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merge conflicts in cmakelist

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This commit is contained in:
abhishandy
2020-08-14 22:33:10 -04:00
parent a33c0081cd 6d725c9b1c
commit 194fe17263
121 changed files with 6528 additions and 214 deletions
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2
cmake/Modules/Documentation.cmake
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@ -29,8 +29,8 @@ if(BUILD_DOC)
OUTPUT requirements.txt
DEPENDS docenv
COMMAND ${CMAKE_COMMAND} -E copy ${LAMMPS_DOC_DIR}/utils/requirements.txt requirements.txt
COMMAND ${DOCENV_BINARY_DIR}/pip install -r requirements.txt --upgrade
COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade ${LAMMPS_DOC_DIR}/utils/converters
COMMAND ${DOCENV_BINARY_DIR}/pip install --use-feature=2020-resolver -r requirements.txt --upgrade
)
# download mathjax distribution and unpack to folder "mathjax"

2
doc/Makefile
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@ -194,7 +194,7 @@ $(VENV):
$(VIRTUALENV) -p $(PYTHON) $(VENV); \
. $(VENV)/bin/activate; \
pip install --upgrade pip; \
pip install -r requirements.txt; \
pip install --use-feature=2020-resolver -r requirements.txt; \
deactivate;\
)

60
doc/src/Build_development.rst
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@ -159,8 +159,8 @@ A test run is then a a collection multiple individual test runs each
with many comparisons to reference results based on template input
files, individual command settings, relative error margins, and
reference data stored in a YAML format file with ``.yaml``
suffix. Currently the programs ``pair_style``, ``bond_style``, and
``angle_style`` are implemented. They will compare forces, energies and
suffix. Currently the programs ``test_pair_style``, ``test_bond_style``, and
``test_angle_style`` are implemented. They will compare forces, energies and
(global) stress for all atoms after a ``run 0`` calculation and after a
few steps of MD with :doc:`fix nve <fix_nve>`, each in multiple variants
with different settings and also for multiple accelerated styles. If a
@ -172,7 +172,7 @@ Below is an example command and output:
.. parsed-literal::
[tests]$ pair_style mol-pair-lj_cut.yaml
[tests]$ test_pair_style mol-pair-lj_cut.yaml
[==========] Running 6 tests from 1 test suite.
[----------] Global test environment set-up.
[----------] 6 tests from PairStyle
@ -259,13 +259,61 @@ and working.
of mis-compiled code (or an undesired large loss of precision due
to significant reordering of operations and thus less error cancellation).
Unit tests for timestepping related fixes
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
A substantial subset of :doc:`fix styles <fix>` are invoked regularly
during MD timestepping and manipulate per-atom properties like
positions, velocities, and forces. For those fix styles, testing can be
done in a very similar fashion as for force fields and thus there is a
test program `test_fix_timestep` that shares a lot of code, properties,
and command line flags with the force field style testers described in
the previous section.
This tester will set up a small molecular system run with verlet run
style for 4 MD steps, then write a binary restart and continue for
another 4 MD steps. At this point coordinates and velocities are
recorded and compared to reference data. Then the system is cleared,
restarted and running the second 4 MD steps again and the data is
compared to the same reference. That is followed by another restart
after which per atom type masses are replaced with per-atom masses and
the second 4 MD steps are repeated again and compared to the same
reference. Also global scalar and vector data of the fix is recorded
and compared. If the fix is a thermostat and thus the internal property
``t_target`` can be extracted, then this is compared to the reference
data. The tests are repeated with the respa run style.
If the fix has a multi-threaded version in the USER-OMP package, then
the entire set of tests is repeated for that version as well.
For this to work, some additional conditions have to be met by the
YAML format test inputs.
- The fix to be tested (and only this fix), should be listed in the
``prerequisites:`` section
- The fix to be tested must be specified in the ``post_commands:``
section with the fix-ID ``test``. This section may contain other
commands and other fixes (e.g. an instance of fix nve for testing
a thermostat or force manipulation fix)
- For fixes that can tally contributions to the global virial, the
line ``fix_modify test virial yes`` should be included in the
``post_commands:`` section of the test input.
- For thermostat fixes the target temperature should be ramped from
an arbitrary value (e.g. 50K) to a pre-defined target temperature
entered as ``${t_target}``.
- For fixes that have thermostatting support included, but do not
have it enabled in the input (e.g. fix rigid with default settings),
the ``post_commands:`` section should contain the line
``variable t_target delete`` to disable the target temperature ramp
check to avoid false positives.
Use custom linker for faster link times when ENABLE_TESTING is active
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
When compiling LAMMPS with enabled tests, most test executables will
need to be linked against the LAMMPS library. Since this can be a
large with many C++ objects when many packages are enabled, link times
can become very long on machines that use the GNU BFD linker (e.g.
need to be linked against the LAMMPS library. Since this can be a very
large library with many C++ objects when many packages are enabled, link
times can become very long on machines that use the GNU BFD linker (e.g.
Linux systems). Alternatives like the ``lld`` linker of the LLVM project
or the ``gold`` linker available with GNU binutils can speed up this step
substantially. CMake will by default test if any of the two can be

1
doc/src/Commands_bond.rst
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@ -46,6 +46,7 @@ OPT.
* :doc:`oxdna2/fene <bond_oxdna>`
* :doc:`oxrna2/fene <bond_oxdna>`
* :doc:`quartic (o) <bond_quartic>`
* :doc:`special <bond_special>`
* :doc:`table (o) <bond_table>`
.. _angle:

106
doc/src/bond_special.rst Normal file
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@ -0,0 +1,106 @@
.. index:: bond_style special
bond_style special command
=================================
Syntax
""""""
.. code-block:: LAMMPS
bond_style special
Examples
""""""""
.. code-block:: LAMMPS
bond_style special
bond_coeff 0.5 0.5
Description
"""""""""""
The *special* bond style can be used to create conceptual bonds which
effectively impose weightings on the pairwise Lennard Jones and/or
Coulombic interactions between selected pairs of particles in the
system. The form of the pairwise interaction will be whatever is
computed by the :doc:`pair_style <pair_style>` command defined for the
system; this command defines the weightings for its two terms.
This command can thus be useful to apply weightings that cannot be
handled by the :doc:`special_bonds <special_bonds>` command, such as
on 1-5 or 1-6 interactions. Or it can be used to add pairwise forces
between one or more pairs of atoms that otherwise would not be include
in the :doc:`pair_style <pair_style>` computation.
The potential for this bond style has the form
.. math::
E = w_{LJ} E_{LJ} + w_{Coul} E_{Coul}
The following coefficients must be defined for each bond type via the
:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <read_restart>` commands:
* :math:`w_{LJ}` weight (0.0 to 1.0) on pairwise Lennard-Jones interactions
* :math:`w_{Coul}` weight (0.0 to 1.0) on pairwise Coulombic interactions
----------
Normally this bond style should be used in conjunction with one (or
more) other bond styles which compute forces between atoms directly
bonded to each other in a molecule. This means the :doc:`bond_style
hybrid <bond_hybrid>` command should be used with bond_style special
as one of its sub-styles.
Note that the same as for any other bond style, pairs of bonded atoms
must be enumerated in the data file read by the :doc:`read_data
<read_data>` command. Thus if this command is used to weight all 1-5
interactions in the system, all the 1-5 pairs of atoms must be listed
in the "Bonds" section of the data file.
This bond style imposes strict requirements on settings made with the
:doc:`special_bonds <special_bonds>` command. These requirements
ensure that the new bonds created by this style do not create spurious
1-2, 1-3, or 1-4 interactions within the molecular topology.
Specifically 1-2 interactions must have weights of zero, 1-3
interactions must either have weights of unity or :doc:`special_bonds
angle yes <special_bonds>` must be used, and 1-4 interactions must
have weights of unity or :doc:`special_bonds dihedral yes <special_bonds>`
must be used.
If this command is used to create bonded interactions between
particles that are further apart than usual (e.g. 1-5 or 1-6
interactions), this style may require an increase in the communication
cutoff via the :doc:`comm_modify cutoff <comm_modify>` command. If
LAMMPS cannot find a partner atom in a bond, an error will be issued.
Restrictions
""""""""""""
This bond style can only be used if LAMMPS was built with the
USER-MISC package. See the :doc:`Build package <Build_package>` doc
page for more info.
This bond style requires the use of a :doc:`pair_style <pair_style>` which
computes a pairwise additive interaction and provides the ability to
compute interactions for individual pairs of atoms. Manybody potentials
are not compatible in general, but also some other pair styles are missing
the required functionality and thus will cause an error.
This command is not compatible with long-range Coulombic interactions. If a
`kspace_style <kspace_style>` is declared, an error will be issued.
Related commands
""""""""""""""""
:doc:`bond_coeff <bond_coeff>`, :doc:`special_bonds <special_bonds>`
**Default:** none

6
doc/src/fix_temp_berendsen.rst
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@ -119,7 +119,11 @@ thermal degrees of freedom, and the bias is added back in.
**Restart, fix_modify, output, run start/stop, minimize info:**
No information about this fix is written to :doc:`binary restart files <restart>`.
This fix writes the cumulative global energy change to
:doc:`binary restart files <restart>`. See the
:doc:`read_restart <read_restart>` command for info on how to
re-specify a fix in an input script that reads a restart file,
so that the fix continues in an uninterrupted fashion.
The :doc:`fix_modify <fix_modify>` *temp* option is supported by this
fix. You can use it to assign a temperature :doc:`compute <compute>`

8
doc/src/fix_temp_csvr.rst
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@ -127,6 +127,14 @@ thermal degrees of freedom, and the bias is added back in.
**Restart, fix_modify, output, run start/stop, minimize info:**
These fixes write the cumulative global energy change and the
random number generator states to :doc:`binary restart files <restart>`.
See the :doc:`read_restart <read_restart>` command for info on how to
re-specify a fix in an input script that reads a restart file,
so that the selected fix continues in an uninterrupted fashion. The
random number generator state can only be restored when the number
of processors remains unchanged from what is recorded in the restart file.
No information about these fixes are written to :doc:`binary restart files <restart>`.
The :doc:`fix_modify <fix_modify>` *temp* option is supported by these

16
doc/src/lattice.rst
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@ -260,12 +260,8 @@ of Aidan Thompson), with its 8 atom unit cell.
variable b equal $a*sqrt(3.0)
variable c equal $a*sqrt(8.0/3.0)
variable 1_3 equal 1.0/3.0
variable 2_3 equal 2.0/3.0
variable 1_6 equal 1.0/6.0
variable 5_6 equal 5.0/6.0
variable 1_12 equal 1.0/12.0
variable 5_12 equal 5.0/12.0
variable third equal 1.0/3.0
variable five6 equal 5.0/6.0
lattice custom 1.0 &
a1 $a 0.0 0.0 &
@ -273,12 +269,12 @@ of Aidan Thompson), with its 8 atom unit cell.
a3 0.0 0.0 $c &
basis 0.0 0.0 0.0 &
basis 0.5 0.5 0.0 &
basis ${1_3} 0.0 0.5 &
basis ${5_6} 0.5 0.5 &
basis ${third} 0.0 0.5 &
basis ${five6} 0.5 0.5 &
basis 0.0 0.0 0.625 &
basis 0.5 0.5 0.625 &
basis ${1_3} 0.0 0.125 &
basis ${5_6} 0.5 0.125
basis ${third} 0.0 0.125 &
basis ${five6} 0.5 0.125
region myreg block 0 1 0 1 0 1
create_box 2 myreg

8
doc/src/pair_fep_soft.rst
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@ -161,11 +161,11 @@ Examples
pair_style coul/long/soft 1.0 10.0 9.5
pair_coeff * * 1.0
pair_coeff 1 1 1.0 9.5
pair_coeff 1 1 1.0
pair_style tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8
pair_coeff * * 1.0
pair_coeff 1 1 1.0 9.5
pair_coeff 1 1 1.0
pair_style morse/soft 4 0.9 10.0
pair_coeff * * 100.0 2.0 1.5 1.0
@ -284,7 +284,9 @@ core. Hence, if used by themselves, there will be no repulsion to keep two
oppositely charged particles from overlapping each other. In this case, if
:math:`\lambda = 1`, a singularity may occur. These sub-styles are suitable to
represent charges embedded in the Lennard-Jones radius of another site (for
example hydrogen atoms in several water models).
example hydrogen atoms in several water models). The :math:`\lambda` must
be defined for each pair, and *coul/cut/soft* can accept an optional cutoff as
the second coefficient.
.. note::

2
doc/src/pair_table.rst
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@ -60,7 +60,7 @@ For the *linear* style, the distance *R* is used to find the 2
surrounding table values from which an energy or force is computed by
linear interpolation.
For the *spline* style, a cubic spline coefficients are computed and
For the *spline* style, cubic spline coefficients are computed and
stored for each of the *N* values in the table, one set of splines for
energy, another for force. Note that these splines are different than
the ones used to pre-compute the *N* values. Those splines were fit

2
src/GRANULAR/fix_wall_gran.cpp
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@ -1541,6 +1541,7 @@ int FixWallGran::pack_restart(int i, double *buf)
if (!use_history) return 0;
int n = 0;
// pack buf[0] this way because other fixes unpack it
buf[n++] = size_history + 1;
for (int m = 0; m < size_history; m++)
buf[n++] = history_one[i][m];
@ -1558,6 +1559,7 @@ void FixWallGran::unpack_restart(int nlocal, int nth)
double **extra = atom->extra;
// skip to Nth set of extra values
// unpack the Nth first values this way because other fixes pack them
int m = 0;
for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);

2
src/GRANULAR/fix_wall_gran_region.cpp
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@ -479,6 +479,7 @@ int FixWallGranRegion::pack_restart(int i, double *buf)
for (m = 0; m < size_history; m++)
buf[n++] = history_many[i][iwall][m];
}
// pack buf[0] this way because other fixes unpack it
buf[0] = n;
return n;
}
@ -496,6 +497,7 @@ void FixWallGranRegion::unpack_restart(int nlocal, int nth)
double **extra = atom->extra;
// skip to Nth set of extra values
// unpack the Nth first values this way because other fixes pack them
int m = 0;
for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);

4
src/KSPACE/pair_lj_charmm_coul_long.cpp
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@ -689,7 +689,7 @@ void PairLJCharmmCoulLong::init_style()
int irequest;
int respa = 0;
if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) {
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
}
@ -718,7 +718,7 @@ void PairLJCharmmCoulLong::init_style()
// set & error check interior rRESPA cutoffs
if (strstr(update->integrate_style,"respa") &&
if (utils::strmatch(update->integrate_style,"^respa") &&
((Respa *) update->integrate)->level_inner >= 0) {
cut_respa = ((Respa *) update->integrate)->cutoff;
cut_in_off = cut_respa[0];

