TYPE>
TYPE ****create3d_offset(TYPE ****&array, int n1lo, int n1hi,
int n2, int n3, const char *name)
{fail(name);}
/* ----------------------------------------------------------------------
free a 3d array with 1st index offset
------------------------------------------------------------------------- */
template <typename TYPE>
void destroy3d_offset(TYPE ***array, int offset)
{
if (array) destroy(&array[offset]);
}
/* ----------------------------------------------------------------------
create a 3d array with
1st index from n1lo to n1hi inclusive,
2nd index from n2lo to n2hi inclusive,
3rd index from n3lo to n3hi inclusive
cannot grow it
------------------------------------------------------------------------- */
template <typename TYPE>
TYPE ***create3d_offset(TYPE ***&array, int n1lo, int n1hi,
int n2lo, int n2hi, int n3lo, int n3hi,
const char *name)
{
int n1 = n1hi - n1lo + 1;
int n2 = n2hi - n2lo + 1;
int n3 = n3hi - n3lo + 1;
create(array,n1,n2,n3,name);
for (int i = 0; i < n1*n2; i++) array[0][i] -= n3lo;
for (int i = 0; i < n1; i++) array[i] -= n2lo;
array -= n1lo;
return array;
}
template <typename TYPE>
TYPE ****create3d_offset(TYPE ****&array, int n1lo, int n1hi,
int n2lo, int n2hi, int n3lo, int n3hi,
const char *name)
{fail(name);}
/* ----------------------------------------------------------------------
free a 3d array with all 3 indices offset
------------------------------------------------------------------------- */
template <typename TYPE>
void destroy3d_offset(TYPE ***array,
int n1_offset, int n2_offset, int n3_offset)
{
if (array == NULL) return;
sfree(&array[n1_offset][n2_offset][n3_offset]);
sfree(&array[n1_offset][n2_offset]);
sfree(&array[n1_offset]);
}
/* ----------------------------------------------------------------------
create a 4d array
------------------------------------------------------------------------- */
template <typename TYPE>
TYPE ****create(TYPE ****&array, int n1, int n2, int n3, int n4,
const char *name)
{
bigint nbytes = sizeof(TYPE) * n1*n2*n3*n4;
TYPE *data = (double *) smalloc(nbytes,name);
nbytes = sizeof(TYPE *) * n1*n2*n3;
TYPE **cube = (double **) smalloc(nbytes,name);
nbytes = sizeof(TYPE **) * n1*n2;
TYPE ***plane = (double ***) smalloc(nbytes,name);
nbytes = sizeof(TYPE ***) * n1;
array = (double ****) smalloc(nbytes,name);
int i,j,k;
int n = 0;
for (i = 0; i < n1; i++) {
array[i] = &plane[i*n2];
for (j = 0; j < n2; j++) {
plane[i*n2+j] = &cube[i*n2*n3+j*n3];
for (k = 0; k < n3; k++) {
cube[i*n2*n3+j*n3+k] = &data[n];
n += n4;
}
}
}
return array;
}
template <typename TYPE>
TYPE *****create(TYPE *****&array, int n1, int n2, int n3, int n4,
const char *name)
{fail(name);}
/* ----------------------------------------------------------------------
destroy a 4d array
------------------------------------------------------------------------- */
template <typename TYPE>
void destroy(TYPE ****array)
{
if (array == NULL) return;
sfree(array[0][0][0]);
sfree(array[0][0]);
sfree(array[0]);
sfree(array);
}
/* ----------------------------------------------------------------------
memory usage of arrays, including pointers
------------------------------------------------------------------------- */
------------------------------------------------------------------------- */
template <typename TYPE>
bigint usage(TYPE *array, int n)
bigint usage(TYPE *, int n)
{
bigint bytes = sizeof(TYPE) * n;
return bytes;
}
template <typename TYPE>
bigint usage(TYPE **array, int n1, int n2)
bigint usage(TYPE **, int n1, int n2)
{
bigint bytes = sizeof(TYPE) * n1*n2;
bytes += sizeof(TYPE *) * n1;
return bytes;
}
template <typename TYPE>
bigint usage(TYPE ***array, int n1, int n2, int n3)
{
bigint bytes = sizeof(TYPE) * n1*n2*n3;
bytes += sizeof(TYPE *) * n1*n2;
bytes += sizeof(TYPE **) * n1;
return bytes;
}
template <typename TYPE>
bigint usage(TYPE ****array, int n1, int n2, int n3, int n4)
{
bigint bytes = sizeof(TYPE) * n1*n2*n3*n4;
bytes += sizeof(TYPE *) * n1*n2*n3;
bytes += sizeof(TYPE **) * n1*n2;
bytes += sizeof(TYPE ***) * n1;
return bytes;
}
};
#endif