9
src/KSPACE/pair_lj_cut_coul_long.cpp
View File

@ -545,10 +545,7 @@ void PairLJCutCoulLong::compute_outer(int eflag, int vflag)
}
} else forcecoul = 0.0;
if (rsq <= cut_in_off_sq) {
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
} else if (rsq <= cut_in_on_sq) {
if (rsq < cut_ljsq[itype][jtype]) {
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
}
@ -659,7 +656,7 @@ void PairLJCutCoulLong::init_style()
int irequest;
int respa = 0;
if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) {
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
}
@ -676,7 +673,7 @@ void PairLJCutCoulLong::init_style()
// set rRESPA cutoffs
if (strstr(update->integrate_style,"respa") &&
if (utils::strmatch(update->integrate_style,"^respa") &&
((Respa *) update->integrate)->level_inner >= 0)
cut_respa = ((Respa *) update->integrate)->cutoff;
else cut_respa = NULL;

2
src/MISC/fix_gld.cpp
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@ -547,6 +547,7 @@ int FixGLD::unpack_exchange(int nlocal, double *buf)
int FixGLD::pack_restart(int i, double *buf)
{
int m = 0;
// pack buf[0] this way because other fixes unpack it
buf[m++] = 3*prony_terms + 1;
for (int k = 0; k < 3*prony_terms; k=k+3)
{
@ -566,6 +567,7 @@ void FixGLD::unpack_restart(int nlocal, int nth)
double **extra = atom->extra;
// skip to the nth set of extended variables
// unpack the Nth first values this way because other fixes pack them
int m = 0;
for (int i = 0; i< nth; i++) m += static_cast<int> (extra[nlocal][m]);

2
src/MISC/fix_ttm.cpp
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@ -656,6 +656,7 @@ void FixTTM::restart(char *buf)
int FixTTM::pack_restart(int i, double *buf)
{
// pack buf[0] this way because other fixes unpack it
buf[0] = 4;
buf[1] = flangevin[i][0];
buf[2] = flangevin[i][1];
@ -672,6 +673,7 @@ void FixTTM::unpack_restart(int nlocal, int nth)
double **extra = atom->extra;
// skip to Nth set of extra values
// unpack the Nth first values this way because other fixes pack them
int m = 0;
for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);

4
src/MOLECULE/fix_cmap.cpp
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@ -1041,7 +1041,7 @@ void FixCMAP::read_data_header(char *line)
sscanf(line,BIGINT_FORMAT,&ncmap);
} else error->all(FLERR,"Invalid read data header line for fix cmap");
// didn't set in constructor b/c this fix could be defined
// didn't set in constructor because this fix could be defined
// before newton command
newton_bond = force->newton_bond;
@ -1291,6 +1291,7 @@ int FixCMAP::pack_restart(int i, double *buf)
buf[n++] = ubuf(crossterm_atom4[i][m]).d;
buf[n++] = ubuf(crossterm_atom5[i][m]).d;
}
// pack buf[0] this way because other fixes unpack it
buf[0] = n;
return n;
@ -1305,6 +1306,7 @@ void FixCMAP::unpack_restart(int nlocal, int nth)
double **extra = atom->extra;
// skip to Nth set of extra values
// unpack the Nth first values this way because other fixes pack them
int n = 0;
for (int i = 0; i < nth; i++) n += static_cast<int> (extra[nlocal][n]);

2
src/PERI/fix_peri_neigh.cpp
View File

@ -579,6 +579,7 @@ void FixPeriNeigh::restart(char *buf)
int FixPeriNeigh::pack_restart(int i, double *buf)
{
int m = 0;
// pack buf[0] this way b/c other fixes unpack it
if (isVES) buf[m++] = 4*npartner[i] + 4;
else if (isEPS) buf[m++] = 3*npartner[i] + 5;
else buf[m++] = 2*npartner[i] + 4;
@ -608,6 +609,7 @@ void FixPeriNeigh::unpack_restart(int nlocal, int nth)
double **extra = atom->extra;
// skip to Nth set of extra values
// unpack the Nth first values this way b/c other fixes pack them
int m = 0;
for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);

38
src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp
View File

@ -691,38 +691,20 @@ void PairLJCharmmCoulLongSoft::init_style()
// request regular or rRESPA neighbor lists
int irequest;
if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
int respa = 0;
if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) {
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
if (respa == 0) irequest = neighbor->request(this,instance_me);
else if (respa == 1) {
irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->id = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->respainner = 1;
irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->id = 3;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->respaouter = 1;
} else {
irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->id = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->respainner = 1;
irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->id = 2;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->respamiddle = 1;
irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->id = 3;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->respaouter = 1;
}
} else irequest = neighbor->request(this,instance_me);
irequest = neighbor->request(this,instance_me);
if (respa >= 1) {
neighbor->requests[irequest]->respaouter = 1;
neighbor->requests[irequest]->respainner = 1;
}
if (respa == 2) neighbor->requests[irequest]->respamiddle = 1;
// require cut_lj_inner < cut_lj
@ -739,7 +721,7 @@ void PairLJCharmmCoulLongSoft::init_style()
// set & error check interior rRESPA cutoffs
if (strstr(update->integrate_style,"respa") &&
if (utils::strmatch(update->integrate_style,"^respa") &&
((Respa *) update->integrate)->level_inner >= 0) {
cut_respa = ((Respa *) update->integrate)->cutoff;
if (MIN(cut_lj,cut_coul) < cut_respa[3])

38
src/USER-FEP/pair_lj_cut_coul_long_soft.cpp
View File

@ -634,44 +634,26 @@ void PairLJCutCoulLongSoft::init_style()
// request regular or rRESPA neighbor lists
int irequest;
if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
int respa = 0;
if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) {
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
if (respa == 0) irequest = neighbor->request(this,instance_me);
else if (respa == 1) {
irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->id = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->respainner = 1;
irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->id = 3;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->respaouter = 1;
} else {
irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->id = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->respainner = 1;
irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->id = 2;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->respamiddle = 1;
irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->id = 3;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->respaouter = 1;
}
} else irequest = neighbor->request(this,instance_me);
irequest = neighbor->request(this,instance_me);
if (respa >= 1) {
neighbor->requests[irequest]->respaouter = 1;
neighbor->requests[irequest]->respainner = 1;
}
if (respa == 2) neighbor->requests[irequest]->respamiddle = 1;
cut_coulsq = cut_coul * cut_coul;
// set rRESPA cutoffs
if (strstr(update->integrate_style,"respa") &&
if (utils::strmatch(update->integrate_style,"^respa") &&
((Respa *) update->integrate)->level_inner >= 0)
cut_respa = ((Respa *) update->integrate)->cutoff;
else cut_respa = NULL;

39
src/USER-FEP/pair_lj_cut_soft.cpp
View File

@ -512,46 +512,27 @@ void PairLJCutSoft::init_style()
// request regular or rRESPA neighbor lists
int irequest;
if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
int respa = 0;
if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) {
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
if (respa == 0) irequest = neighbor->request(this,instance_me);
else if (respa == 1) {
irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->id = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->respainner = 1;
irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->id = 3;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->respaouter = 1;
} else {
irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->id = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->respainner = 1;
irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->id = 2;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->respamiddle = 1;
irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->id = 3;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->respaouter = 1;
}
} else irequest = neighbor->request(this,instance_me);
irequest = neighbor->request(this,instance_me);
if (respa >= 1) {
neighbor->requests[irequest]->respaouter = 1;
neighbor->requests[irequest]->respainner = 1;
}
if (respa == 2) neighbor->requests[irequest]->respamiddle = 1;
// set rRESPA cutoffs
if (strstr(update->integrate_style,"respa") &&
if (utils::strmatch(update->integrate_style,"^respa") &&
((Respa *) update->integrate)->level_inner >= 0)
cut_respa = ((Respa *) update->integrate)->cutoff;
else cut_respa = NULL;
}
/* ----------------------------------------------------------------------

31
src/USER-FEP/pair_morse_soft.cpp
View File

@ -333,6 +333,37 @@ void PairMorseSoft::read_restart(FILE *fp)
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairMorseSoft::write_restart_settings(FILE *fp)
{
fwrite(&nlambda,sizeof(double),1,fp);
fwrite(&shift_range,sizeof(double),1,fp);
fwrite(&cut_global,sizeof(double),1,fp);
fwrite(&offset_flag,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairMorseSoft::read_restart_settings(FILE *fp)
{
int me = comm->me;
if (me == 0) {
utils::sfread(FLERR,&nlambda,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&shift_range,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
}
MPI_Bcast(&nlambda,1,MPI_DOUBLE,0,world);
MPI_Bcast(&shift_range,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
}
/* ----------------------------------------------------------------------
proc 0 writes to data file

2
src/USER-FEP/pair_morse_soft.h
View File

@ -38,6 +38,8 @@ class PairMorseSoft : public PairMorse {
virtual double init_one(int, int);
virtual void write_restart(FILE *);
virtual void read_restart(FILE *);
virtual void write_restart_settings(FILE *);
virtual void read_restart_settings(FILE *);
void write_data(FILE *);
void write_data_all(FILE *);

1
src/USER-MISC/README
View File

@ -26,6 +26,7 @@ angle_style dipole, Mario Orsi, orsimario at gmail.com, 10 Jan 12
angle_style quartic, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12
bond_style harmonic/shift, Carsten Svaneborg, science at zqex.dk, 8 Aug 11
bond_style harmonic/shift/cut, Carsten Svaneborg, science at zqex.dk, 8 Aug 11
bond_style special, David Nicholson, davidanich at gmail.com, 31 Jan 2020
compute ackland/atom, Gerolf Ziegenhain, gerolf at ziegenhain.com, 4 Oct 2007
compute basal/atom, Christopher Barrett, cdb333 at cavs.msstate.edu, 3 Mar 2013
compute cnp/atom, Paulo Branicio (USC), branicio at usc.edu, 31 May 2017

222
src/USER-MISC/bond_special.cpp Normal file
View File

@ -0,0 +1,222 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
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.
Contributing Author: David Nicholson (MIT)
------------------------------------------------------------------------- */
#include <cmath>
#include <cstdlib>
#include <cstring>
#include "bond_special.h"
#include "atom.h"
#include "neighbor.h"
#include "domain.h"
#include "comm.h"
#include "force.h"
#include "pair.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
BondSpecial::BondSpecial(LAMMPS *lmp) : Bond(lmp) {}
/* ---------------------------------------------------------------------- */
BondSpecial::~BondSpecial()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(factor_lj);
memory->destroy(factor_coul);
}
}
/* ---------------------------------------------------------------------- */
void BondSpecial::init_style()
{
if (force->pair == NULL) error->all(FLERR,"No pair style defined");
else if ((force->pair->single_enable == 0) || force->pair->manybody_flag)
error->all(FLERR,"Pair style does not support bond style special");
if (force->special_lj[1] != 0.0 || force->special_coul[1] != 0)
error->all(FLERR,"Invalid 1-2 setting for bond style special.");
if (force->special_angle != 1 && (force->special_lj[2] != 1.0 ||
force->special_coul[2] != 1.0))
error->all(FLERR,"Invalid 1-3 setting for bond style special.");
if (force->special_dihedral != 1 && (force->special_lj[3] != 1.0 ||
force->special_coul[3] != 1.0))
error->all(FLERR,"Invalid 1-4 setting for bond style special.");
if (force->kspace != NULL)
error->all(FLERR,"Bond style special is not compatible with long range "
"Coulombic interactions");
}
/* ---------------------------------------------------------------------- */
void BondSpecial::compute(int eflag, int vflag)
{
int i1,i2,i1type,i2type,n,type;
double delx,dely,delz,ebond,fbond;
double rsq;
ev_init(eflag,vflag);
double **x = atom->x;
double **f = atom->f;
int **bondlist = neighbor->bondlist;
int nbondlist = neighbor->nbondlist;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
for (n = 0; n < nbondlist; n++) {
i1 = bondlist[n][0];
i2 = bondlist[n][1];
type = bondlist[n][2];
i1type = atom->type[i1];
i2type = atom->type[i2];
delx = x[i1][0] - x[i2][0];
dely = x[i1][1] - x[i2][1];
delz = x[i1][2] - x[i2][2];
rsq = delx*delx + dely*dely + delz*delz;
ebond = force->pair->single(i1,i2,i1type,i2type,rsq,factor_lj[type],
factor_coul[type],fbond);
// apply force to each of 2 atoms
if (newton_bond || i1 < nlocal) {
f[i1][0] += delx*fbond;
f[i1][1] += dely*fbond;
f[i1][2] += delz*fbond;
}
if (newton_bond || i2 < nlocal) {
f[i2][0] -= delx*fbond;
f[i2][1] -= dely*fbond;
f[i2][2] -= delz*fbond;
}
if (evflag) ev_tally(i1,i2,nlocal,newton_bond,ebond,fbond,delx,dely,delz);
}
}
/* ---------------------------------------------------------------------- */
void BondSpecial::allocate()
{
allocated = 1;
int n = atom->nbondtypes;
memory->create(factor_lj,n+1,"bond:factor_lj");
memory->create(factor_coul,n+1,"bond:factor_coul");
memory->create(setflag,n+1,"bond:setflag");
for (int i = 1; i <= n; i++) setflag[i] = 0;
}
/* ----------------------------------------------------------------------
set coeffs for one or more types
------------------------------------------------------------------------- */
void BondSpecial::coeff(int narg, char **arg)
{
if (narg != 3) error->all(FLERR,"Incorrect args for bond coefficients");
if (!allocated) allocate();
int ilo,ihi;
force->bounds(FLERR,arg[0],atom->nbondtypes,ilo,ihi);
double factor_lj_one = force->numeric(FLERR,arg[1]);
double factor_coul_one = force->numeric(FLERR,arg[2]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
factor_lj[i] = factor_lj_one;
factor_coul[i] = factor_coul_one;
setflag[i] = 1;
count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for bond coefficients");
}
/* ----------------------------------------------------------------------
return an equilbrium bond length
------------------------------------------------------------------------- */
double BondSpecial::equilibrium_distance(int i)
{
return 0.;
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void BondSpecial::write_restart(FILE *fp)
{
fwrite(&factor_lj[1],sizeof(double),atom->nbondtypes,fp);
fwrite(&factor_coul[1],sizeof(double),atom->nbondtypes,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void BondSpecial::read_restart(FILE *fp)
{
allocate();
if (comm->me == 0) {
fread(&factor_lj[1],sizeof(double),atom->nbondtypes,fp);
fread(&factor_coul[1],sizeof(double),atom->nbondtypes,fp);
}
MPI_Bcast(&factor_lj[1],atom->nbondtypes,MPI_DOUBLE,0,world);
MPI_Bcast(&factor_coul[1],atom->nbondtypes,MPI_DOUBLE,0,world);
for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1;
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void BondSpecial::write_data(FILE *fp)
{
for (int i = 1; i <= atom->nbondtypes; i++)
fprintf(fp,"%d %g %g\n",i,factor_lj[i],factor_coul[i]);
}
/* ---------------------------------------------------------------------- */
double BondSpecial::single(int type, double rsq, int i, int j,
double &fforce)
{
int itype = atom->type[i];
int jtype = atom->type[j];
double ebond;
ebond = force->pair->single(i,j,itype,jtype,rsq,factor_lj[type],
factor_coul[type],fforce);
return ebond;
}

78
src/USER-MISC/bond_special.h Normal file
View File

@ -0,0 +1,78 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
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.
Contributing Author: David Nicholson (MIT)
------------------------------------------------------------------------- */
#ifdef BOND_CLASS
BondStyle(special,BondSpecial)
#else
#ifndef LMP_BOND_SPECIAL_H
#define LMP_BOND_SPECIAL_H
#include <cstdio>
#include "bond.h"
namespace LAMMPS_NS {
class BondSpecial: public Bond {
public:
BondSpecial(class LAMMPS *);
virtual ~BondSpecial();
void init_style();
void compute(int, int);
void coeff(int, char **);
double equilibrium_distance(int);
void write_restart(FILE *);
void read_restart(FILE *);
void write_data(FILE *);
double single(int, double, int, int, double &);
protected:
double *factor_lj,*factor_coul;
void allocate();
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Incorrect args for bond coefficients
Self-explanatory. Check the input script or data file.
E: Invalid 1-2 setting for bond style special.
Bond style special must be used with zero factors for 1-2 special bonds.
E: Invalid 1-3 setting for bond style special.
Bond style special must be used with 1.0 factors for 1-3 special bonds or the
angle keyword set to yes.
E: Invalid 1-4 setting for bond style special.
Bond style special must be used with 1.0 factors for 1-4 special bonds or the
dihedral keyword set to yes.
E: Bond style special is not compatible with long range Coulombic interactions.
Self-explanatory.
*/

2
src/USER-MISC/fix_gle.cpp
View File

@ -822,6 +822,7 @@ int FixGLE::unpack_exchange(int nlocal, double *buf)
int FixGLE::pack_restart(int i, double *buf)
{
int m = 0;
// pack buf[0] this way because other fixes unpack it
buf[m++] = 3*ns + 1;
for (int k = 0; k < 3*ns; k=k+3)
{
@ -841,6 +842,7 @@ void FixGLE::unpack_restart(int nlocal, int nth)
double **extra = atom->extra;
// skip to the nth set of extended variables
// unpack the Nth first values this way because other fixes pack them
int m = 0;
for (int i = 0; i< nth; i++) m += static_cast<int> (extra[nlocal][m]);

2
src/USER-MISC/fix_pimd.cpp
View File

@ -794,6 +794,7 @@ int FixPIMD::pack_restart(int i, double *buf)
{
int offset=0;
int pos = i * 3;
// pack buf[0] this way because other fixes unpack it
buf[offset++] = size_peratom_cols+1;
memcpy(buf+offset, nhc_eta[pos], nhc_size_one_1); offset += nhc_offset_one_1;
@ -811,6 +812,7 @@ void FixPIMD::unpack_restart(int nlocal, int nth)
double **extra = atom->extra;
// skip to Nth set of extra values
// unpack the Nth first values this way because other fixes pack them
int m = 0;
for (int i=0; i<nth; i++) m += static_cast<int> (extra[nlocal][m]);

7
src/USER-MISC/fix_srp.cpp
View File

@ -114,7 +114,7 @@ void FixSRP::init()
error->all(FLERR,"Illegal bond particle type");
// this fix must come before any fix which migrates atoms in its pre_exchange()
// b/c this fix's pre_exchange() creates per-atom data structure
// because this fix's pre_exchange() creates per-atom data structure
// that data must be current for atom migration to carry it along
for (int i = 0; i < modify->nfix; i++) {
@ -555,6 +555,7 @@ void FixSRP::post_run()
int FixSRP::pack_restart(int i, double *buf)
{
int m = 0;
// pack buf[0] this way because other fixes unpack it
buf[m++] = 3;
buf[m++] = array[i][0];
buf[m++] = array[i][1];
@ -570,9 +571,11 @@ void FixSRP::unpack_restart(int nlocal, int nth)
double **extra = atom->extra;
// skip to Nth set of extra values
// unpack the Nth first values this way because other fixes pack them
int m = 0;
for (int i = 0; i < nth; i++){
m += extra[nlocal][m];
m += static_cast<int> (extra[nlocal][m]);
}
m++;

2
src/USER-MISC/fix_ti_spring.cpp
View File

@ -315,6 +315,7 @@ int FixTISpring::unpack_exchange(int nlocal, double *buf)
int FixTISpring::pack_restart(int i, double *buf)
{
// pack buf[0] this way because other fixes unpack it
buf[0] = 4;
buf[1] = xoriginal[i][0];
buf[2] = xoriginal[i][1];
@ -331,6 +332,7 @@ void FixTISpring::unpack_restart(int nlocal, int nth)
double **extra = atom->extra;
// skip to Nth set of extra values
// unpack the Nth first values this way because other fixes pack them
int m = 0;
for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);

2
src/USER-MISC/fix_ttm_mod.cpp
View File

@ -980,6 +980,7 @@ void FixTTMMod::restart(char *buf)
int FixTTMMod::pack_restart(int i, double *buf)
{
// pack buf[0] this way because other fixes unpack it
buf[0] = 4;
buf[1] = flangevin[i][0];
buf[2] = flangevin[i][1];
@ -996,6 +997,7 @@ void FixTTMMod::unpack_restart(int nlocal, int nth)
double **extra = atom->extra;
// skip to Nth set of extra values
// unpack the Nth first values this way because other fixes pack them
int m = 0;
for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);

4
src/USER-MISC/pair_e3b.cpp
View File

@ -382,8 +382,6 @@ void PairE3B::settings(int narg, char **arg)
{
if (narg != 1) error->all(FLERR,"Illegal pair_style command");
typeO=force->inumeric(FLERR,arg[0]);
if (typeO<1 || typeO>atom->ntypes)
error->all(FLERR,"Invalid Otype: out of bounds");
}
/* ----------------------------------------------------------------------
@ -477,6 +475,8 @@ void PairE3B::init_style()
error->all(FLERR,"Pair style E3B requires atom IDs");
if (force->newton_pair == 0)
error->all(FLERR,"Pair style E3B requires newton pair on");
if (typeO<1 || typeO>atom->ntypes)
error->all(FLERR,"Invalid Otype: out of bounds");
// need a half neighbor list
neighbor->request(this,instance_me);

11
src/USER-MISC/pair_edip.cpp
View File

@ -51,7 +51,13 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairEDIP::PairEDIP(LAMMPS *lmp) : Pair(lmp)
PairEDIP::PairEDIP(LAMMPS *lmp) :
Pair(lmp), preInvR_ij(NULL), preExp3B_ij(NULL), preExp3BDerived_ij(NULL),
preExp2B_ij(NULL), preExp2BDerived_ij(NULL), prePow2B_ij(NULL),
preForceCoord(NULL), cutoffFunction(NULL), cutoffFunctionDerived(NULL),
pow2B(NULL), exp2B(NULL), exp3B(NULL), qFunctionGrid(NULL),
expMinusBetaZeta_iZeta_iGrid(NULL), tauFunctionGrid(NULL),
tauFunctionDerivedGrid(NULL)
{
single_enable = 0;
restartinfo = 0;
@ -503,6 +509,8 @@ void PairEDIP::allocateGrids(void)
double maxArgumentExpMinusBetaZeta_iZeta_i;
double const leftLimitToZero = -DBL_MIN * 1000.0;
deallocateGrids();
// tauFunctionGrid
maxArgumentTauFunctionGrid = leadDimInteractionList;
@ -561,6 +569,7 @@ void PairEDIP::allocatePreLoops(void)
{
int nthreads = comm->nthreads;
deallocatePreLoops();
memory->create(preInvR_ij,nthreads*leadDimInteractionList,"edip:preInvR_ij");
memory->create(preExp3B_ij,nthreads*leadDimInteractionList,"edip:preExp3B_ij");
memory->create(preExp3BDerived_ij,nthreads*leadDimInteractionList,

10
src/USER-MISC/pair_lennard_mdf.cpp
View File

@ -226,8 +226,8 @@ void PairLennardMDF::coeff(int narg, char **arg)
cut_inner_one = force->numeric(FLERR,arg[4]);
cut_one = force->numeric(FLERR,arg[5]);
}
if (cut_inner_global <= 0.0 || cut_inner_global > cut_global)
error->all(FLERR,"Illegal pair_style command");
if (cut_inner_one <= 0.0 || cut_inner_one > cut_one)
error->all(FLERR,"Illegal pair_coeff command");
int count = 0;
for (int i = ilo; i <= ihi; i++) {
@ -328,6 +328,8 @@ void PairLennardMDF::read_restart(FILE *fp)
void PairLennardMDF::write_restart_settings(FILE *fp)
{
fwrite(&mix_flag,sizeof(int),1,fp);
fwrite(&cut_global,sizeof(double),1,fp);
fwrite(&cut_inner_global,sizeof(double),1,fp);
}
/* ----------------------------------------------------------------------
@ -339,8 +341,12 @@ void PairLennardMDF::read_restart_settings(FILE *fp)
int me = comm->me;
if (me == 0) {
utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
utils::sfread(FLERR,&cut_inner_global,sizeof(double),1,fp,NULL,error);
}
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_inner_global,1,MPI_DOUBLE,0,world);
}
/* ----------------------------------------------------------------------

48
src/USER-MISC/pair_lj_expand_coul_long.cpp
View File

@ -53,6 +53,7 @@ PairLJExpandCoulLong::PairLJExpandCoulLong(LAMMPS *lmp) : Pair(lmp)
writedata = 1;
ftable = NULL;
qdist = 0.0;
cut_respa = NULL;
}
/* ---------------------------------------------------------------------- */
@ -167,7 +168,7 @@ void PairLJExpandCoulLong::compute(int eflag, int vflag)
rshift2inv = 1.0/rshiftsq;
r6inv = rshift2inv*rshift2inv*rshift2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
forcelj = factor_lj*forcelj/rshift/r;
forcelj *= factor_lj/rshift/r;
} else forcelj = 0.0;
fpair = forcecoul*r2inv + forcelj;
@ -276,7 +277,7 @@ void PairLJExpandCoulLong::compute_inner()
rshift2inv = 1.0/rshiftsq;
r6inv = rshift2inv*rshift2inv*rshift2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
forcelj = factor_lj*forcelj/rshift/r;
forcelj *= factor_lj/rshift/r;
} else forcelj = 0.0;
fpair = forcecoul*r2inv + forcelj;
@ -371,7 +372,7 @@ void PairLJExpandCoulLong::compute_middle()
rshift2inv = 1.0/rshiftsq;
r6inv = rshift2inv*rshift2inv*rshift2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
forcelj = factor_lj*forcelj/rshift/r;
forcelj *= factor_lj/rshift/r;
} else forcelj = 0.0;
fpair = forcecoul*r2inv + forcelj;
@ -506,7 +507,7 @@ void PairLJExpandCoulLong::compute_outer(int eflag, int vflag)
rshift2inv = 1.0/rshiftsq;
r6inv = rshift2inv*rshift2inv*rshift2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
forcelj = factor_lj*forcelj/rshift/r;
forcelj *= factor_lj/rshift/r;
if (rsq < cut_in_on_sq) {
rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff;
forcelj *= rsw*rsw*(3.0 - 2.0*rsw);
@ -524,6 +525,7 @@ void PairLJExpandCoulLong::compute_outer(int eflag, int vflag)
f[j][2] -= delz*fpair;
}
if (evflag) ecoul = evdwl = 0.0;
if (eflag) {
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq) {
@ -538,14 +540,18 @@ void PairLJExpandCoulLong::compute_outer(int eflag, int vflag)
ecoul -= (1.0-factor_coul)*prefactor;
}
}
} else ecoul = 0.0;
}
if (rsq < cut_ljsq[itype][jtype]) {
r6inv = r2inv*r2inv*r2inv;
r = sqrt(rsq);
rshift = r - shift[itype][jtype];
rshiftsq = rshift*rshift;
rshift2inv = 1.0/rshiftsq;
r6inv = rshift2inv*rshift2inv*rshift2inv;
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
offset[itype][jtype];
evdwl *= factor_lj;
} else evdwl = 0.0;
}
}
if (vflag) {
@ -564,15 +570,18 @@ void PairLJExpandCoulLong::compute_outer(int eflag, int vflag)
}
} else forcecoul = 0.0;
if (rsq <= cut_in_off_sq) {
r6inv = r2inv*r2inv*r2inv;
if (rsq < cut_ljsq[itype][jtype]) {
r = sqrt(rsq);
rshift = r - shift[itype][jtype];
rshiftsq = rshift*rshift;
rshift2inv = 1.0/rshiftsq;
r6inv = rshift2inv*rshift2inv*rshift2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
} else if (rsq <= cut_in_on_sq) {
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
}
fpair = (forcecoul + factor_lj*forcelj) * r2inv;
}
forcelj *= factor_lj/rshift/r;
} else forcelj = 0.0;
fpair = forcecoul*r2inv + forcelj;
} else fpair = 0.0;
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,ecoul,fpair,delx,dely,delz);
@ -946,11 +955,16 @@ double PairLJExpandCoulLong::single(int i, int j, int itype, int jtype,
} else forcecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
r6inv = r2inv*r2inv*r2inv;
r = sqrt(rsq);
double rshift = r - shift[itype][jtype];
double rshiftsq = rshift*rshift;
double rshift2inv = 1.0/rshiftsq;
r6inv = rshift2inv*rshift2inv*rshift2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
forcelj *= factor_lj/rshift/r;
} else forcelj = 0.0;
fforce = (forcecoul + factor_lj*forcelj) * r2inv;
fforce = forcecoul*r2inv + forcelj;
double eng = 0.0;
if (rsq < cut_coulsq) {