176
tools/phonon/phonon.cpp
View File

@ -1,9 +1,18 @@
#include <vector>
#include "string.h"
#include "phonon.h"
#include "green.h"
#include "timer.h"
#include "global.h"
#include "dynmat.h"
#include "green.h"
#include "input.h"
#include "memory.h"
#include "timer.h"
#include "zheevd.h"
#include <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#ifdef UseSPG
extern "C"{
@ -27,6 +36,7 @@ Phonon::Phonon(DynMat *dm)
dynmat = dm;
sysdim = dynmat->sysdim;
ndim = dynmat->fftdim;
input = dm->input;
dos = NULL;
ldos = NULL;
qpts = NULL;
@ -42,10 +52,7 @@ Phonon::Phonon(DynMat *dm)
// display the menu
char str[MAXLINE];
while ( 1 ){
printf("\n");
for (int i = 0; i < 37; ++i) printf("=");
printf(" Menu ");
for (int i = 0; i < 37; ++i) printf("="); printf("\n");
puts("\n===================================== Menu =====================================");
printf(" 1. Phonon DOS evaluation;\n");
printf(" 2. Phonon dispersion curves;\n");
printf(" 3. Dynamical matrix at arbitrary q;\n");
@ -64,9 +71,10 @@ Phonon::Phonon(DynMat *dm)
// read user choice
int job = 0;
printf("Your choice [0]: ");
if (count_words(fgets(str,MAXLINE,stdin)) > 0) job = atoi(strtok(str," \t\n\r\f"));
input->read_stdin(str);
if (count_words(str) > 0) job = atoi(strtok(str," \t\n\r\f"));
printf("\nYour selection: %d\n", job);
for (int i = 0; i < 80; ++i) printf("=");printf("\n\n");
puts("================================================================================\n");
// now to do the job according to user's choice
if (job == 1) pdos();
@ -138,7 +146,8 @@ void Phonon::pdos()
// Now to ask for the output frequency range
printf("\nThe frequency range of all q-points are: [%g %g]\n", fmin, fmax);
printf("Please input the desired range to get DOS [%g %g]: ", fmin, fmax);
if (count_words(fgets(str,MAXLINE,stdin)) >= 2){
input->read_stdin(str);
if (count_words(str) >= 2){
fmin = atof(strtok(str," \t\n\r\f"));
fmax = atof(strtok(NULL," \t\n\r\f"));
}
@ -147,7 +156,8 @@ void Phonon::pdos()
ndos = 201;
printf("Please input the number of intervals [%d]: ", ndos);
if (count_words(fgets(str,MAXLINE,stdin)) > 0) ndos = atoi(strtok(str," \t\n\r\f"));
input->read_stdin(str);
if (count_words(str) > 0) ndos = atoi(strtok(str," \t\n\r\f"));
ndos += (ndos+1)%2; ndos = MAX(2,ndos);
@ -170,7 +180,8 @@ void Phonon::pdos()
// smooth dos ?
printf("Would you like to smooth the phonon dos? (y/n)[n]: ");
if (count_words(fgets(str,MAXLINE,stdin)) > 0){
input->read_stdin(str);
if (count_words(str) > 0){
char *flag = strtok(str," \t\n\r\f");
if (strcmp(flag,"y") == 0 || strcmp(flag,"Y") == 0) smooth(dos, ndos);
}
@ -194,7 +205,8 @@ void Phonon::writeDOS()
char str[MAXLINE];
// now to output the phonon DOS
printf("\nPlease input the filename to write DOS [pdos.dat]: ");
if (count_words(fgets(str,MAXLINE,stdin)) < 1) strcpy(str, "pdos.dat");
input->read_stdin(str);
if (count_words(str) < 1) strcpy(str, "pdos.dat");
char *fname = strtok(str," \t\n\r\f");
printf("The total phonon DOS will be written to file: %s\n", fname);
@ -234,7 +246,7 @@ void Phonon::writeLDOS()
const double one3 = 1./double(sysdim);
char str[MAXLINE];
for (int ilocal = 0; ilocal < nlocal; ++ilocal){
sprintf(str,"pldos_%d.dat", locals[ilocal]);
snprintf(str, MAXLINE-1, "pldos_%d.dat", locals[ilocal]);
char *fname = strtok(str," \t\n\r\f");
FILE *fp = fopen(fname, "w"); fname = NULL;
@ -281,7 +293,7 @@ void Phonon::ldos_rsgf()
fmin = fmax = egvs[0];
for (int i = 1; i < ndim; ++i){fmin = MIN(fmin, egvs[i]); fmax = MAX(fmax, egvs[i]);}
delete []egvs;
delete[] egvs;
} else {
fmin = 0.; fmax = 20.;
@ -297,7 +309,8 @@ void Phonon::ldos_rsgf()
printf("\nThere are %d atoms in each unit cell of your lattice.\n", dynmat->nucell);
printf("Please input the index/index range/index range and increment of atom(s)\n");
printf("in the unit cell to evaluate LDOS, q to exit [%d]: ", ik);
int nr = count_words( fgets(str,MAXLINE,stdin) );
input->read_stdin(str);
int nr = count_words(str);
if (nr < 1){
istr = iend = ik;
iinc = 1;
@ -327,7 +340,8 @@ void Phonon::ldos_rsgf()
}
printf("Please input the frequency range to evaluate LDOS [%g %g]: ", fmin, fmax);
if (count_words(fgets(str,MAXLINE,stdin)) >= 2){
input->read_stdin(str);
if (count_words(str) >= 2){
fmin = atof(strtok(str," \t\n\r\f"));
fmax = atof(strtok(NULL," \t\n\r\f"));
}
@ -335,16 +349,19 @@ void Phonon::ldos_rsgf()
printf("The frequency range for your LDOS is [%g %g].\n", fmin, fmax);
printf("Please input the desired number of points in LDOS [%d]: ", ndos);
if (count_words(fgets(str,MAXLINE,stdin)) > 0) ndos = atoi(strtok(str," \t\n\r\f"));
input->read_stdin(str);
if (count_words(str) > 0) ndos = atoi(strtok(str," \t\n\r\f"));
if (ndos < 2) break;
ndos += (ndos+1)%2;
printf("Please input the maximum # of Lanczos iterations [%d]: ", nit);
if (count_words(fgets(str,MAXLINE,stdin)) > 0) nit = atoi(strtok(str," \t\n\r\f"));
input->read_stdin(str);
if (count_words(str) > 0) nit = atoi(strtok(str," \t\n\r\f"));
if (nit < 1) break;
printf("Please input the value of epsilon for delta-function [%g]: ", eps);
if (count_words(fgets(str,MAXLINE,stdin)) > 0) eps = atof(strtok(str," \t\n\r\f"));
input->read_stdin(str);
if (count_words(str) > 0) eps = atof(strtok(str," \t\n\r\f"));
if (eps <= 0.) break;
// prepare array for local pdos
@ -395,8 +412,11 @@ void Phonon::dmanyq()
{
char str[MAXLINE];
double q[3];
do printf("Please input the q-point to output the dynamical matrix:");
while (count_words(fgets(str,MAXLINE,stdin)) < 3);
while ( 1 ){
printf("Please input the q-point to output the dynamical matrix: ");
input->read_stdin(str);
if (count_words(str) >= 3) break;
}
q[0] = atof(strtok(str," \t\n\r\f"));
q[1] = atof(strtok(NULL," \t\n\r\f"));
q[2] = atof(strtok(NULL," \t\n\r\f"));
@ -413,11 +433,13 @@ void Phonon::dmanyq()
void Phonon::vfanyq()
{
char str[MAXLINE];
double q[3], egvs[ndim];
double q[3];
double *egvs = new double[ndim];
while ( 1 ){
printf("Please input the q-point to compute the frequencies, q to exit: ");
if (count_words(fgets(str,MAXLINE,stdin)) < 3) break;
input->read_stdin(str);
if (count_words(str) < 3) break;
q[0] = atof(strtok(str, " \t\n\r\f"));
q[1] = atof(strtok(NULL," \t\n\r\f"));
@ -427,9 +449,11 @@ void Phonon::vfanyq()
dynmat->geteigen(egvs, 0);
printf("q-point: [%lg %lg %lg], ", q[0], q[1], q[2]);
printf("vibrational frequencies at this q-point:\n");
for (int i = 0; i < ndim; ++i) printf("%lg ", egvs[i]); printf("\n\n");
for (int i = 0; i < ndim; ++i) printf("%lg ", egvs[i]);
printf("\n\n");
}
delete[] egvs;
return;
}
@ -439,15 +463,18 @@ void Phonon::vfanyq()
void Phonon::vecanyq()
{
char str[MAXLINE];
double q[3], egvs[ndim];
double q[3];
double *egvs = new double[ndim];
doublecomplex **eigvec = dynmat->DM_q;
printf("Please input the filename to output the result [eigvec.dat]: ");
if (count_words(fgets(str,MAXLINE,stdin)) < 1) strcpy(str,"eigvec.dat");
input->read_stdin(str);
if (count_words(str) < 1) strcpy(str,"eigvec.dat");
FILE *fp = fopen(strtok(str," \t\n\r\f"), "w");
while ( 1 ){
printf("Please input the q-point to compute the frequencies, q to exit: ");
if (count_words(fgets(str,MAXLINE,stdin)) < 3) break;
input->read_stdin(str);
if (count_words(str) < 3) break;
q[0] = atof(strtok(str, " \t\n\r\f"));
q[1] = atof(strtok(NULL," \t\n\r\f"));
@ -475,6 +502,7 @@ void Phonon::vecanyq()
fprintf(fp,"\n");
}
fclose(fp);
delete[] egvs;
eigvec = NULL;
return;
}
@ -488,7 +516,8 @@ void Phonon::DMdisp()
char str[MAXLINE];
printf("Please input the filename to output the DM data [DMDisp.dat]: ");
if (count_words(fgets(str,MAXLINE,stdin)) < 1) strcpy(str, "DMDisp.dat");
input->read_stdin(str);
if (count_words(str) < 1) strcpy(str, "DMDisp.dat");
char *fname = strtok(str," \t\n\r\f");
FILE *fp = fopen(fname, "w"); fname = NULL;
@ -503,7 +532,8 @@ void Phonon::DMdisp()
for (int i = 0; i < 3; ++i) qstr[i] = qend[i];
printf("\nPlease input the start q-point in unit of B1->B3, q to exit [%g %g %g]: ", qstr[0], qstr[1], qstr[2]);
int n = count_words(fgets(str,MAXLINE,stdin));
input->read_stdin(str);
int n = count_words(str);
char *ptr = strtok(str," \t\n\r\f");
if ((n == 1) && (strcmp(ptr,"q") == 0)) break;
else if (n >= 3){
@ -512,14 +542,18 @@ void Phonon::DMdisp()