21
src/USER-MISC/pair_meam_spline.cpp
View File

@ -57,6 +57,7 @@ PairMEAMSpline::PairMEAMSpline(LAMMPS *lmp) : Pair(lmp)
nelements = 0;
elements = NULL;
map = NULL;
Uprime_values = NULL;
nmax = 0;
@ -65,6 +66,14 @@ PairMEAMSpline::PairMEAMSpline(LAMMPS *lmp) : Pair(lmp)
comm_forward = 1;
comm_reverse = 0;
phis = NULL;
Us = NULL;
rhos = NULL;
fs = NULL;
gs = NULL;
zero_atom_energies = NULL;
}
/* ---------------------------------------------------------------------- */
@ -332,6 +341,8 @@ void PairMEAMSpline::allocate()
allocated = 1;
int n = nelements;
memory->destroy(setflag);
memory->destroy(cutsq);
memory->create(setflag,n+1,n+1,"pair:setflag");
memory->create(cutsq,n+1,n+1,"pair:cutsq");
@ -339,14 +350,21 @@ void PairMEAMSpline::allocate()
//Change the functional form
//f_ij->f_i
//g_i(cos\theta_ijk)->g_jk(cos\theta_ijk)
delete[] phis;
delete[] Us;
delete[] rhos;
delete[] fs;
delete[] gs;
phis = new SplineFunction[nmultichoose2];
Us = new SplineFunction[n];
rhos = new SplineFunction[n];
fs = new SplineFunction[n];
gs = new SplineFunction[nmultichoose2];
delete[] zero_atom_energies;
zero_atom_energies = new double[n];
delete[] map;
map = new int[n+1];
for (int i=0; i <= n; ++i) map[i] = -1;
}
@ -470,6 +488,9 @@ void PairMEAMSpline::read_file(const char* filename)
if (nelements < 1)
error->one(FLERR, "Invalid number of atomic species on"
" meam/spline line in potential file");
if (elements)
for (int i = 0; i < nelements; i++) delete [] elements[i];
delete [] elements;
elements = new char*[nelements];
for (int i=0; i<nelements; ++i) {
ptr = strtok(NULL," \t\n\r\f");

11
src/USER-MISC/pair_morse_smooth_linear.cpp
View File

@ -201,14 +201,6 @@ void PairMorseSmoothLinear::coeff(int narg, char **arg)
alpha[i][j] = alpha_one;
r0[i][j] = r0_one;
cut[i][j] = cut_one;
morse1[i][j] = 2.0*d0[i][j]*alpha[i][j];
double alpha_dr = -alpha[i][j] * (cut[i][j] - r0[i][j]);
offset[i][j] = d0[i][j] * (exp(2.0*alpha_dr) - 2.0*exp(alpha_dr));
der_at_cutoff[i][j] = -2.0*alpha[i][j]*d0[i][j] * (exp(2.0*alpha_dr) - exp(alpha_dr));
setflag[i][j] = 1;
count++;
}
@ -227,6 +219,9 @@ double PairMorseSmoothLinear::init_one(int i, int j)
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
morse1[i][j] = 2.0*d0[i][j]*alpha[i][j];
double alpha_dr = -alpha[i][j] * (cut[i][j] - r0[i][j]);
offset[i][j] = d0[i][j] * (exp(2.0*alpha_dr) - 2.0*exp(alpha_dr));
der_at_cutoff[i][j] = -2.0*alpha[i][j]*d0[i][j] * (exp(2.0*alpha_dr) - exp(alpha_dr));
d0[j][i] = d0[i][j];
alpha[j][i] = alpha[i][j];

8
src/USER-OMP/pair_morse_smooth_linear_omp.cpp
View File

@ -35,8 +35,6 @@ PairMorseSmoothLinearOMP::PairMorseSmoothLinearOMP(LAMMPS *lmp) :
respa_enable = 0;
}
/* ---------------------------------------------------------------------- */
void PairMorseSmoothLinearOMP::compute(int eflag, int vflag)
@ -76,8 +74,6 @@ void PairMorseSmoothLinearOMP::compute(int eflag, int vflag)
} // end of omp parallel region
}
template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
void PairMorseSmoothLinearOMP::eval(int iifrom, int iito, ThrData * const thr)
{
@ -129,7 +125,7 @@ void PairMorseSmoothLinearOMP::eval(int iifrom, int iito, ThrData * const thr)
dexp = exp(-alpha[itype][jtype] * dr);
fpartial = morse1[itype][jtype] * (dexp*dexp - dexp) / r;
fpair = factor_lj * ( fpartial - der_at_cutoff[itype][jtype] / r);
fpair = factor_lj * ( fpartial + der_at_cutoff[itype][jtype] / r);
fxtmp += delx*fpair;
fytmp += dely*fpair;
@ -143,7 +139,7 @@ void PairMorseSmoothLinearOMP::eval(int iifrom, int iito, ThrData * const thr)
if (EFLAG) {
evdwl = d0[itype][jtype] * (dexp*dexp - 2.0*dexp) -
offset[itype][jtype];
evdwl += ( r - cut[itype][jtype] ) * der_at_cutoff[itype][jtype];
evdwl -= ( r - cut[itype][jtype] ) * der_at_cutoff[itype][jtype];
evdwl *= factor_lj;
}

2
src/USER-SDPD/fix_meso_move.cpp
View File

@ -948,6 +948,7 @@ int FixMesoMove::unpack_exchange (int nlocal, double *buf) {
------------------------------------------------------------------------- */
int FixMesoMove::pack_restart (int i, double *buf) {
// pack buf[0] this way because other fixes unpack it
buf[0] = 4;
buf[1] = xoriginal[i][0];
buf[2] = xoriginal[i][1];
@ -963,6 +964,7 @@ void FixMesoMove::unpack_restart (int nlocal, int nth) {
double **extra = atom->extra;
// skip to Nth set of extra values
// unpack the Nth first values this way because other fixes pack them
int m = 0;
for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);

2
src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp
View File

@ -450,6 +450,7 @@ int FixSMD_TLSPH_ReferenceConfiguration::unpack_exchange(int nlocal, double *buf
int FixSMD_TLSPH_ReferenceConfiguration::pack_restart(int i, double *buf) {
int m = 0;
// pack buf[0] this way because other fixes unpack it
buf[m++] = 4 * npartner[i] + 2;
buf[m++] = npartner[i];
for (int n = 0; n < npartner[i]; n++) {
@ -470,6 +471,7 @@ void FixSMD_TLSPH_ReferenceConfiguration::unpack_restart(int /*nlocal*/, int /*n
// ipage = NULL if being called from granular pair style init()
// skip to Nth set of extra values
// unpack the Nth first values this way because other fixes pack them
// double **extra = atom->extra;
//

14
src/create_atoms.cpp
View File

@ -71,6 +71,20 @@ void CreateAtoms::command(int narg, char **arg)
error->all(FLERR,"Cannot create_atoms after "
"reading restart file with per-atom info");
// check for compatible lattice
int latsty = domain->lattice->style;
if (domain->dimension == 2) {
if (latsty == Lattice::SC || latsty == Lattice::BCC
|| latsty == Lattice::FCC || latsty == Lattice::HCP
|| latsty == Lattice::DIAMOND)
error->all(FLERR,"Lattice style incompatible with simulation dimension");
} else {
if (latsty == Lattice::SQ ||latsty == Lattice::SQ2
|| latsty == Lattice::HEX)
error->all(FLERR,"Lattice style incompatible with simulation dimension");
}
// parse arguments
if (narg < 2) error->all(FLERR,"Illegal create_atoms command");

2
src/fix_move.cpp
View File

@ -1193,6 +1193,7 @@ int FixMove::pack_restart(int i, double *buf)
buf[n++] = qoriginal[i][2];
buf[n++] = qoriginal[i][3];
}
// pack buf[0] this way because other fixes unpack it
buf[0] = n;
return n;
}
@ -1206,6 +1207,7 @@ void FixMove::unpack_restart(int nlocal, int nth)
double **extra = atom->extra;
// skip to Nth set of extra values
// unpack the Nth first values this way because other fixes pack them
int m = 0;
for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);

18
src/fix_neigh_history.cpp
View File

@ -149,7 +149,7 @@ void FixNeighHistory::init()
error->all(FLERR,"Neighbor history requires atoms have IDs");
// this fix must come before any fix which migrates atoms in its pre_exchange()
// b/c this fix's pre_exchange() creates per-atom data structure
// because this fix's pre_exchange() creates per-atom data structure
// that data must be current for atom migration to carry it along
for (int i = 0; i < modify->nfix; i++) {
@ -215,7 +215,7 @@ void FixNeighHistory::setup_post_neighbor()
called during run before atom exchanges, including for restart files
called at end of run via post_run()
do not call during setup of run (setup_pre_exchange)
b/c there is no guarantee of a current NDS (even on continued run)
because there is no guarantee of a current NDS (even on continued run)
if run command does a 2nd run with pre = no, then no neigh list
will be built, but old neigh list will still have the info
onesided and newton on and newton off versions
@ -242,7 +242,7 @@ void FixNeighHistory::pre_exchange_onesided()
double *allvalues,*onevalues;
// NOTE: all operations until very end are with nlocal_neigh <= current nlocal
// b/c previous neigh list was built with nlocal_neigh
// because previous neigh list was built with nlocal_neigh
// nlocal can be larger if other fixes added atoms at this pre_exchange()
// clear two paged data structures
@ -335,7 +335,7 @@ void FixNeighHistory::pre_exchange_newton()
// NOTE: all operations until very end are with
// nlocal_neigh <= current nlocal and nall_neigh
// b/c previous neigh list was built with nlocal_neigh & nghost_neigh
// because previous neigh list was built with nlocal_neigh & nghost_neigh
// nlocal can be larger if other fixes added atoms at this pre_exchange()
// clear two paged data structures
@ -430,7 +430,7 @@ void FixNeighHistory::pre_exchange_newton()
// perform reverse comm to augment
// owned atom partner/valuepartner with ghost info
// use variable variant b/c size of packed data can be arbitrarily large
// use variable variant because size of packed data can be arbitrarily large
// if many touching neighbors for large particle
commflag = PERPARTNER;
@ -463,7 +463,7 @@ void FixNeighHistory::pre_exchange_no_newton()
double *allvalues,*onevalues,*jvalues;
// NOTE: all operations until very end are with nlocal_neigh <= current nlocal
// b/c previous neigh list was built with nlocal_neigh
// because previous neigh list was built with nlocal_neigh
// nlocal can be larger if other fixes added atoms at this pre_exchange()
// clear two paged data structures
@ -708,10 +708,10 @@ void FixNeighHistory::grow_arrays(int nmax)
void FixNeighHistory::copy_arrays(int i, int j, int /*delflag*/)
{
// just copy pointers for partner and valuepartner
// b/c can't overwrite chunk allocation inside ipage_atom,dpage_atom
// because can't overwrite chunk allocation inside ipage_atom,dpage_atom
// incoming atoms in unpack_exchange just grab new chunks
// so are orphaning chunks for migrating atoms
// OK, b/c will reset ipage_atom,dpage_atom on next reneighboring
// OK, because will reset ipage_atom,dpage_atom on next reneighboring
npartner[j] = npartner[i];
partner[j] = partner[i];
@ -853,6 +853,7 @@ int FixNeighHistory::pack_restart(int i, double *buf)
memcpy(&buf[m],&valuepartner[i][dnum*n],dnumbytes);
m += dnum;
}
// pack buf[0] this way because other fixes unpack it
buf[0] = m;
return m;
}
@ -868,6 +869,7 @@ void FixNeighHistory::unpack_restart(int nlocal, int nth)
if (ipage_atom == NULL) allocate_pages();
// skip to Nth set of extra values
// unpack the Nth first values this way because other fixes pack them
double **extra = atom->extra;

4
src/fix_property_atom.cpp
View File

@ -192,7 +192,7 @@ int FixPropertyAtom::setmask()
void FixPropertyAtom::init()
{
// error if atom style has changed since fix was defined
// don't allow this b/c user could change to style that defines molecule,q
// don't allow this because user could change to style that defines molecule,q
if (strcmp(astyle,atom->atom_style) != 0)
error->all(FLERR,"Atom style was redefined after using fix property/atom");
@ -579,6 +579,7 @@ int FixPropertyAtom::unpack_exchange(int nlocal, double *buf)
int FixPropertyAtom::pack_restart(int i, double *buf)
{
// pack buf[0] this way because other fixes unpack it
buf[0] = nvalue+1;
int m = 1;
@ -602,6 +603,7 @@ void FixPropertyAtom::unpack_restart(int nlocal, int nth)
double **extra = atom->extra;
// skip to Nth set of extra values
// unpack the Nth first values this way because other fixes pack them
int m = 0;
for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);

13
src/fix_setforce.cpp
View File

@ -297,8 +297,14 @@ void FixSetForce::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
// set force to desired value on requested level, 0.0 on other levels
if (ilevel == ilevel_respa) post_force(vflag);
else {
if (ilevel == 0) foriginal_saved[0] = foriginal_saved[1] = foriginal_saved[2] = 0.0;
if (ilevel == ilevel_respa) {
post_force(vflag);
foriginal[0] += foriginal_saved[0];
foriginal[1] += foriginal_saved[1];
foriginal[2] += foriginal_saved[2];
} else {
Region *region = NULL;
if (iregion >= 0) {
region = domain->regions[iregion];
@ -313,6 +319,9 @@ void FixSetForce::post_force_respa(int vflag, int ilevel, int /*iloop*/)
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (region && !region->match(x[i][0],x[i][1],x[i][2])) continue;
foriginal_saved[0] += f[i][0];
foriginal_saved[1] += f[i][1];
foriginal_saved[2] += f[i][2];
if (xstyle) f[i][0] = 0.0;
if (ystyle) f[i][1] = 0.0;
if (zstyle) f[i][2] = 0.0;

2
src/fix_setforce.h
View File

@ -45,7 +45,7 @@ class FixSetForce : public Fix {
char *xstr,*ystr,*zstr;
char *idregion;
int xvar,yvar,zvar,xstyle,ystyle,zstyle;
double foriginal[3],foriginal_all[3];
double foriginal[3],foriginal_all[3],foriginal_saved[3];
int force_flag;
int nlevels_respa,ilevel_respa;

2
src/fix_spring_self.cpp
View File

@ -264,6 +264,7 @@ int FixSpringSelf::unpack_exchange(int nlocal, double *buf)
int FixSpringSelf::pack_restart(int i, double *buf)
{
// pack buf[0] this way because other fixes unpack it
buf[0] = 4;
buf[1] = xoriginal[i][0];
buf[2] = xoriginal[i][1];
@ -280,6 +281,7 @@ void FixSpringSelf::unpack_restart(int nlocal, int nth)
double **extra = atom->extra;
// skip to Nth set of extra values
// unpack the Nth first values this way because other fixes pack them
int m = 0;
for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);

6
src/fix_store.cpp
View File

@ -280,7 +280,8 @@ int FixStore::pack_restart(int i, double *buf)
return 1;
}
buf[0] = ubuf(nvalues+1).d;
// pack buf[0] this way because other fixes unpack it
buf[0] = nvalues+1;
if (vecflag) buf[1] = vstore[i];
else
for (int m = 0; m < nvalues; m++)
@ -299,9 +300,10 @@ void FixStore::unpack_restart(int nlocal, int nth)
double **extra = atom->extra;
// skip to Nth set of extra values
// unpack the Nth first values this way because other fixes pack them
int m = 0;
for (int i = 0; i < nth; i++) m += (int) ubuf(extra[nlocal][m]).i;
for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);
m++;
if (vecflag) vstore[nlocal] = extra[nlocal][m];

2
src/fix_store_state.cpp
View File

@ -611,6 +611,7 @@ int FixStoreState::unpack_exchange(int nlocal, double *buf)
int FixStoreState::pack_restart(int i, double *buf)
{
// pack buf[0] this way because other fixes unpack it
buf[0] = nvalues+1;
for (int m = 0; m < nvalues; m++) buf[m+1] = values[i][m];
return nvalues+1;
@ -625,6 +626,7 @@ void FixStoreState::unpack_restart(int nlocal, int nth)
double **extra = atom->extra;
// skip to Nth set of extra values
// unpack the Nth first values this way because other fixes pack them
int m = 0;
for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);

29
src/fix_temp_berendsen.cpp
View File

@ -43,6 +43,7 @@ FixTempBerendsen::FixTempBerendsen(LAMMPS *lmp, int narg, char **arg) :
// Berendsen thermostat should be applied every step
restart_global = 1;
dynamic_group_allow = 1;
nevery = 1;
scalar_flag = 1;
@ -241,6 +242,34 @@ double FixTempBerendsen::compute_scalar()
return energy;
}
/* ----------------------------------------------------------------------
pack entire state of Fix into one write
------------------------------------------------------------------------- */
void FixTempBerendsen::write_restart(FILE *fp)
{
int n = 0;
double list[1];
list[n++] = energy;
if (comm->me == 0) {
int size = n * sizeof(double);
fwrite(&size,sizeof(int),1,fp);
fwrite(list,sizeof(double),n,fp);
}
}
/* ----------------------------------------------------------------------
use state info from restart file to restart the Fix
------------------------------------------------------------------------- */
void FixTempBerendsen::restart(char *buf)
{
double *list = (double *) buf;
energy = list[0];
}
/* ----------------------------------------------------------------------
extract thermostat properties
------------------------------------------------------------------------- */

2
src/fix_temp_berendsen.h
View File

@ -34,6 +34,8 @@ class FixTempBerendsen : public Fix {
int modify_param(int, char **);
void reset_target(double);
double compute_scalar();
void write_restart(FILE *);
void restart(char *buf);
virtual void *extract(const char *, int &);
private:

41
src/fix_temp_csld.cpp
View File

@ -49,6 +49,7 @@ FixTempCSLD::FixTempCSLD(LAMMPS *lmp, int narg, char **arg) :
// CSLD thermostat should be applied every step
restart_global = 1;
nevery = 1;
scalar_flag = 1;
global_freq = nevery;
@ -297,6 +298,46 @@ double FixTempCSLD::compute_scalar()
return energy;
}
/* ----------------------------------------------------------------------
pack entire state of Fix into one write
------------------------------------------------------------------------- */
void FixTempCSLD::write_restart(FILE *fp)
{
int nsize = (98+2+3)*comm->nprocs+2; // pRNG state per proc + nprocs + energy
double *list;
if (comm->me == 0) list = new double[nsize];
list[0] = energy;
list[1] = comm->nprocs;
double state[103];
random->get_state(state);
MPI_Gather(state,103,MPI_DOUBLE,list+2,103*comm->nprocs,MPI_DOUBLE,0,world);
if (comm->me == 0) {
int size = nsize * sizeof(double);
fwrite(&size,sizeof(int),1,fp);
fwrite(list,sizeof(double),nsize,fp);
}
if (comm->me == 0) delete[] list;
}
/* ----------------------------------------------------------------------
use state info from restart file to restart the Fix
------------------------------------------------------------------------- */
void FixTempCSLD::restart(char *buf)
{
double *list = (double *) buf;
energy = list[0];
int nprocs = (int) list[1];
if (nprocs != comm->nprocs) {
if (comm->me == 0)
error->warning(FLERR,"Different number of procs. Cannot restore RNG state.");
} else random->set_state(list+2+comm->me*103);
}
/* ----------------------------------------------------------------------
extract thermostat properties
------------------------------------------------------------------------- */

2
src/fix_temp_csld.h
View File

@ -34,6 +34,8 @@ class FixTempCSLD : public Fix {
int modify_param(int, char **);
void reset_target(double);
virtual double compute_scalar();
void write_restart(FILE *);
void restart(char *buf);
virtual void *extract(const char *, int &);
private:

40
src/fix_temp_csvr.cpp
View File

@ -126,6 +126,7 @@ FixTempCSVR::FixTempCSVR(LAMMPS *lmp, int narg, char **arg) :
// CSVR thermostat should be applied every step
restart_global = 1;
nevery = 1;
scalar_flag = 1;
global_freq = nevery;
@ -331,6 +332,45 @@ double FixTempCSVR::compute_scalar()
return energy;
}
/* ----------------------------------------------------------------------
pack entire state of Fix into one write
------------------------------------------------------------------------- */
void FixTempCSVR::write_restart(FILE *fp)
{
int nsize = (98+2+3)*comm->nprocs+2; // pRNG state per proc + nprocs + energy
double *list;
if (comm->me == 0) list = new double[nsize];
list[0] = energy;
list[1] = comm->nprocs;
double state[103];
random->get_state(state);
MPI_Gather(state,103,MPI_DOUBLE,list+2,103*comm->nprocs,MPI_DOUBLE,0,world);
if (comm->me == 0) {
int size = nsize * sizeof(double);
fwrite(&size,sizeof(int),1,fp);
fwrite(list,sizeof(double),nsize,fp);
}
if (comm->me == 0) delete[] list;
}
/* ----------------------------------------------------------------------
use state info from restart file to restart the Fix
------------------------------------------------------------------------- */
void FixTempCSVR::restart(char *buf)
{
double *list = (double *) buf;
energy = list[0];
int nprocs = (int) list[1];
if (nprocs != comm->nprocs) {
if (comm->me == 0)
error->warning(FLERR,"Different number of procs. Cannot restore RNG state.");
} else random->set_state(list+2+comm->me*103);
}
/* ----------------------------------------------------------------------
extract thermostat properties
------------------------------------------------------------------------- */

2
src/fix_temp_csvr.h
View File

@ -34,6 +34,8 @@ class FixTempCSVR : public Fix {
int modify_param(int, char **);
void reset_target(double);
virtual double compute_scalar();
void write_restart(FILE *);
void restart(char *buf);
virtual void *extract(const char *, int &);
private:

7
src/lammps.cpp
View File

@ -854,9 +854,6 @@ void LAMMPS::destroy()
delete neighbor;
neighbor = NULL;
delete comm;
comm = NULL;
delete force;
force = NULL;
@ -870,6 +867,10 @@ void LAMMPS::destroy()
// since they delete fixes
modify = NULL;
delete comm; // comm must come after modify
// since fix destructors may access comm
comm = NULL;
delete domain; // domain must come after modify
// since fix destructors access domain
domain = NULL;

2
src/lattice.cpp
View File

@ -28,8 +28,6 @@ using namespace LAMMPS_NS;
#define BIG 1.0e30
enum{NONE,SC,BCC,FCC,HCP,DIAMOND,SQ,SQ2,HEX,CUSTOM};
/* ---------------------------------------------------------------------- */
Lattice::Lattice(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)

2
src/lattice.h
View File

@ -20,6 +20,8 @@ namespace LAMMPS_NS {
class Lattice : protected Pointers {
public:
enum{NONE,SC,BCC,FCC,HCP,DIAMOND,SQ,SQ2,HEX,CUSTOM};
int style; // NONE,SC,FCC,etc
double xlattice,ylattice,zlattice; // lattice scale factors in 3 dims
double a1[3],a2[3],a3[3]; // edge vectors of unit cell

4
src/pair_lj_cut.cpp
View File

@ -484,7 +484,7 @@ void PairLJCut::init_style()
int irequest;
int respa = 0;
if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) {
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
}
@ -499,7 +499,7 @@ void PairLJCut::init_style()
// set rRESPA cutoffs
if (strstr(update->integrate_style,"respa") &&
if (utils::strmatch(update->integrate_style,"^respa") &&
((Respa *) update->integrate)->level_inner >= 0)
cut_respa = ((Respa *) update->integrate)->cutoff;
else cut_respa = NULL;

14
src/pair_table.cpp
View File

@ -458,25 +458,25 @@ void PairTable::read_table(Table *tb, char *file, char *keyword)
}
if (ferror)
error->warning(FLERR,fmt::format("{} of {} force values in table are "
error->warning(FLERR,fmt::format("{} of {} force values in table {} are "
"inconsistent with -dE/dr.\n Should "
"only be flagged at inflection points",
ferror,tb->ninput));
ferror,tb->ninput,keyword));
// warn if re-computed distance values differ from file values
if (rerror)
error->warning(FLERR,fmt::format("{} of {} distance values in table with "
"relative error\n over {} to "
error->warning(FLERR,fmt::format("{} of {} distance values in table {} "
"with relative error\n over {} to "
"re-computed values",
rerror,tb->ninput,EPSILONR));
rerror,tb->ninput,EPSILONR,keyword));
// warn if data was read incompletely, e.g. columns were missing
if (cerror)
error->warning(FLERR,fmt::format("{} of {} lines in table were "
error->warning(FLERR,fmt::format("{} of {} lines in table {} were "
"incomplete\n or could not be parsed "
"completely",cerror,tb->ninput));
"completely",cerror,tb->ninput,keyword));
}
/* ----------------------------------------------------------------------

36
src/random_mars.cpp
View File

@ -16,6 +16,7 @@
#include "random_mars.h"
#include <cmath>
#include <cstring>
#include "error.h"
#include "math_const.h"
@ -36,6 +37,7 @@ RanMars::RanMars(LAMMPS *lmp, int seed) : Pointers(lmp),
save = 0;
u = new double[97+1];
memset(u,0,98*sizeof(double));
ij = (seed-1)/30082;
kl = (seed-1) - 30082*ij;
@ -181,7 +183,7 @@ double RanMars::besselexp(double theta, double alpha, double cp)
void RanMars::select_subset(bigint ntarget, int nmine, int *mark, int *next)
{
int mode,index,oldindex,newvalue,nflip,which,niter;
int active[2],first[2],last[2];
int active[2],first[2];
int newactive[2],newfirst[2],newlast[2];
bigint nmark,nflipall;
bigint activeall[2],bsum[3],bsumall[3];
@ -191,8 +193,6 @@ void RanMars::select_subset(bigint ntarget, int nmine, int *mark, int *next)
active[1] = 0;
first[0] = 0;
first[1] = -1;
last[0] = nmine-1;
last[1] = -1;
bigint bnmine = nmine;
bigint bnall;
@ -266,8 +266,6 @@ void RanMars::select_subset(bigint ntarget, int nmine, int *mark, int *next)
active[1] = newactive[1];
first[0] = newfirst[0];
first[1] = newfirst[1];
last[0] = newlast[0];
last[1] = newlast[1];
}
// update nmark and activeall
@ -291,3 +289,31 @@ void RanMars::select_subset(bigint ntarget, int nmine, int *mark, int *next)
// niter,nmark,nactiveall,thresh,nflipall);
}
}
/* ----------------------------------------------------------------------
store state in buffer
------------------------------------------------------------------------- */
void RanMars::get_state(double *state)
{
for (int i=0; i < 98; ++i) state[i] = u[i];
state[98] = i97;
state[99] = j97;
state[100]= c;
state[101]= cd;
state[102]= cm;
}
/* ----------------------------------------------------------------------
restore state from buffer
------------------------------------------------------------------------- */
void RanMars::set_state(double *state)
{
for (int i=0; i < 98; ++i) u[i] = state[i];
i97 = state[98];
j97 = state[99];
c = state[100];
cd = state[101];
cm = state[102];
}

2
src/random_mars.h
View File

@ -28,6 +28,8 @@ class RanMars : protected Pointers {
double rayleigh(double sigma);
double besselexp(double theta, double alpha, double cp);
void select_subset(bigint, int, int *, int *);
void get_state(double *);
void set_state(double *);
private:
int save;

6
src/velocity.cpp
View File

@ -67,7 +67,7 @@ void Velocity::command(int narg, char **arg)
// check if velocities of atoms in rigid bodies are updated
if (modify->check_rigid_group_overlap(groupbit))
if (modify->check_rigid_group_overlap(groupbit) && (comm->me == 0))
error->warning(FLERR,"Changing velocities of atoms in rigid bodies. "
"This has no effect unless rigid bodies are rebuild");
@ -200,7 +200,7 @@ void Velocity::create(double t_desired, int seed)
// initialize temperature computation(s)
// warn if groups don't match
if (igroup != temperature->igroup && comm->me == 0)
if ((igroup != temperature->igroup) && (comm->me == 0))
error->warning(FLERR,"Mismatch between velocity and compute groups");
temperature->init();
temperature->setup();
@ -596,7 +596,7 @@ void Velocity::scale(int /*narg*/, char **arg)
// initialize temperature computation
// warn if groups don't match
if (igroup != temperature->igroup && comm->me == 0)
if ((igroup != temperature->igroup) && (comm->me == 0))
error->warning(FLERR,"Mismatch between velocity and compute groups");
temperature->init();
temperature->setup();

2
unittest/CMakeLists.txt
View File

@ -1,9 +1,9 @@
include(GTest)
add_subdirectory(force-styles)
add_subdirectory(utils)
add_subdirectory(formats)
add_subdirectory(commands)
add_subdirectory(force-styles)
find_package(ClangFormat 8.0)

4
unittest/commands/CMakeLists.txt
View File

@ -3,6 +3,10 @@ add_executable(test_simple_commands test_simple_commands.cpp)
target_link_libraries(test_simple_commands PRIVATE lammps GTest::GMock GTest::GTest)
add_test(NAME SimpleCommands COMMAND test_simple_commands WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
add_executable(test_lattice_region test_lattice_region.cpp)
target_link_libraries(test_lattice_region PRIVATE lammps GTest::GMock GTest::GTest)
add_test(NAME LatticeRegion COMMAND test_lattice_region WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
add_executable(test_kim_commands test_kim_commands.cpp)
target_link_libraries(test_kim_commands PRIVATE lammps GTest::GMock GTest::GTest)
add_test(NAME KimCommands COMMAND test_kim_commands WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})