qstr[2] = atof(strtok(NULL," \t\n\r\f"));
}
do printf("Please input the end q-point in unit of B1->B3: ");
while (count_words(fgets(str,MAXLINE,stdin)) < 3);
while ( 1 ){
printf("Please input the end q-point in unit of B1->B3: ");
input->read_stdin(str);
if (count_words(str) >= 3) break;
}
qend[0] = atof(strtok(str," \t\n\r\f"));
qend[1] = atof(strtok(NULL," \t\n\r\f"));
qend[2] = atof(strtok(NULL," \t\n\r\f"));
printf("Please input the # of points along the line [%d]: ", nq);
if (count_words(fgets(str,MAXLINE,stdin)) > 0) nq = atoi(strtok(str," \t\n\r\f"));
input->read_stdin(str);
if (count_words(str) > 0) nq = atoi(strtok(str," \t\n\r\f"));
nq = MAX(nq,2);
for (int i=0; i<3; i++) qinc[i] = (qend[i]-qstr[i])/double(nq-1);
@ -588,7 +622,8 @@ void Phonon::therm()
char str[MAXLINE];
printf("\nPlease input the filename to output thermal properties [therm.dat]:");
if (count_words(fgets(str,MAXLINE,stdin)) < 1) strcpy(str, "therm.dat");
input->read_stdin(str);
if (count_words(str) < 1) strcpy(str, "therm.dat");
char *fname = strtok(str," \t\n\r\f");
FILE *fp = fopen(fname, "a"); fname = NULL;
// header line
@ -630,7 +665,8 @@ void Phonon::therm()
fprintf(fp,"%lg %lg %lg %lg %lg %lg\n", T, Uvib, Svib, Fvib, ZPE, Cvib);
printf("Please input the desired temperature (K), enter to exit: ");
if (count_words(fgets(str,MAXLINE,stdin)) < 1) break;
input->read_stdin(str);
if (count_words(str) < 1) break;
T = atof(strtok(str," \t\n\r\f"));
} while (T > 0.);
@ -646,12 +682,14 @@ void Phonon::local_therm()
{
char str[MAXLINE];
printf("\nWould you like to compute the local thermal properties (y/n)[n]: ");
if (count_words(fgets(str,MAXLINE,stdin)) < 1) return;
input->read_stdin(str);
if (count_words(str) < 1) return;
char *ptr = strtok(str," \t\n\r\f");
if (strcmp(ptr,"y") != 0 && strcmp(ptr, "Y") != 0 && strcmp(ptr, "yes") != 0) return;
printf("Please input the filename to output vibrational thermal info [localtherm.dat]: ");
if (count_words(fgets(str,MAXLINE,stdin)) < 1) strcpy(str, "localtherm.dat");
input->read_stdin(str);
if (count_words(str) < 1) strcpy(str, "localtherm.dat");
FILE *fp = fopen(strtok(str," \t\n\r\f"), "w");
fprintf(fp,"# atom Temp U_vib (eV) S_vib (kB) F_vib (eV) C_vib (kB) ZPE (eV)\n");
@ -672,7 +710,8 @@ void Phonon::local_therm()
while ( 1 ){
printf("\nPlease input the temperature at which to evaluate the local vibrational\n");
printf("thermal properties, non-positive number to exit [%g]: ", T);
if (count_words(fgets(str,MAXLINE,stdin)) > 0){
input->read_stdin(str);
if (count_words(str) > 0){
T = atoi(strtok(str," \t\n\r\f"));
if (T <= 0.) break;
}
@ -765,7 +804,8 @@ void Phonon::QMesh()
printf("\nThe q-mesh size from the read dynamical matrix is: %d x %d x %d\n", nx, ny, nz);
printf("A denser mesh can be interpolated, but NOTE a too dense mesh can cause segmentation fault.\n");
printf("Please input your desired q-mesh size [%d %d %d]: ", nx, ny, nz);
if (count_words(fgets(str,MAXLINE,stdin)) >= 3){
input->read_stdin(str);
if (count_words(str) >= 3){
nx = atoi(strtok(str," \t\n\r\f"));
ny = atoi(strtok(NULL," \t\n\r\f"));
nz = atoi(strtok(NULL," \t\n\r\f"));
@ -780,7 +820,8 @@ void Phonon::QMesh()
int method = 2;
printf("Please select your method to generate the q-points:\n");
printf(" 1. uniform;\n 2. Monkhost-Pack mesh;\nYour choice [2]: ");
if (count_words(fgets(str,MAXLINE,stdin)) > 0) method = atoi(strtok(str," \t\n\r\f"));
input->read_stdin(str);
if (count_words(str) > 0) method = atoi(strtok(str," \t\n\r\f"));
method = 2 - method%2;
printf("Your selection: %d\n", method);
#endif
@ -831,7 +872,7 @@ void Phonon::QMesh()
for (int idim = 0; idim < sysdim; ++idim) atpos[i][idim] = dynmat->basis[i][idim];
// display the unit cell info read
printf("\n");for (int ii = 0; ii < 80; ++ii) printf("="); printf("\n");
puts("\n================================================================================");
printf("The basis vectors of the unit cell:\n");
for (int idim = 0; idim < 3; ++idim)
printf(" A%d = %lg %lg %lg\n", idim+1, latvec[0][idim], latvec[1][idim], latvec[2][idim]);
@ -845,14 +886,21 @@ void Phonon::QMesh()
mesh[0] = nx; mesh[1] = ny; mesh[2] = nz;
shift[0] = shift[1] = shift[2] = 0;
int num_grid = mesh[0]*mesh[1]*mesh[2];
int grid_point[num_grid][3], map[num_grid];
double symprec = 1.e-4, pos[num_atom][3];
int **grid_point;
memory->create(grid_point, num_grid, 3, "phonon:grid_point");
int *map = new int[num_grid];
double symprec = 1.0e-3;
double **pos;
memory->create(pos, num_atom, 3, "phonon:pos");
if (dynmat->symprec > 0.) symprec = dynmat->symprec;
for (int i = 0; i < num_atom; ++i)
for (int j = 0; j < 3; ++j) pos[i][j] = atpos[i][j];
for (int j = 0; j < 3; ++j)
pos[i][j] = atpos[i][j];
// if spglib >= 1.0.3 is used
nq = spg_get_ir_reciprocal_mesh(grid_point, map, mesh, shift, is_time_reversal, latvec, pos, attyp, num_atom, symprec);
nq = spg_get_ir_reciprocal_mesh((int (*)[3])grid_point, map, mesh, shift, is_time_reversal,
latvec, (double (*)[3])pos, attyp, num_atom, symprec);
memory->create(wt, nq, "QMesh:wt");
memory->create(qpts, nq,3,"QMesh:qpts");
@ -873,11 +921,14 @@ void Phonon::QMesh()
qpts[numq][2] = double(grid_point[i][2])/double(mesh[2]);
numq++;
}
wt[iq2idx[iq]] += 1.;
wt[iq2idx[iq]] += 1.0;
}
delete []iq2idx;
double wsum = 0.;
delete[] iq2idx;
delete[] map;
memory->destroy(grid_point);
memory->destroy(pos);
double wsum = 0.0;
for (int iq = 0; iq < nq; ++iq) wsum += wt[iq];
for (int iq = 0; iq < nq; ++iq) wt[iq] /= wsum;
@ -898,7 +949,8 @@ void Phonon::ldos_egv()
char str[MAXLINE], *ptr;
printf("\nThe # of atoms per cell is: %d, please input the atom IDs to compute\n", dynmat->nucell);
printf("local PDOS, IDs begin with 0: ");
int nmax = count_words(fgets(str,MAXLINE,stdin));
input->read_stdin(str);
int nmax = count_words(str);
if (nmax < 1) return;
memory->destroy(locals);
@ -920,7 +972,8 @@ void Phonon::ldos_egv()
fmin = 0.; fmax = 10.;
printf("Please input the freqency (nv, THz) range to compute PDOS [%g %g]: ", fmin, fmax);
if (count_words(fgets(str,MAXLINE,stdin)) >= 2) {
input->read_stdin(str);
if (count_words(str) >= 2) {
fmin = atof(strtok(str," \t\n\r\f"));
fmax = atof(strtok(NULL," \t\n\r\f"));
}
@ -928,7 +981,8 @@ void Phonon::ldos_egv()
ndos = 201;
printf("Please input your desired # of points in PDOS [%d]: ", ndos);
if (count_words(fgets(str,MAXLINE,stdin)) > 0) ndos = atoi(strtok(str," \t\n\r\f"));
input->read_stdin(str);
if (count_words(str) > 0) ndos = atoi(strtok(str," \t\n\r\f"));
if (ndos < 2) return;
ndos += (ndos+1)%2;
@ -957,7 +1011,8 @@ void Phonon::ldos_egv()
Timer *time = new Timer();
// memory and pointer for eigenvalues and eigenvectors
double egval[ndim], offset=fmin-0.5*df;
double offset=fmin-0.5*df;
double *egval = new double[ndim];
doublecomplex **egvec = dynmat->DM_q;
printf("\nNow to compute the phonons and DOSs "); fflush(stdout);
@ -985,6 +1040,7 @@ void Phonon::ldos_egv()
}
}
}
delete[] egval;
egvec = NULL;
printf("Done!\nNow to normalize the DOSs ..."); fflush(stdout);
@ -1008,10 +1064,7 @@ void Phonon::ldos_egv()
* ---------------------------------------------------------------------------- */
void Phonon::ShowCell()
{
printf("\n");
for (int i = 0; i < 30; ++i) printf("=");
printf(" Unit Cell Info ");
for (int i = 0; i < 30; ++i) printf("="); printf("\n");
puts("============================== Unit Cell Info ==============================");
printf("Number of atoms in the unit cell: %d\n", dynmat->nucell);
printf("Basis vectors of the unit cell:\n");
printf(" %15.8f %15.8f %15.8f\n", dynmat->basevec[0], dynmat->basevec[1], dynmat->basevec[2]);
@ -1024,8 +1077,7 @@ void Phonon::ShowCell()
printf("Atomic type and fractional coordinates:\n");
for (int i = 0; i < dynmat->nucell; ++i)
printf("%4d %12.8f %12.8f %12.8f\n", dynmat->attyp[i], dynmat->basis[i][0], dynmat->basis[i][1], dynmat->basis[i][2]);
for (int i = 0; i < 80; ++i) printf("=");
printf("\n");
puts("================================================================================");
return;
}
@ -1101,7 +1153,7 @@ int Phonon::count_words(const char *line)
strcpy(copy,line);
char *ptr;
if (ptr = strchr(copy,'#')) *ptr = '\0';
if ((ptr = strchr(copy,'#'))) *ptr = '\0';
if (strtok(copy," \t\n\r\f") == NULL) {
memory->destroy(copy);