703
unittest/commands/test_lattice_region.cpp Normal file
View File

@ -0,0 +1,703 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
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 "atom.h"
#include "domain.h"
#include "fmt/format.h"
#include "info.h"
#include "input.h"
#include "lammps.h"
#include "lattice.h"
#include "region.h"
#include "utils.h"
#include "gmock/gmock.h"
#include "gtest/gtest.h"
#include <cstdio>
#include <cstring>
#include <fstream>
#include <iostream>
#include <mpi.h>
// whether to print verbose output (i.e. not capturing LAMMPS screen output).
bool verbose = false;
#if defined(OMPI_MAJOR_VERSION)
const bool have_openmpi = true;
#else
const bool have_openmpi = false;
#endif
using LAMMPS_NS::utils::split_words;
namespace LAMMPS_NS {
using ::testing::ExitedWithCode;
using ::testing::MatchesRegex;
using ::testing::StrEq;
#define TEST_FAILURE(errmsg, ...) \
if (Info::has_exceptions()) { \
::testing::internal::CaptureStdout(); \
ASSERT_ANY_THROW({__VA_ARGS__}); \
auto mesg = ::testing::internal::GetCapturedStdout(); \
ASSERT_THAT(mesg, MatchesRegex(errmsg)); \
} else { \
if (!have_openmpi) { \
::testing::internal::CaptureStdout(); \
ASSERT_DEATH({__VA_ARGS__}, ""); \
auto mesg = ::testing::internal::GetCapturedStdout(); \
ASSERT_THAT(mesg, MatchesRegex(errmsg)); \
} \
}
class LatticeRegionTest : public ::testing::Test {
protected:
LAMMPS *lmp;
void SetUp() override
{
const char *args[] = {"LatticeRegionTest", "-log", "none", "-echo", "screen", "-nocite"};
char **argv = (char **)args;
int argc = sizeof(args) / sizeof(char *);
if (!verbose) ::testing::internal::CaptureStdout();
lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD);
lmp->input->one("units metal");
if (!verbose) ::testing::internal::GetCapturedStdout();
}
void TearDown() override
{
if (!verbose) ::testing::internal::CaptureStdout();
delete lmp;
if (!verbose) ::testing::internal::GetCapturedStdout();
}
};
TEST_F(LatticeRegionTest, lattice_none)
{
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("lattice none 2.0");
if (!verbose) ::testing::internal::GetCapturedStdout();
auto lattice = lmp->domain->lattice;
ASSERT_EQ(lattice->style, Lattice::NONE);
ASSERT_EQ(lattice->xlattice, 2.0);
ASSERT_EQ(lattice->ylattice, 2.0);
ASSERT_EQ(lattice->zlattice, 2.0);
ASSERT_EQ(lattice->nbasis, 0);
ASSERT_EQ(lattice->basis, nullptr);
TEST_FAILURE(".*ERROR: Illegal lattice command.*", lmp->input->one("lattice"););
TEST_FAILURE(".*ERROR: Illegal lattice command.*", lmp->input->one("lattice xxx"););
TEST_FAILURE(".*ERROR: Illegal lattice command.*", lmp->input->one("lattice none 1.0 origin"););
TEST_FAILURE(".*ERROR: Expected floating point.*", lmp->input->one("lattice none xxx"););
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("units lj");
lmp->input->one("lattice none 1.0");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_EQ(lattice->xlattice, 1.0);
ASSERT_EQ(lattice->ylattice, 1.0);
ASSERT_EQ(lattice->zlattice, 1.0);
}
TEST_F(LatticeRegionTest, lattice_sc)
{
::testing::internal::CaptureStdout();
lmp->input->one("lattice sc 1.0 spacing 1.5 2.0 3.0");
auto output = ::testing::internal::GetCapturedStdout();
if (verbose) std::cout << output;
ASSERT_THAT(output, MatchesRegex(".*Lattice spacing in x,y,z = 1.50* 2.0* 3.0*.*"));
auto lattice = lmp->domain->lattice;
ASSERT_EQ(lattice->xlattice, 1.5);
ASSERT_EQ(lattice->ylattice, 2.0);
ASSERT_EQ(lattice->zlattice, 3.0);
::testing::internal::CaptureStdout();
lmp->input->one("lattice sc 2.0");
output = ::testing::internal::GetCapturedStdout();
if (verbose) std::cout << output;
ASSERT_THAT(output, MatchesRegex(".*Lattice spacing in x,y,z = 2.0* 2.0* 2.0*.*"));
lattice = lmp->domain->lattice;
ASSERT_EQ(lattice->style, Lattice::SC);
ASSERT_EQ(lattice->xlattice, 2.0);
ASSERT_EQ(lattice->ylattice, 2.0);
ASSERT_EQ(lattice->zlattice, 2.0);
ASSERT_EQ(lattice->nbasis, 1);
ASSERT_NE(lattice->basis, nullptr);
ASSERT_EQ(lattice->a1[0], 1.0);
ASSERT_EQ(lattice->a1[1], 0.0);
ASSERT_EQ(lattice->a1[2], 0.0);
ASSERT_EQ(lattice->a2[0], 0.0);
ASSERT_EQ(lattice->a2[1], 1.0);
ASSERT_EQ(lattice->a2[2], 0.0);
ASSERT_EQ(lattice->a3[0], 0.0);
ASSERT_EQ(lattice->a3[1], 0.0);
ASSERT_EQ(lattice->a3[2], 1.0);
ASSERT_EQ(lattice->basis[0][0], 0.0);
ASSERT_EQ(lattice->basis[0][1], 0.0);
ASSERT_EQ(lattice->basis[0][2], 0.0);
TEST_FAILURE(".*ERROR: Illegal lattice command.*",
lmp->input->one("lattice sc 1.0 origin 1.0 1.0 1.0"););
TEST_FAILURE(".*ERROR: Illegal lattice command.*",
lmp->input->one("lattice sc 1.0 origin 1.0"););
TEST_FAILURE(".*ERROR: Illegal lattice command.*",
lmp->input->one("lattice sc 1.0 origin 0.0 0.0 0.0 xxx"););
TEST_FAILURE(".*ERROR: Expected floating point.*",
lmp->input->one("lattice sc 1.0 origin xxx 1.0 1.0"););
TEST_FAILURE(".*ERROR: Lattice orient vectors are not orthogonal.*",
lmp->input->one("lattice sc 1.0 orient x 2 2 0"););
TEST_FAILURE(".*ERROR: Lattice orient vectors are not right-handed.*",
lmp->input->one("lattice sc 1.0 orient y 0 -1 0"););
TEST_FAILURE(".*ERROR: Lattice spacings are invalid.*",
lmp->input->one("lattice sc 1.0 spacing 0.0 1.0 1.0"););
TEST_FAILURE(".*ERROR: Lattice spacings are invalid.*",
lmp->input->one("lattice sc 1.0 spacing 1.0 -0.1 1.0"););
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("units lj");
lmp->input->one("lattice sc 2.0");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_DOUBLE_EQ(lattice->xlattice, pow(0.5, 1.0 / 3.0));
ASSERT_DOUBLE_EQ(lattice->ylattice, pow(0.5, 1.0 / 3.0));
ASSERT_DOUBLE_EQ(lattice->zlattice, pow(0.5, 1.0 / 3.0));
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("dimension 2");
if (!verbose) ::testing::internal::GetCapturedStdout();
TEST_FAILURE(".*ERROR: Lattice style incompatible with simulation dimension.*",
lmp->input->one("lattice sc 1.0"););
}
TEST_F(LatticeRegionTest, lattice_bcc)
{
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("lattice bcc 4.2 orient x 1 1 0 orient y -1 1 0");
if (!verbose) ::testing::internal::GetCapturedStdout();
auto lattice = lmp->domain->lattice;
ASSERT_EQ(lattice->style, Lattice::BCC);
ASSERT_DOUBLE_EQ(lattice->xlattice, sqrt(2.0) * 4.2);
ASSERT_DOUBLE_EQ(lattice->ylattice, sqrt(2.0) * 4.2);
ASSERT_DOUBLE_EQ(lattice->zlattice, 4.2);
ASSERT_EQ(lattice->nbasis, 2);
ASSERT_EQ(lattice->basis[0][0], 0.0);
ASSERT_EQ(lattice->basis[0][1], 0.0);
ASSERT_EQ(lattice->basis[0][2], 0.0);
ASSERT_EQ(lattice->basis[1][0], 0.5);
ASSERT_EQ(lattice->basis[1][1], 0.5);
ASSERT_EQ(lattice->basis[1][2], 0.5);
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("dimension 2");
if (!verbose) ::testing::internal::GetCapturedStdout();
TEST_FAILURE(".*ERROR: Lattice style incompatible with simulation dimension.*",
lmp->input->one("lattice bcc 1.0"););
}
TEST_F(LatticeRegionTest, lattice_fcc)
{
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("lattice fcc 3.5 origin 0.5 0.5 0.5");
if (!verbose) ::testing::internal::GetCapturedStdout();
auto lattice = lmp->domain->lattice;
ASSERT_EQ(lattice->style, Lattice::FCC);
ASSERT_DOUBLE_EQ(lattice->xlattice, 3.5);
ASSERT_DOUBLE_EQ(lattice->ylattice, 3.5);
ASSERT_DOUBLE_EQ(lattice->zlattice, 3.5);
ASSERT_EQ(lattice->nbasis, 4);
ASSERT_EQ(lattice->basis[0][0], 0.0);
ASSERT_EQ(lattice->basis[0][1], 0.0);
ASSERT_EQ(lattice->basis[0][2], 0.0);
ASSERT_EQ(lattice->basis[1][0], 0.5);
ASSERT_EQ(lattice->basis[1][1], 0.5);
ASSERT_EQ(lattice->basis[1][2], 0.0);
ASSERT_EQ(lattice->basis[2][0], 0.5);
ASSERT_EQ(lattice->basis[2][1], 0.0);
ASSERT_EQ(lattice->basis[2][2], 0.5);
ASSERT_EQ(lattice->basis[3][0], 0.0);
ASSERT_EQ(lattice->basis[3][1], 0.5);
ASSERT_EQ(lattice->basis[3][2], 0.5);
TEST_FAILURE(".*ERROR: Invalid option in lattice command for non-custom style.*",
lmp->input->one("lattice fcc 1.0 basis 0.0 0.0 0.0"););
TEST_FAILURE(".*ERROR: Invalid option in lattice command for non-custom style.*",
lmp->input->one("lattice fcc 1.0 a1 0.0 1.0 0.0"););
TEST_FAILURE(".*ERROR: Illegal lattice command.*",
lmp->input->one("lattice fcc 1.0 orient w 1 0 0"););
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("dimension 2");
if (!verbose) ::testing::internal::GetCapturedStdout();
TEST_FAILURE(".*ERROR: Lattice style incompatible with simulation dimension.*",
lmp->input->one("lattice fcc 1.0"););
}
TEST_F(LatticeRegionTest, lattice_hcp)
{
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("lattice hcp 3.0 orient z 0 0 1");
if (!verbose) ::testing::internal::GetCapturedStdout();
auto lattice = lmp->domain->lattice;
ASSERT_EQ(lattice->style, Lattice::HCP);
ASSERT_DOUBLE_EQ(lattice->xlattice, 3.0);
ASSERT_DOUBLE_EQ(lattice->ylattice, 3.0 * sqrt(3.0));
ASSERT_DOUBLE_EQ(lattice->zlattice, 2.0 * sqrt(6.0));
ASSERT_EQ(lattice->nbasis, 4);
ASSERT_EQ(lattice->basis[0][0], 0.0);
ASSERT_EQ(lattice->basis[0][1], 0.0);
ASSERT_EQ(lattice->basis[0][2], 0.0);
ASSERT_EQ(lattice->basis[1][0], 0.5);
ASSERT_EQ(lattice->basis[1][1], 0.5);
ASSERT_EQ(lattice->basis[1][2], 0.0);
ASSERT_EQ(lattice->basis[2][0], 0.5);
ASSERT_DOUBLE_EQ(lattice->basis[2][1], 5.0 / 6.0);
ASSERT_EQ(lattice->basis[2][2], 0.5);
ASSERT_EQ(lattice->basis[3][0], 0.0);
ASSERT_DOUBLE_EQ(lattice->basis[3][1], 1.0 / 3.0);
ASSERT_EQ(lattice->basis[3][2], 0.5);
ASSERT_EQ(lattice->a1[0], 1.0);
ASSERT_EQ(lattice->a1[1], 0.0);
ASSERT_EQ(lattice->a1[2], 0.0);
ASSERT_EQ(lattice->a2[0], 0.0);
ASSERT_DOUBLE_EQ(lattice->a2[1], sqrt(3.0));
ASSERT_EQ(lattice->a2[2], 0.0);
ASSERT_EQ(lattice->a3[0], 0.0);
ASSERT_EQ(lattice->a3[1], 0.0);
ASSERT_DOUBLE_EQ(lattice->a3[2], sqrt(8.0 / 3.0));
TEST_FAILURE(".*ERROR: Invalid option in lattice command for non-custom style.*",
lmp->input->one("lattice hcp 1.0 a2 0.0 1.0 0.0"););
TEST_FAILURE(".*ERROR: Invalid option in lattice command for non-custom style.*",
lmp->input->one("lattice hcp 1.0 a3 0.0 1.0 0.0"););
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("dimension 2");
if (!verbose) ::testing::internal::GetCapturedStdout();
TEST_FAILURE(".*ERROR: Lattice style incompatible with simulation dimension.*",
lmp->input->one("lattice hcp 1.0"););
}
TEST_F(LatticeRegionTest, lattice_diamond)
{
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("lattice diamond 4.1 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1");
if (!verbose) ::testing::internal::GetCapturedStdout();
auto lattice = lmp->domain->lattice;
ASSERT_EQ(lattice->style, Lattice::DIAMOND);
ASSERT_DOUBLE_EQ(lattice->xlattice, 6.6952719636073539);
ASSERT_DOUBLE_EQ(lattice->ylattice, 5.7982756057296889);
ASSERT_DOUBLE_EQ(lattice->zlattice, 7.1014083110323973);
ASSERT_EQ(lattice->nbasis, 8);
ASSERT_EQ(lattice->basis[0][0], 0.0);
ASSERT_EQ(lattice->basis[0][1], 0.0);
ASSERT_EQ(lattice->basis[0][2], 0.0);
ASSERT_EQ(lattice->basis[1][0], 0.0);
ASSERT_EQ(lattice->basis[1][1], 0.5);
ASSERT_EQ(lattice->basis[1][2], 0.5);
ASSERT_EQ(lattice->basis[2][0], 0.5);
ASSERT_EQ(lattice->basis[2][1], 0.0);
ASSERT_EQ(lattice->basis[2][2], 0.5);
ASSERT_EQ(lattice->basis[3][0], 0.5);
ASSERT_EQ(lattice->basis[3][1], 0.5);
ASSERT_EQ(lattice->basis[3][2], 0.0);
ASSERT_EQ(lattice->basis[4][0], 0.25);
ASSERT_EQ(lattice->basis[4][1], 0.25);
ASSERT_EQ(lattice->basis[4][2], 0.25);
ASSERT_EQ(lattice->basis[5][0], 0.25);
ASSERT_EQ(lattice->basis[5][1], 0.75);
ASSERT_EQ(lattice->basis[5][2], 0.75);
ASSERT_EQ(lattice->basis[6][0], 0.75);
ASSERT_EQ(lattice->basis[6][1], 0.25);
ASSERT_EQ(lattice->basis[6][2], 0.75);
ASSERT_EQ(lattice->basis[7][0], 0.75);
ASSERT_EQ(lattice->basis[7][1], 0.75);
ASSERT_EQ(lattice->basis[7][2], 0.25);
ASSERT_EQ(lattice->a1[0], 1.0);
ASSERT_EQ(lattice->a1[1], 0.0);
ASSERT_EQ(lattice->a1[2], 0.0);
ASSERT_EQ(lattice->a2[0], 0.0);
ASSERT_EQ(lattice->a2[1], 1.0);
ASSERT_EQ(lattice->a2[2], 0.0);
ASSERT_EQ(lattice->a3[0], 0.0);
ASSERT_EQ(lattice->a3[1], 0.0);
ASSERT_EQ(lattice->a3[2], 1.0);
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("dimension 2");
if (!verbose) ::testing::internal::GetCapturedStdout();
TEST_FAILURE(".*ERROR: Lattice style incompatible with simulation dimension.*",
lmp->input->one("lattice diamond 1.0"););
}
TEST_F(LatticeRegionTest, lattice_sq)
{
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("dimension 2");
lmp->input->one("lattice sq 3.0");
if (!verbose) ::testing::internal::GetCapturedStdout();
auto lattice = lmp->domain->lattice;
ASSERT_EQ(lattice->style, Lattice::SQ);
ASSERT_DOUBLE_EQ(lattice->xlattice, 3.0);