16
tools/phonon/phonon.h
View File

@ -1,22 +1,16 @@
#ifndef PHONON_H
#define PHONON_H
#include "stdio.h"
#include "stdlib.h"
#include <complex>
#include "dynmat.h"
#include "memory.h"
using namespace std;
class Phonon{
public:
Phonon(DynMat *);
Phonon(class DynMat *);
~Phonon();
DynMat *dynmat;
class DynMat *dynmat;
private:
class UserInput *input;
int nq, ndim, sysdim;
double **qpts, *wt;
double **eigs;
@ -25,7 +19,7 @@ private:
double *dos, fmin, fmax, df, rdf;
double ***ldos;
Memory *memory;
class Memory *memory;
void QMesh();
void ComputeAll();

144
tools/phonon/phonopy.cpp
View File

@ -1,9 +1,20 @@
#ifdef FFTW3
#include <map>
#include "phonopy.h"
#include "math.h"
#include "kpath.h"
#include "fftw3.h"
#include "global.h"
#include "dynmat.h"
#include "input.h"
#include "memory.h"
#include <fftw3.h>
#include <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include <map>
/* ----------------------------------------------------------------------------
* Class Phonopy is designed to interface with phonopy.
@ -14,13 +25,16 @@ Phonopy::Phonopy(DynMat *dynmat)
memory = new Memory();
sysdim = dm->sysdim;
fftdim = dm->fftdim;
input = dm->input;
fftdim2 = fftdim * fftdim;
nucell = dm->nucell;
nx = ny = nz = 5;
write(1);
char str[MAXLINE];
if (count_words(fgets(str,MAXLINE,stdin)) >= 3){
if (input == NULL) input = new UserInput(0);
input->read_stdin(str);
if (count_words(str) >= 3){
nx = atoi(strtok(str," \t\n\r\f"));
ny = atoi(strtok(NULL," \t\n\r\f"));
nz = atoi(strtok(NULL," \t\n\r\f"));
@ -36,7 +50,7 @@ Phonopy::Phonopy(DynMat *dynmat)
memory->create(mass, nucell, "Phonopy:mass");
for (int i = 0; i < nucell; ++i){
double m = 1./dm->M_inv_sqrt[i];
double m = 1.0/dm->M_inv_sqrt[i];
mass[i] = m * m;
}
@ -68,7 +82,7 @@ return;
void Phonopy::write(int flag)
{
if (flag == 1){ // basic information
for (int ii = 0; ii < 80; ++ii) printf("="); printf("\n");
puts("================================================================================");
printf("Now to prepare the input files for phonopy.\n");
printf("The dimension of your present supercell is : %d x %d x %d.\n", dm->nx, dm->ny, dm->nz);
printf("The size of the force constant matrix will be: %d x %d.\n", dm->npt*3, dm->npt*3);
@ -84,19 +98,18 @@ void Phonopy::write(int flag)
} else if (flag == 4){
printf("Done!\nThe force constants information is extracted and written to FORCE_CONSTANTS,\n");
printf("the primitive cell is written to POSCAR.primitive, and the input file for\n");
printf("phonopy band evaluation is written to band.conf.\n");
printf("One should be able to obtain the phonon band structure after correcting\n");
printf("the element names in POSCAR.primitive and band.conf by running\n");
printf("`phonopy --readfc -c POSCAR.primitive -p band.conf`.\n");
for (int ii = 0; ii < 80; ++ii) printf("-");
printf("\n*** Remember to change the element names. ***\n");
#ifdef UseSPG
for (int ii = 0; ii < 80; ++ii) printf("-");
#endif
printf("phonopy band evaluation is written to band.conf.\n\n");
printf("One should be able to obtain the phonon band structure after\n");
printf(" 1) Correcting the `element names` in POSCAR.primitive and band.conf;\n");
printf(" 2) Running `phonopy --readfc -c POSCAR.primitive -p band.conf`.\n\n");
printf("Or the phonon density of states after\n");
printf(" 1) Correcting the `element names` in POSCAR.primitive and mesh.conf;\n");
printf(" 2) Running `phonopy --readfc -c POSCAR.primitive -p mesh.conf`.\n");
puts("--------------------------------------------------------------------------------");
printf("*** Remember to modify the `element names`. ***\n");
} else if (flag == 5){
for (int ii = 0; ii < 80; ++ii) printf("="); printf("\n");
puts("================================================================================");
}
return;
}
@ -162,7 +175,9 @@ void Phonopy::phonopy()
memory->destroy(out);
// in POSCAR, atoms are sorted/aggregated by type, while for LAMMPS there is no such requirment
int type_id[nucell], num_type[nucell], ntype = 0;
int *type_id = new int[nucell];
int *num_type = new int[nucell];
int ntype = 0;
for (int i = 0; i < nucell; ++i) num_type[i] = 0;
for (int i = 0; i < nucell; ++i){
int ip = ntype;
@ -221,14 +236,22 @@ void Phonopy::phonopy()
// write the primitive cell in POSCAR format
fp = fopen("POSCAR.primitive", "w");
fprintf(fp, "Fix-phonon unit cell");
for (int ip = 0; ip < ntype; ++ip) fprintf(fp, ", Elem-%d: %lg", type_id[ip], mass[ip]);
for (int ip = 0; ip < ntype; ++ip){
for (int i = 0; i < nucell; ++i){
if (dm->attyp[i] == type_id[ip]){
fprintf(fp, ", Elem-%d: %lg", type_id[ip], mass[i]);
break;
}
}
}
fprintf(fp, "\n1.\n");
int ndim = 0;
for (int idim = 0; idim < 3; ++idim){
for (int jdim = 0; jdim < 3; ++jdim) fprintf(fp, "%lg ", dm->basevec[ndim++]);
fprintf(fp, "\n");
}
for (int ip = 0; ip < ntype; ++ip) fprintf(fp, "Elem-%d ", type_id[ip]); fprintf(fp, "\n");
for (int ip = 0; ip < ntype; ++ip) fprintf(fp, "Elem-%d ", type_id[ip]);
fprintf(fp, "\n");
for (int ip = 0; ip < ntype; ++ip) fprintf(fp, "%d ", num_type[ip]);
fprintf(fp, "\nDirect\n");
for (int ip = 0; ip < ntype; ++ip){
@ -240,57 +263,48 @@ void Phonopy::phonopy()
}
fclose(fp);
#ifdef UseSPG
// Get high symmetry k-path
QNodes *q = new QNodes();
kPath *kp = new kPath(dm, q);
kp->kpath();
#endif
// mesh.conf
fp = fopen("mesh.conf", "w");
fprintf(fp, "# From Fix-phonon");
for (int ip = 0; ip < ntype; ++ip){
for (int i = 0; i < nucell; ++i){
if (dm->attyp[i] == type_id[ip]){
fprintf(fp, ", Elem-%d: %lg", type_id[ip], mass[i]);
break;
}
}
}
fprintf(fp, "\n\nATOM_NAME = ");
for (int ip = 0; ip < ntype; ++ip) fprintf(fp, "Elem-%d ", type_id[ip]);
fprintf(fp, "\nDIM = %d %d %d\n", nx, ny, nz);
fprintf(fp, "MP = 31 31 31\nFORCE_CONSTANTS = READ\n");
fprintf(fp, "#FC_SYMMETRY = .TRUE.\n#SYMMETRY_TOLERANCE = 0.01\n");
fclose(fp);
// band.conf
fp = fopen("band.conf", "w");
fprintf(fp, "# From Fix-phonon");
for (int ip = 0; ip < ntype; ++ip) fprintf(fp, ", Elem-%d: %lg", type_id[ip], mass[ip]);
for (int ip = 0; ip < ntype; ++ip){
for (int i = 0; i < nucell; ++i){
if (dm->attyp[i] == type_id[ip]){
fprintf(fp, ", Elem-%d: %lg", type_id[ip], mass[i]);
break;
}
}
}
fprintf(fp, "\n\nATOM_NAME = ");
for (int ip = 0; ip < ntype; ++ip) fprintf(fp, "Elem-%d ", type_id[ip]);
fprintf(fp, "\nDIM = %d %d %d\nBAND = ", nx, ny, nz);
#ifdef UseSPG
int nsect = q->qs.size();
for (int i = 0; i < nsect; ++i){
fprintf(fp, " %lg %lg %lg", q->qs[i][0], q->qs[i][1], q->qs[i][2]);
if (i+1 < nsect){
double dq = 0.;
for (int j = 0; j < 3; ++j) dq += (q->qe[i][j] - q->qs[i+1][j]) * (q->qe[i][j] - q->qs[i+1][j]);
if (dq > ZERO) {
fprintf(fp, " %lg %lg %lg,", q->qe[i][0], q->qe[i][1], q->qe[i][2]);
}
} else if (i+1 == nsect){
fprintf(fp, " %lg %lg %lg\n", q->qe[i][0], q->qe[i][1], q->qe[i][2]);
}
}
#endif
fprintf(fp, "\nBAND_POINTS = 21\nBAND_LABELS =");
#ifdef UseSPG
for (int i = 0; i < q->ndstr.size(); ++i){
std::size_t found = q->ndstr[i].find("{/Symbol G}");
if (found != std::string::npos) q->ndstr[i].replace(found, found+11, "$\\Gamma$");
found = q->ndstr[i].find("/");
if (found != std::string::npos) q->ndstr[i].replace(found, found, " ");
fprintf(fp, " %s", q->ndstr[i].c_str());
}
#endif
fprintf(fp, "\nFORCE_CONSTANTS = READ\nBAND_CONNECTION = .TRUE.\n");
fprintf(fp, "\nDIM = %d %d %d\nBAND = AUTO\n", nx, ny, nz);
fprintf(fp, "BAND_POINTS = 21\nFORCE_CONSTANTS = READ\nBAND_CONNECTION = .TRUE.\n");
fprintf(fp, "#FC_SYMMETRY = .TRUE.\n#SYMMETRY_TOLERANCE = 0.01\n");
// output info
write(4);
#ifdef UseSPG
kp->show_path();
delete kp;
delete q;
#endif
write(5);
return;
delete[] type_id;
delete[] num_type;
return;
}
/*------------------------------------------------------------------------------
@ -304,7 +318,7 @@ int Phonopy::count_words(const char *line)
strcpy(copy,line);
char *ptr;
if (ptr = strchr(copy,'#')) *ptr = '\0';
if ((ptr = strchr(copy,'#'))) *ptr = '\0';
if (strtok(copy," \t\n\r\f") == NULL) {
memory->destroy(copy);
@ -314,7 +328,7 @@ int Phonopy::count_words(const char *line)
while (strtok(NULL," \t\n\r\f")) n++;
memory->destroy(copy);
return n;
return n;
}
/*----------------------------------------------------------------------------*/
#endif

16
tools/phonon/phonopy.h
View File

@ -4,22 +4,16 @@
#ifndef PHONOPY_H
#define PHONOPY_H
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "memory.h"
#include "qnodes.h"
#include "dynmat.h"
#include "global.h"
#include "zheevd.h"
class Phonopy {
public:
Phonopy(DynMat *);
Phonopy(class DynMat *);
~Phonopy();
private:
Memory *memory;
char str[MAXLINE];
class UserInput *input;
class Memory *memory;
int npt, fftdim2; // local variables
int nx, ny, nz, nucell; // local variables
int sysdim, fftdim; // local variables
@ -27,7 +21,7 @@ private:
doublecomplex **FC_all;
DynMat *dm;
class DynMat *dm;
void write(int);
void get_my_FC();
void phonopy();

3
tools/phonon/timer.cpp
View File

@ -1,4 +1,7 @@
#include "timer.h"
#include <cstdio>
/* -----------------------------------------------------------------------------
* Initialization of time
* -------------------------------------------------------------------------- */

4
tools/phonon/timer.h
View File

@ -1,9 +1,7 @@
#ifndef TIMER_H
#define TIMER_H
#include "stdio.h"
#include "stdlib.h"
#include "time.h"
#include <ctime>
class Timer {
public:

18
tools/phonon/tricubic/CMakeLists.txt Normal file
View File

@ -0,0 +1,18 @@
# Support Linux from Ubuntu 20.04LTS onward, CentOS 7.x (with EPEL),
# macOS, MSVC 2019 (=Version 16)
cmake_minimum_required(VERSION 3.10)
# set up project
project(tricubic VERSION 1.1 DESCRIPTION "Tricubic library" LANGUAGES CXX)
set(CMAKE_POSITION_INDEPENDENT_CODE ON)
# hacks for MSVC to prevent lots of pointless warnings about "unsafe" functions
if(MSVC)
add_compile_options(/wd4244)
add_compile_options(/wd4267)
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
endif()
add_library(tricubic STATIC tricubic.cpp)
target_include_directories(tricubic PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})

340
tools/phonon/tricubic/LICENSE Normal file
View File

@ -0,0 +1,340 @@
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59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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28
tools/phonon/tricubic/README.md Normal file
View File

@ -0,0 +1,28 @@
# libtricubic
This folder contains a slightly refactored version of version 1.0 of
the _libtricubic_ library, developed by François Lekien in 2004.
The following paper explaining the method was published in 2005:
> Lekien, F., & Marsden, J. (2005). _Tricubic interpolation in three
> dimensions._ International Journal for Numerical Methods in Engineering,
> 63(3), 455–471. doi:10.1002/nme.1296
Some additional notes and the full matrix can be found in the technical notes:
> Lekien, F., Coulliette, C., & Marsden, J. (2004). _Tricubic Engine - Technical
> Notes and Full Matrix.
The main article refers to the author's website
(http://gyre.cds.caltech.edu/pub/software/tricubic/) to download the code and
documentation. Unfortunately, this website no longer exists. Even the
archive.org snapshot is useless; [A single snapshot from December 3rd 2009 is
available](https://web.archive.org/web/20091203115835/http://gyre.cds.caltech.edu/pub/software/tricubic)
which seems like an FTP listing. No files are accessible.
The source code was obtained from https://github.com/nbigaouette/libtricubic/
Only the sources for the library were retained. No functional changes were
made, but some common programming conventions were applied, source files
merged, and build support for CMake added.