ASSERT_DOUBLE_EQ(lattice->ylattice, 3.0);
ASSERT_DOUBLE_EQ(lattice->zlattice, 3.0);
ASSERT_EQ(lattice->nbasis, 1);
ASSERT_EQ(lattice->basis[0][0], 0.0);
ASSERT_EQ(lattice->basis[0][1], 0.0);
ASSERT_EQ(lattice->basis[0][2], 0.0);
TEST_FAILURE(
".*ERROR: Lattice settings are not compatible with 2d simulation.*",
lmp->input->one("lattice sq 1.0 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1"););
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("dimension 3");
if (!verbose) ::testing::internal::GetCapturedStdout();
TEST_FAILURE(".*ERROR: Lattice style incompatible with simulation dimension.*",
lmp->input->one("lattice sq 1.0"););
}
TEST_F(LatticeRegionTest, lattice_sq2)
{
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("dimension 2");
lmp->input->one("lattice sq2 2.0");
if (!verbose) ::testing::internal::GetCapturedStdout();
auto lattice = lmp->domain->lattice;
ASSERT_EQ(lattice->style, Lattice::SQ2);
ASSERT_DOUBLE_EQ(lattice->xlattice, 2.0);
ASSERT_DOUBLE_EQ(lattice->ylattice, 2.0);
ASSERT_DOUBLE_EQ(lattice->zlattice, 2.0);
ASSERT_EQ(lattice->nbasis, 2);
ASSERT_EQ(lattice->basis[0][0], 0.0);
ASSERT_EQ(lattice->basis[0][1], 0.0);
ASSERT_EQ(lattice->basis[0][2], 0.0);
ASSERT_EQ(lattice->basis[1][0], 0.5);
ASSERT_EQ(lattice->basis[1][1], 0.5);
ASSERT_EQ(lattice->basis[1][2], 0.0);
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("dimension 3");
if (!verbose) ::testing::internal::GetCapturedStdout();
TEST_FAILURE(".*ERROR: Lattice style incompatible with simulation dimension.*",
lmp->input->one("lattice sq2 1.0"););
}
TEST_F(LatticeRegionTest, lattice_hex)
{
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("dimension 2");
lmp->input->one("lattice hex 2.0");
if (!verbose) ::testing::internal::GetCapturedStdout();
auto lattice = lmp->domain->lattice;
ASSERT_EQ(lattice->style, Lattice::HEX);
ASSERT_DOUBLE_EQ(lattice->xlattice, 2.0);
ASSERT_DOUBLE_EQ(lattice->ylattice, 3.4641016151377544);
ASSERT_DOUBLE_EQ(lattice->zlattice, 2.0);
ASSERT_EQ(lattice->nbasis, 2);
ASSERT_EQ(lattice->basis[0][0], 0.0);
ASSERT_EQ(lattice->basis[0][1], 0.0);
ASSERT_EQ(lattice->basis[0][2], 0.0);
ASSERT_EQ(lattice->basis[1][0], 0.5);
ASSERT_EQ(lattice->basis[1][1], 0.5);
ASSERT_EQ(lattice->basis[1][2], 0.0);
ASSERT_EQ(lattice->a1[0], 1.0);
ASSERT_EQ(lattice->a1[1], 0.0);
ASSERT_EQ(lattice->a1[2], 0.0);
ASSERT_EQ(lattice->a2[0], 0.0);
ASSERT_DOUBLE_EQ(lattice->a2[1], sqrt(3.0));
ASSERT_EQ(lattice->a2[2], 0.0);
ASSERT_EQ(lattice->a3[0], 0.0);
ASSERT_EQ(lattice->a3[1], 0.0);
ASSERT_EQ(lattice->a3[2], 1.0);
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("dimension 3");
if (!verbose) ::testing::internal::GetCapturedStdout();
TEST_FAILURE(".*ERROR: Lattice style incompatible with simulation dimension.*",
lmp->input->one("lattice hex 1.0"););
}
TEST_F(LatticeRegionTest, lattice_custom)
{
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("variable a equal 4.34");
lmp->input->one("variable b equal $a*sqrt(3.0)");
lmp->input->one("variable c equal $a*sqrt(8.0/3.0)");
lmp->input->one("variable t equal 1.0/3.0");
lmp->input->one("variable f equal 5.0/6.0");
lmp->input->one("lattice custom 1.0 "
"a1 $a 0.0 0.0 "
"a2 0.0 $b 0.0 "
"a3 0.0 0.0 $c "
"basis 0.0 0.0 0.0 "
"basis 0.5 0.5 0.0 "
"basis $t 0.0 0.5 "
"basis $f 0.5 0.5 "
"basis 0.0 0.0 0.625 "
"basis 0.5 0.5 0.625 "
"basis $t 0.0 0.125 "
"basis $f 0.5 0.125 ");
if (!verbose) ::testing::internal::GetCapturedStdout();
auto lattice = lmp->domain->lattice;
ASSERT_EQ(lattice->style, Lattice::CUSTOM);
ASSERT_DOUBLE_EQ(lattice->xlattice, 4.34);
ASSERT_DOUBLE_EQ(lattice->ylattice, 4.34 * sqrt(3.0));
ASSERT_DOUBLE_EQ(lattice->zlattice, 4.34 * sqrt(8.0 / 3.0));
ASSERT_EQ(lattice->nbasis, 8);
ASSERT_DOUBLE_EQ(lattice->basis[0][0], 0.0);
ASSERT_DOUBLE_EQ(lattice->basis[0][1], 0.0);
ASSERT_DOUBLE_EQ(lattice->basis[0][2], 0.0);
ASSERT_DOUBLE_EQ(lattice->basis[1][0], 0.5);
ASSERT_DOUBLE_EQ(lattice->basis[1][1], 0.5);
ASSERT_DOUBLE_EQ(lattice->basis[1][2], 0.0);
ASSERT_NEAR(lattice->basis[2][0], 1.0 / 3.0, 1.0e-14);
ASSERT_DOUBLE_EQ(lattice->basis[2][1], 0.0);
ASSERT_DOUBLE_EQ(lattice->basis[2][2], 0.5);
ASSERT_DOUBLE_EQ(lattice->basis[3][0], 5.0 / 6.0);
ASSERT_DOUBLE_EQ(lattice->basis[3][1], 0.5);
ASSERT_DOUBLE_EQ(lattice->basis[3][2], 0.5);
ASSERT_DOUBLE_EQ(lattice->basis[4][0], 0.0);
ASSERT_DOUBLE_EQ(lattice->basis[4][1], 0.0);
ASSERT_DOUBLE_EQ(lattice->basis[4][2], 0.625);
ASSERT_DOUBLE_EQ(lattice->basis[5][0], 0.5);
ASSERT_DOUBLE_EQ(lattice->basis[5][1], 0.5);
ASSERT_DOUBLE_EQ(lattice->basis[5][2], 0.625);
ASSERT_NEAR(lattice->basis[6][0], 1.0 / 3.0, 1.0e-14);
ASSERT_DOUBLE_EQ(lattice->basis[6][1], 0.0);
ASSERT_DOUBLE_EQ(lattice->basis[6][2], 0.125);
ASSERT_DOUBLE_EQ(lattice->basis[7][0], 5.0 / 6.0);
ASSERT_DOUBLE_EQ(lattice->basis[7][1], 0.5);
ASSERT_DOUBLE_EQ(lattice->basis[7][2], 0.125);
ASSERT_DOUBLE_EQ(lattice->a1[0], 4.34);
ASSERT_DOUBLE_EQ(lattice->a1[1], 0.0);
ASSERT_DOUBLE_EQ(lattice->a1[2], 0.0);
ASSERT_DOUBLE_EQ(lattice->a2[0], 0.0);
ASSERT_DOUBLE_EQ(lattice->a2[1], 4.34 * sqrt(3.0));
ASSERT_DOUBLE_EQ(lattice->a2[2], 0.0);
ASSERT_DOUBLE_EQ(lattice->a3[0], 0.0);
ASSERT_DOUBLE_EQ(lattice->a3[1], 0.0);
ASSERT_DOUBLE_EQ(lattice->a3[2], 4.34 * sqrt(8.0 / 3.0));
TEST_FAILURE(".*ERROR: Illegal lattice command.*",
lmp->input->one("lattice custom 1.0 basis -0.1 0 0"););
TEST_FAILURE(".*ERROR: Illegal lattice command.*",
lmp->input->one("lattice custom 1.0 basis 0.0 1.0 0"););
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("dimension 2");
if (!verbose) ::testing::internal::GetCapturedStdout();
TEST_FAILURE(".*ERROR: No basis atoms in lattice.*", lmp->input->one("lattice custom 1.0"););
TEST_FAILURE(".*ERROR: Lattice settings are not compatible with 2d simulation.*",
lmp->input->one("lattice custom 1.0 origin 0.5 0.5 0.5 basis 0.0 0.0 0.0"););
TEST_FAILURE(".*ERROR: Lattice settings are not compatible with 2d simulation.*",
lmp->input->one("lattice custom 1.0 a1 1.0 1.0 1.0 basis 0.0 0.0 0.0"););
TEST_FAILURE(".*ERROR: Lattice settings are not compatible with 2d simulation.*",
lmp->input->one("lattice custom 1.0 a2 1.0 1.0 1.0 basis 0.0 0.0 0.0"););
TEST_FAILURE(".*ERROR: Lattice settings are not compatible with 2d simulation.*",
lmp->input->one("lattice custom 1.0 a3 1.0 1.0 1.0 basis 0.0 0.0 0.0"););
}
TEST_F(LatticeRegionTest, region_fail)
{
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("lattice none 2.0");
lmp->input->one("region box block 0 1 0 1 0 1");
if (!verbose) ::testing::internal::GetCapturedStdout();
TEST_FAILURE(".*ERROR: Create_atoms command before simulation box is defined.*",
lmp->input->one("create_atoms 1 box"););
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("create_box 1 box");
if (!verbose) ::testing::internal::GetCapturedStdout();
TEST_FAILURE(".*ERROR: Cannot create atoms with undefined lattice.*",
lmp->input->one("create_atoms 1 box"););
}
TEST_F(LatticeRegionTest, region_block_lattice)
{
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("lattice sc 1.5");
lmp->input->one("region box block 0 2 0 2 0 2 units lattice");
lmp->input->one("create_box 1 box");
lmp->input->one("create_atoms 1 box");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_EQ(lmp->domain->triclinic, 0);
auto x = lmp->atom->x;
ASSERT_EQ(lmp->atom->natoms, 8);
ASSERT_DOUBLE_EQ(x[0][0], 0.0);
ASSERT_DOUBLE_EQ(x[0][1], 0.0);
ASSERT_DOUBLE_EQ(x[0][2], 0.0);
ASSERT_DOUBLE_EQ(x[1][0], 1.5);
ASSERT_DOUBLE_EQ(x[1][1], 0.0);
ASSERT_DOUBLE_EQ(x[1][2], 0.0);
ASSERT_DOUBLE_EQ(x[2][0], 0.0);
ASSERT_DOUBLE_EQ(x[2][1], 1.5);
ASSERT_DOUBLE_EQ(x[2][2], 0.0);
ASSERT_DOUBLE_EQ(x[3][0], 1.5);
ASSERT_DOUBLE_EQ(x[3][1], 1.5);
ASSERT_DOUBLE_EQ(x[3][2], 0.0);
}
TEST_F(LatticeRegionTest, region_block_box)
{
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("lattice sc 1.5 origin 0.75 0.75 0.75");
lmp->input->one("region box block 0 2 0 2 0 2 units box");
lmp->input->one("create_box 1 box");
lmp->input->one("create_atoms 1 box");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_EQ(lmp->domain->triclinic, 0);
auto x = lmp->atom->x;
ASSERT_EQ(lmp->atom->natoms, 1);
ASSERT_DOUBLE_EQ(x[0][0], 1.125);
ASSERT_DOUBLE_EQ(x[0][1], 1.125);
ASSERT_DOUBLE_EQ(x[0][2], 1.125);
}
TEST_F(LatticeRegionTest, region_cone)
{
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("lattice fcc 2.5 origin 0.5 0.5 0.5");
lmp->input->one("region box cone x 1.0 1.0 0.5 2.1 0.0 2.0");
lmp->input->one("create_box 1 box");
lmp->input->one("create_atoms 1 region box");
lmp->input->one("write_dump all atom init.lammpstrj");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_EQ(lmp->domain->triclinic, 0);
auto x = lmp->atom->x;
ASSERT_EQ(lmp->atom->natoms, 42);
}
TEST_F(LatticeRegionTest, region_cylinder)
{
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("lattice fcc 2.5 origin 0.5 0.5 0.5");
lmp->input->one("region box cylinder z 1.0 1.0 2.1 0.0 2.0 ");
lmp->input->one("create_box 1 box");
lmp->input->one("create_atoms 1 region box");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_EQ(lmp->domain->triclinic, 0);
auto x = lmp->atom->x;
ASSERT_EQ(lmp->atom->natoms, 114);
}
TEST_F(LatticeRegionTest, region_prism)
{
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("lattice bcc 2.5 origin 0.75 0.75 0.75");
lmp->input->one("region box prism 0 2 0 2 0 2 0.5 0.0 0.0");
lmp->input->one("create_box 1 box");
lmp->input->one("create_atoms 1 box");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_EQ(lmp->domain->triclinic, 1);
auto x = lmp->atom->x;
ASSERT_EQ(lmp->atom->natoms, 16);
}
TEST_F(LatticeRegionTest, region_sphere)
{
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("lattice fcc 2.5 origin 0.5 0.5 0.5");
lmp->input->one("region box sphere 1.0 1.0 1.0 1.1");
lmp->input->one("create_box 1 box");
lmp->input->one("create_atoms 1 region box");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_EQ(lmp->domain->triclinic, 0);
auto x = lmp->atom->x;
ASSERT_EQ(lmp->atom->natoms, 14);
}
TEST_F(LatticeRegionTest, region_union)
{
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("lattice fcc 2.5 origin 0.5 0.5 0.5");
lmp->input->one("region part1 sphere 2.0 1.0 1.0 1.1");
lmp->input->one("region part2 block 0.0 2.0 0.0 2.0 0.0 2.0");
lmp->input->one("region box union 2 part1 part2");
lmp->input->one("create_box 1 box");
lmp->input->one("create_atoms 1 region box");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_EQ(lmp->domain->triclinic, 0);
auto x = lmp->atom->x;
ASSERT_EQ(lmp->atom->natoms, 67);
}
TEST_F(LatticeRegionTest, region_intersect)
{
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("lattice fcc 2.5 origin 0.5 0.5 0.5");
lmp->input->one("region part1 sphere 2.0 1.0 1.0 1.8");
lmp->input->one("region part2 block 0.0 2.0 0.0 2.0 0.0 2.0");
lmp->input->one("region box intersect 2 part1 part2");
lmp->input->one("create_box 1 box");
lmp->input->one("create_atoms 1 region box");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_EQ(lmp->domain->triclinic, 0);
auto x = lmp->atom->x;
ASSERT_EQ(lmp->atom->natoms, 21);
}
TEST_F(LatticeRegionTest, region_plane)
{
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("lattice fcc 2.5 origin 0.5 0.5 0.5");
lmp->input->one("region box block 0.0 2.0 0.0 2.0 0.0 2.0");
lmp->input->one("region part1 plane 0.5 1.0 0.0 0.75 0.0 0.0");
lmp->input->one("region part2 plane 1.5 1.0 0.0 0.75 0.0 0.0 side out");
lmp->input->one("region atoms intersect 2 part1 part2");
lmp->input->one("create_box 1 box");
lmp->input->one("create_atoms 1 region atoms");
lmp->input->one("write_dump all atom init.lammpstrj");
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_EQ(lmp->domain->triclinic, 0);
auto x = lmp->atom->x;
ASSERT_EQ(lmp->atom->natoms, 16);
}
} // namespace LAMMPS_NS
int main(int argc, char **argv)
{
MPI_Init(&argc, &argv);
::testing::InitGoogleMock(&argc, argv);
if (have_openmpi && !LAMMPS_NS::Info::has_exceptions())
std::cout << "Warning: using OpenMPI without exceptions. "
"Death tests will be skipped\n";
// handle arguments passed via environment variable
if (const char *var = getenv("TEST_ARGS")) {
std::vector<std::string> env = split_words(var);
for (auto arg : env) {
if (arg == "-v") {
verbose = true;
}
}
}
if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true;
int rv = RUN_ALL_TESTS();
MPI_Finalize();
return rv;
}