185
tools/phonon/tricubic/tricubic.cpp Normal file
View File

@ -0,0 +1,185 @@
#include "tricubic.h"
#include <cmath>
static const int A[64][64] = {
{ 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{ 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{-3, 3, 0, 0, 0, 0, 0, 0,-2,-1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{ 2,-2, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,-3, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,-2,-1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2,-2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{-3, 0, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,-2, 0,-1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{ 0, 0, 0, 0, 0, 0, 0, 0,-3, 0, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,-2, 0,-1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{ 9,-9,-9, 9, 0, 0, 0, 0, 6, 3,-6,-3, 0, 0, 0, 0, 6,-6, 3,-3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 2, 2, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{-6, 6, 6,-6, 0, 0, 0, 0,-3,-3, 3, 3, 0, 0, 0, 0,-4, 4,-2, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,-2,-2,-1,-1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{ 2, 0,-2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{ 0, 0, 0, 0, 0, 0, 0, 0, 2, 0,-2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{-6, 6, 6,-6, 0, 0, 0, 0,-4,-2, 4, 2, 0, 0, 0, 0,-3, 3,-3, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,-2,-1,-2,-1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{ 4,-4,-4, 4, 0, 0, 0, 0, 2, 2,-2,-2, 0, 0, 0, 0, 2,-2, 2,-2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,-3, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,-2,-1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2,-2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0},
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,-3, 3, 0, 0, 0, 0, 0, 0,-2,-1, 0, 0, 0, 0, 0, 0},
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2,-2, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0},
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,-3, 0, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,-2, 0,-1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,-3, 0, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,-2, 0,-1, 0, 0, 0, 0, 0},
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9,-9,-9, 9, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 6, 3,-6,-3, 0, 0, 0, 0, 6,-6, 3,-3, 0, 0, 0, 0, 4, 2, 2, 1, 0, 0, 0, 0},
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,-6, 6, 6,-6, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,-3,-3, 3, 3, 0, 0, 0, 0,-4, 4,-2, 2, 0, 0, 0, 0,-2,-2,-1,-1, 0, 0, 0, 0},
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0,-2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0,-2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0},
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,-6, 6, 6,-6, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,-4,-2, 4, 2, 0, 0, 0, 0,-3, 3,-3, 3, 0, 0, 0, 0,-2,-1,-2,-1, 0, 0, 0, 0},
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 4,-4,-4, 4, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 2,-2,-2, 0, 0, 0, 0, 2,-2, 2,-2, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0},
{-3, 0, 0, 0, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,-2, 0, 0, 0,-1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{ 0, 0, 0, 0, 0, 0, 0, 0,-3, 0, 0, 0, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,-2, 0, 0, 0,-1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{ 9,-9, 0, 0,-9, 9, 0, 0, 6, 3, 0, 0,-6,-3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 6,-6, 0, 0, 3,-3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 2, 0, 0, 2, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{-6, 6, 0, 0, 6,-6, 0, 0,-3,-3, 0, 0, 3, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,-4, 4, 0, 0,-2, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,-2,-2, 0, 0,-1,-1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,-3, 0, 0, 0, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,-2, 0, 0, 0,-1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,-3, 0, 0, 0, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,-2, 0, 0, 0,-1, 0, 0, 0},
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9,-9, 0, 0,-9, 9, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 6, 3, 0, 0,-6,-3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 6,-6, 0, 0, 3,-3, 0, 0, 4, 2, 0, 0, 2, 1, 0, 0},
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,-6, 6, 0, 0, 6,-6, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,-3,-3, 0, 0, 3, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,-4, 4, 0, 0,-2, 2, 0, 0,-2,-2, 0, 0,-1,-1, 0, 0},
{ 9, 0,-9, 0,-9, 0, 9, 0, 0, 0, 0, 0, 0, 0, 0, 0, 6, 0, 3, 0,-6, 0,-3, 0, 6, 0,-6, 0, 3, 0,-3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, 2, 0, 2, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{ 0, 0, 0, 0, 0, 0, 0, 0, 9, 0,-9, 0,-9, 0, 9, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 6, 0, 3, 0,-6, 0,-3, 0, 6, 0,-6, 0, 3, 0,-3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, 2, 0, 2, 0, 1, 0},
{-27,27,27,-27,27,-27,-27,27,-18,-9,18, 9,18, 9,-18,-9,-18,18,-9, 9,18,-18, 9,-9,-18,18,18,-18,-9, 9, 9,-9,-12,-6,-6,-3,12, 6, 6, 3,-12,-6,12, 6,-6,-3, 6, 3,-12,12,-6, 6,-6, 6,-3, 3,-8,-4,-4,-2,-4,-2,-2,-1},
{18,-18,-18,18,-18,18,18,-18, 9, 9,-9,-9,-9,-9, 9, 9,12,-12, 6,-6,-12,12,-6, 6,12,-12,-12,12, 6,-6,-6, 6, 6, 6, 3, 3,-6,-6,-3,-3, 6, 6,-6,-6, 3, 3,-3,-3, 8,-8, 4,-4, 4,-4, 2,-2, 4, 4, 2, 2, 2, 2, 1, 1},
{-6, 0, 6, 0, 6, 0,-6, 0, 0, 0, 0, 0, 0, 0, 0, 0,-3, 0,-3, 0, 3, 0, 3, 0,-4, 0, 4, 0,-2, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,-2, 0,-2, 0,-1, 0,-1, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{ 0, 0, 0, 0, 0, 0, 0, 0,-6, 0, 6, 0, 6, 0,-6, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,-3, 0,-3, 0, 3, 0, 3, 0,-4, 0, 4, 0,-2, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0,-2, 0,-2, 0,-1, 0,-1, 0},
{18,-18,-18,18,-18,18,18,-18,12, 6,-12,-6,-12,-6,12, 6, 9,-9, 9,-9,-9, 9,-9, 9,12,-12,-12,12, 6,-6,-6, 6, 6, 3, 6, 3,-6,-3,-6,-3, 8, 4,-8,-4, 4, 2,-4,-2, 6,-6, 6,-6, 3,-3, 3,-3, 4, 2, 4, 2, 2, 1, 2, 1},
{-12,12,12,-12,12,-12,-12,12,-6,-6, 6, 6, 6, 6,-6,-6,-6, 6,-6, 6, 6,-6, 6,-6,-8, 8, 8,-8,-4, 4, 4,-4,-3,-3,-3,-3, 3, 3, 3, 3,-4,-4, 4, 4,-2,-2, 2, 2,-4, 4,-4, 4,-2, 2,-2, 2,-2,-2,-2,-2,-1,-1,-1,-1},
{ 2, 0, 0, 0,-2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{ 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 0,-2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{-6, 6, 0, 0, 6,-6, 0, 0,-4,-2, 0, 0, 4, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,-3, 3, 0, 0,-3, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,-2,-1, 0, 0,-2,-1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{ 4,-4, 0, 0,-4, 4, 0, 0, 2, 2, 0, 0,-2,-2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2,-2, 0, 0, 2,-2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 0,-2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 0,-2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0},
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,-6, 6, 0, 0, 6,-6, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,-4,-2, 0, 0, 4, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,-3, 3, 0, 0,-3, 3, 0, 0,-2,-1, 0, 0,-2,-1, 0, 0},
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 4,-4, 0, 0,-4, 4, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 2, 0, 0,-2,-2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2,-2, 0, 0, 2,-2, 0, 0, 1, 1, 0, 0, 1, 1, 0, 0},
{-6, 0, 6, 0, 6, 0,-6, 0, 0, 0, 0, 0, 0, 0, 0, 0,-4, 0,-2, 0, 4, 0, 2, 0,-3, 0, 3, 0,-3, 0, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,-2, 0,-1, 0,-2, 0,-1, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{ 0, 0, 0, 0, 0, 0, 0, 0,-6, 0, 6, 0, 6, 0,-6, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,-4, 0,-2, 0, 4, 0, 2, 0,-3, 0, 3, 0,-3, 0, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0,-2, 0,-1, 0,-2, 0,-1, 0},
{18,-18,-18,18,-18,18,18,-18,12, 6,-12,-6,-12,-6,12, 6,12,-12, 6,-6,-12,12,-6, 6, 9,-9,-9, 9, 9,-9,-9, 9, 8, 4, 4, 2,-8,-4,-4,-2, 6, 3,-6,-3, 6, 3,-6,-3, 6,-6, 3,-3, 6,-6, 3,-3, 4, 2, 2, 1, 4, 2, 2, 1},
{-12,12,12,-12,12,-12,-12,12,-6,-6, 6, 6, 6, 6,-6,-6,-8, 8,-4, 4, 8,-8, 4,-4,-6, 6, 6,-6,-6, 6, 6,-6,-4,-4,-2,-2, 4, 4, 2, 2,-3,-3, 3, 3,-3,-3, 3, 3,-4, 4,-2, 2,-4, 4,-2, 2,-2,-2,-1,-1,-2,-2,-1,-1},
{ 4, 0,-4, 0,-4, 0, 4, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 2, 0,-2, 0,-2, 0, 2, 0,-2, 0, 2, 0,-2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{ 0, 0, 0, 0, 0, 0, 0, 0, 4, 0,-4, 0,-4, 0, 4, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 2, 0,-2, 0,-2, 0, 2, 0,-2, 0, 2, 0,-2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 1, 0, 1, 0},
{-12,12,12,-12,12,-12,-12,12,-8,-4, 8, 4, 8, 4,-8,-4,-6, 6,-6, 6, 6,-6, 6,-6,-6, 6, 6,-6,-6, 6, 6,-6,-4,-2,-4,-2, 4, 2, 4, 2,-4,-2, 4, 2,-4,-2, 4, 2,-3, 3,-3, 3,-3, 3,-3, 3,-2,-1,-2,-1,-2,-1,-2,-1},
{ 8,-8,-8, 8,-8, 8, 8,-8, 4, 4,-4,-4,-4,-4, 4, 4, 4,-4, 4,-4,-4, 4,-4, 4, 4,-4,-4, 4, 4,-4,-4, 4, 2, 2, 2, 2,-2,-2,-2,-2, 2, 2,-2,-2, 2, 2,-2,-2, 2,-2, 2,-2, 2,-2, 2,-2, 1, 1, 1, 1, 1, 1, 1, 1}
};
static const char tricubic_version_stored[] = "1.1";
static int ijk2n(int i, int j, int k) {
return(i+4*j+16*k);
}
static void point2xyz(int p, int *x, int *y, int *z) {
switch (p) {
case 0: *x=0; *y=0; *z=0; break;
case 1: *x=1; *y=0; *z=0; break;
case 2: *x=0; *y=1; *z=0; break;
case 3: *x=1; *y=1; *z=0; break;
case 4: *x=0; *y=0; *z=1; break;
case 5: *x=1; *y=0; *z=1; break;
case 6: *x=0; *y=1; *z=1; break;
case 7: *x=1; *y=1; *z=1; break;
default:*x=0; *y=0; *z=0;
}
}
const char *tricubic_version(void) {
return(tricubic_version_stored);
}
void tricubic_pointID2xyz(int id, int *x, int *y, int *z) {
point2xyz(id,x,y,z);
}
void tricubic_pointID2xyz(int id, double *x, double *y, double *z) {
int x2,y2,z2;
point2xyz(id,&x2,&y2,&z2);
*x=(double)(x2);
*y=(double)(y2);
*z=(double)(z2);
}
void tricubic_get_coeff_stacked(double a[64], double x[64]) {
int i,j;
for (i=0;i<64;i++) {
a[i]=(double)(0.0);
for (j=0;j<64;j++) {
a[i]+=A[i][j]*x[j];
}
}
}
void tricubic_get_coeff(double a[64], double f[8], double dfdx[8], double dfdy[8], double dfdz[8], double d2fdxdy[8], double d2fdxdz[8], double d2fdydz[8], double d3fdxdydz[8]) {
int i;
double x[64];
for (i=0;i<8;i++) {
x[0+i]=f[i];
x[8+i]=dfdx[i];
x[16+i]=dfdy[i];
x[24+i]=dfdz[i];
x[32+i]=d2fdxdy[i];
x[40+i]=d2fdxdz[i];
x[48+i]=d2fdydz[i];
x[56+i]=d3fdxdydz[i];
}
tricubic_get_coeff_stacked(a,x);
}
double tricubic_eval(double a[64], double x, double y, double z) {
int i,j,k;
double ret=(double)(0.0);
/* TRICUBIC EVAL
This is the short version of tricubic_eval. It is used to compute
the value of the function at a given point (x,y,z). To compute
partial derivatives of f, use the full version with the extra args.
*/
for (i=0;i<4;i++) {
for (j=0;j<4;j++) {
for (k=0;k<4;k++) {
ret+=a[ijk2n(i,j,k)]*pow(x,i)*pow(y,j)*pow(z,k);
}
}
}
return(ret);
}
double tricubic_eval(double a[64], double x, double y, double z, int derx, int dery, int derz) {
int i,j,k;
double ret=(double)(0.0);
double cont;
int w;
/* TRICUBIC_EVAL
The full version takes 3 extra integers args that allows to evaluate
any partial derivative of f at the point
derx=dery=derz=0 => f
derx=2 dery=derz=0 => d2f/dx2
derx=dery=derz=1 =? d3f/dxdydz
NOTICE that (derx>3)||(dery>3)||(derz>3) => returns 0.0
this computes \frac{\partial ^{derx+dery+derz} d}{\partial x ^{derx} \partial y ^{dery} \partial z ^{derz}}
*/
for (i=derx;i<4;i++) {
for (j=dery;j<4;j++) {
for (k=derz;k<4;k++) {
cont=a[ijk2n(i,j,k)]*pow(x,i-derx)*pow(y,j-dery)*pow(z,k-derz);
for (w=0;w<derx;w++) {
cont*=(i-w);
}
for (w=0;w<dery;w++) {
cont*=(j-w);
}
for (w=0;w<derz;w++) {
cont*=(k-w);
}
ret+=cont;
}
}
}
return(ret);
}

10
tools/phonon/tricubic/tricubic.h Normal file
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@ -0,0 +1,10 @@
#ifndef TRICUBIC_H
#define TRICUBIC_H
extern const char *tricubic_version(void);
extern void tricubic_get_coeff(double a[64], double f[8], double dfdx[8], double dfdy[8], double dfdz[8], double d2fdxdy[8], double d2fdxdz[8], double d2fdydz[8], double d3fdxdydz[8]);
extern double tricubic_eval(double a[64], double x, double y, double z);
extern double tricubic_eval(double a[64], double x, double y, double z, int derx, int dery, int derz);
extern void tricubic_pointID2xyz(int id, int *x, int *y, int *z);
extern void tricubic_pointID2xyz(int id, double *x, double *y, double *z);
#endif

1
tools/phonon/version.h
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@ -1 +0,0 @@
#define VERSION 21

1
tools/phonon/version.h.in Normal file
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@ -0,0 +1 @@
#define VERSION @CMAKE_PROJECT_VERSION@

16
tools/phonon/zheevd.h Normal file
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@ -0,0 +1,16 @@
#ifndef ZHEEVD_H
#define ZHEEVD_H
#ifdef __cplusplus
extern "C" {
#endif
typedef struct { double r, i; } doublecomplex;
/* Subroutine */ int zheevd_(char *jobz, char *uplo, int *n,
doublecomplex *a, int *lda, double *w, doublecomplex *work,
int *lwork, double *rwork, int *lrwork, int *iwork,
int *liwork, int *info);
#ifdef __cplusplus
}
#endif
#endif

92
unittest/commands/test_compute_global.cpp
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@ -294,6 +294,98 @@ TEST_F(ComputeGlobalTest, Reduction)
EXPECT_DOUBLE_EQ(rep[2], 26);
EXPECT_DOUBLE_EQ(rep[3], max[0]);
}
TEST_F(ComputeGlobalTest, Counts)
{
if (lammps_get_natoms(lmp) == 0.0) GTEST_SKIP();
BEGIN_HIDE_OUTPUT();
command("pair_style zero 10.0");
command("pair_coeff * *");
command("variable t1 atom type==1");
command("variable t2 atom type==2");
command("variable t3 atom type==3");
command("variable t4 atom type==4");
command("variable t5 atom type==5");
command("compute tsum all reduce sum v_t1 v_t2 v_t3 v_t4 v_t5");
command("compute tcnt all count/type atom");
command("compute bcnt all count/type bond");
command("compute acnt all count/type angle");
command("compute dcnt all count/type dihedral");
command("compute icnt all count/type improper");
command("thermo_style custom c_tsum[*] c_tcnt[*] c_bcnt[*] c_acnt[*] c_dcnt[*] c_icnt[*]");
command("run 0 post no");
END_HIDE_OUTPUT();
auto tsum = get_vector("tsum");
auto tcnt = get_vector("tcnt");
auto bcnt = get_vector("bcnt");
auto bbrk = get_scalar("bcnt");
auto acnt = get_vector("acnt");
auto dcnt = get_vector("dcnt");
auto icnt = get_vector("icnt");
EXPECT_DOUBLE_EQ(tsum[0], tcnt[0]);
EXPECT_DOUBLE_EQ(tsum[1], tcnt[1]);
EXPECT_DOUBLE_EQ(tsum[2], tcnt[2]);
EXPECT_DOUBLE_EQ(tsum[3], tcnt[3]);
EXPECT_DOUBLE_EQ(tsum[4], tcnt[4]);
EXPECT_DOUBLE_EQ(bbrk, 0.0);
EXPECT_DOUBLE_EQ(bcnt[0], 3.0);
EXPECT_DOUBLE_EQ(bcnt[1], 6.0);
EXPECT_DOUBLE_EQ(bcnt[2], 3.0);
EXPECT_DOUBLE_EQ(bcnt[3], 2.0);
EXPECT_DOUBLE_EQ(bcnt[4], 10.0);
EXPECT_DOUBLE_EQ(acnt[0], 6.0);
EXPECT_DOUBLE_EQ(acnt[1], 10.0);
EXPECT_DOUBLE_EQ(acnt[2], 5.0);
EXPECT_DOUBLE_EQ(acnt[3], 9.0);
EXPECT_DOUBLE_EQ(dcnt[0], 3.0);
EXPECT_DOUBLE_EQ(dcnt[1], 8.0);
EXPECT_DOUBLE_EQ(dcnt[2], 3.0);
EXPECT_DOUBLE_EQ(dcnt[3], 4.0);
EXPECT_DOUBLE_EQ(dcnt[4], 13.0);
EXPECT_DOUBLE_EQ(icnt[0], 1.0);
EXPECT_DOUBLE_EQ(icnt[1], 1.0);
BEGIN_HIDE_OUTPUT();
command("delete_bonds all bond 3 remove");
command("run 0 post no");
END_HIDE_OUTPUT();
bcnt = get_vector("bcnt");
bbrk = get_scalar("bcnt");
acnt = get_vector("acnt");
dcnt = get_vector("dcnt");
icnt = get_vector("icnt");
EXPECT_DOUBLE_EQ(bbrk, 0.0);
EXPECT_DOUBLE_EQ(bcnt[0], 3.0);
EXPECT_DOUBLE_EQ(bcnt[1], 6.0);
EXPECT_DOUBLE_EQ(bcnt[2], 0.0);
EXPECT_DOUBLE_EQ(bcnt[3], 2.0);
EXPECT_DOUBLE_EQ(bcnt[4], 10.0);
EXPECT_DOUBLE_EQ(acnt[0], 6.0);
EXPECT_DOUBLE_EQ(acnt[1], 10.0);
EXPECT_DOUBLE_EQ(acnt[2], 5.0);
EXPECT_DOUBLE_EQ(acnt[3], 9.0);
EXPECT_DOUBLE_EQ(dcnt[0], 3.0);
EXPECT_DOUBLE_EQ(dcnt[1], 8.0);
EXPECT_DOUBLE_EQ(dcnt[2], 3.0);
EXPECT_DOUBLE_EQ(dcnt[3], 4.0);
EXPECT_DOUBLE_EQ(dcnt[4], 13.0);
EXPECT_DOUBLE_EQ(icnt[0], 1.0);
EXPECT_DOUBLE_EQ(icnt[1], 1.0);
}
} // namespace LAMMPS_NS
int main(int argc, char **argv)