2
unittest/commands/test_reset_ids.cpp
View File

@ -660,6 +660,8 @@ TEST_F(ResetIDsTest, TopologyData)
TEST_F(ResetIDsTest, DeathTests)
{
if (lmp->atom->natoms == 0) GTEST_SKIP();
TEST_FAILURE(".*ERROR: Illegal reset_mol_ids command.*", lmp->input->one("reset_mol_ids"););
TEST_FAILURE(".*ERROR: Illegal reset_mol_ids command.*",
lmp->input->one("reset_mol_ids all offset 1 1"););

12
unittest/force-styles/CMakeLists.txt
View File

@ -125,3 +125,15 @@ foreach(TEST ${IMPROPER_TESTS})
add_test(NAME ${TNAME} COMMAND test_improper_style ${TEST} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
set_tests_properties(${TNAME} PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};PYTHONPATH=${TEST_INPUT_FOLDER}:$ENV{PYTHONPATH}")
endforeach()
# tester for timestepping fixes
add_executable(test_fix_timestep test_fix_timestep.cpp)
target_link_libraries(test_fix_timestep PRIVATE lammps style_tests)
# tests for timestep related fixes (time integration, thermostat, force manipulation, constraints/restraints)
file(GLOB FIX_TIMESTEP_TESTS LIST_DIRECTORIES false ${TEST_INPUT_FOLDER}/fix-timestep-*.yaml)
foreach(TEST ${FIX_TIMESTEP_TESTS})
string(REGEX REPLACE "^.*fix-timestep-(.*)\.yaml" "FixTimestep:\\1" TNAME ${TEST})
add_test(NAME ${TNAME} COMMAND test_fix_timestep ${TEST} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
set_tests_properties(${TNAME} PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};PYTHONPATH=${TEST_INPUT_FOLDER}:$ENV{PYTHONPATH}")
endforeach()

9
unittest/force-styles/check_tests.py
View File

@ -55,6 +55,7 @@ kspace = {}
pair = {}
style_pattern = re.compile("(.+)Style\((.+),(.+)\)")
upper = re.compile("[A-Z]+")
gpu = re.compile("(.+)/gpu$")
intel = re.compile("(.+)/intel$")
kokkos = re.compile("(.+)/kk$")
@ -85,7 +86,7 @@ for header in headers:
for m in matches:
# skip over internal styles w/o explicit documentation
style = m[1]
if style.isupper():
if upper.match(style):
continue
# detect, process, and flag suffix styles:
@ -131,6 +132,8 @@ for header in headers:
register_style(kspace,style,info)
elif m[0] == 'Pair':
register_style(pair,style,info)
elif m[0] == 'Fix':
register_style(fix,style,info)
@ -179,6 +182,8 @@ counter += check_tests('improper',improper,'improper-*.yaml',
'.*improper_style:\s*((\S+).*)?')
counter += check_tests('kspace',kspace,'kspace-*.yaml',
'.*kspace_style\s*((\S+).*)?')
counter += check_tests('fix',fix,'fix-*.yaml',
' fix\s+((\S+)\s*)?')
total = len(pair)+len(bond)+len(angle)+len(dihedral)+len(improper)+len(kspace)
total = len(pair)+len(bond)+len(angle)+len(dihedral)+len(improper)+len(kspace)+len(fix)
print(f"\nTotal tests missing: {counter} of {total}")

1
unittest/force-styles/error_stats.h
View File

@ -29,6 +29,7 @@ public:
double dev() const;
double max() const { return maxerr; }
double idx() const { return maxidx; }
bool has_data() const { return num > 0; }
private:
double sum, sumsq, maxerr;

13
unittest/force-styles/test_config.h
View File

@ -58,15 +58,21 @@ public:
double run_coul;
stress_t init_stress;
stress_t run_stress;
double global_scalar;
std::vector<double> global_vector;
std::vector<coord_t> init_forces;
std::vector<coord_t> run_forces;
std::vector<coord_t> run_pos;
std::vector<coord_t> restart_pos;
std::vector<coord_t> run_vel;
std::vector<coord_t> restart_vel;
TestConfig() :
lammps_version(""), date_generated(""), basename(""), epsilon(1.0e-14), input_file(""),
pair_style("zero"), bond_style("zero"), angle_style("zero"), dihedral_style("zero"),
improper_style("zero"), kspace_style("none"), natoms(0), init_energy(0), run_energy(0),
init_vdwl(0), run_vdwl(0), init_coul(0), run_coul(0), init_stress({0, 0, 0, 0, 0, 0}),
run_stress({0, 0, 0, 0, 0, 0})
run_stress({0, 0, 0, 0, 0, 0}), global_scalar(0)
{
prerequisites.clear();
pre_commands.clear();
@ -79,6 +85,11 @@ public:
extract.clear();
init_forces.clear();
run_forces.clear();
run_pos.clear();
restart_pos.clear();
run_vel.clear();
restart_vel.clear();
global_vector.clear();
}
virtual ~TestConfig(){};

53
unittest/force-styles/test_config_reader.cpp
View File

@ -40,6 +40,8 @@ TestConfigReader::TestConfigReader(TestConfig &config) : YamlReader(), config(co
consumers["run_stress"] = &TestConfigReader::run_stress;
consumers["init_forces"] = &TestConfigReader::init_forces;
consumers["run_forces"] = &TestConfigReader::run_forces;
consumers["run_pos"] = &TestConfigReader::run_pos;
consumers["run_vel"] = &TestConfigReader::run_vel;
consumers["pair_style"] = &TestConfigReader::pair_style;
consumers["pair_coeff"] = &TestConfigReader::pair_coeff;
@ -48,6 +50,9 @@ TestConfigReader::TestConfigReader(TestConfig &config) : YamlReader(), config(co
consumers["run_vdwl"] = &TestConfigReader::run_vdwl;
consumers["run_coul"] = &TestConfigReader::run_coul;
consumers["global_scalar"] = &TestConfigReader::global_scalar;
consumers["global_vector"] = &TestConfigReader::global_vector;
consumers["bond_style"] = &TestConfigReader::bond_style;
consumers["bond_coeff"] = &TestConfigReader::bond_coeff;
consumers["angle_style"] = &TestConfigReader::angle_style;
@ -176,6 +181,36 @@ void TestConfigReader::run_forces(const yaml_event_t &event)
}
}
void TestConfigReader::run_pos(const yaml_event_t &event)
{
config.run_pos.clear();
config.run_pos.resize(config.natoms + 1);
std::stringstream data((char *)event.data.scalar.value);
std::string line;
while (std::getline(data, line, '\n')) {
int tag;
coord_t xyz;
sscanf(line.c_str(), "%d %lg %lg %lg", &tag, &xyz.x, &xyz.y, &xyz.z);
config.run_pos[tag] = xyz;
}
}
void TestConfigReader::run_vel(const yaml_event_t &event)
{
config.run_vel.clear();
config.run_vel.resize(config.natoms + 1);
std::stringstream data((char *)event.data.scalar.value);
std::string line;
while (std::getline(data, line, '\n')) {
int tag;
coord_t xyz;
sscanf(line.c_str(), "%d %lg %lg %lg", &tag, &xyz.x, &xyz.y, &xyz.z);
config.run_vel[tag] = xyz;
}
}
void TestConfigReader::pair_style(const yaml_event_t &event)
{
config.pair_style = (char *)event.data.scalar.value;
@ -267,3 +302,21 @@ void TestConfigReader::run_energy(const yaml_event_t &event)
{
config.run_energy = atof((char *)event.data.scalar.value);
}
void TestConfigReader::global_scalar(const yaml_event_t &event)
{
config.global_scalar = atof((char *)event.data.scalar.value);
}
void TestConfigReader::global_vector(const yaml_event_t &event)
{
std::stringstream data((char *)event.data.scalar.value);
config.global_vector.clear();
double value;
std::size_t num;
data >> num;
for (std::size_t i = 0; i < num; ++i) {
data >> value;
config.global_vector.push_back(value);
}
}

4
unittest/force-styles/test_config_reader.h
View File

@ -36,6 +36,8 @@ public:
void run_stress(const yaml_event_t &event);
void init_forces(const yaml_event_t &event);
void run_forces(const yaml_event_t &event);
void run_pos(const yaml_event_t &event);
void run_vel(const yaml_event_t &event);
void pair_style(const yaml_event_t &event);
void pair_coeff(const yaml_event_t &event);
void bond_style(const yaml_event_t &event);
@ -49,6 +51,8 @@ public:
void run_coul(const yaml_event_t &event);
void init_energy(const yaml_event_t &event);
void run_energy(const yaml_event_t &event);
void global_scalar(const yaml_event_t &event);
void global_vector(const yaml_event_t &event);
};
#endif

2
unittest/force-styles/test_error_stats.cpp
View File

@ -29,12 +29,14 @@ TEST(ErrorStats, test)
ASSERT_EQ(out.str(), "Average: 5.800e-01 StdDev: 7.305e-01 MaxErr: 2.000e+00 @ item: 3.0");
stats.reset();
ASSERT_EQ(stats.has_data(), false);
ASSERT_DOUBLE_EQ(stats.avg(), 0.0);
ASSERT_DOUBLE_EQ(stats.dev(), 0.0);
ASSERT_DOUBLE_EQ(stats.max(), 0.0);
ASSERT_EQ(stats.idx(), -1);
stats.add(1.0);
ASSERT_EQ(stats.has_data(), true);
ASSERT_DOUBLE_EQ(stats.avg(), 1.0);
ASSERT_DOUBLE_EQ(stats.dev(), 0.0);
ASSERT_DOUBLE_EQ(stats.max(), 1.0);

1166
unittest/force-styles/test_fix_timestep.cpp Normal file
View File

File diff suppressed because it is too large Load Diff

5
unittest/force-styles/test_main.cpp
View File

@ -102,13 +102,16 @@ int main(int argc, char **argv)
if (strcmp(argv[iarg], "-g") == 0) {
if (iarg + 1 < argc) {
generate_yaml_file(argv[iarg + 1], test_config);
MPI_Finalize();
return 0;
} else {
usage(std::cerr, argv[0]);
MPI_Finalize();
return 1;
}
} else if (strcmp(argv[iarg], "-u") == 0) {
generate_yaml_file(argv[1], test_config);
MPI_Finalize();
return 0;
} else if (strcmp(argv[iarg], "-d") == 0) {
if (iarg + 1 < argc) {
@ -116,6 +119,7 @@ int main(int argc, char **argv)
iarg += 2;
} else {
usage(std::cerr, argv[0]);
MPI_Finalize();
return 1;
}
} else if (strcmp(argv[iarg], "-s") == 0) {
@ -127,6 +131,7 @@ int main(int argc, char **argv)
} else {
std::cerr << "unknown option: " << argv[iarg] << "\n\n";
usage(std::cerr, argv[0]);
MPI_Finalize();
return 1;
}
}

3
unittest/force-styles/test_pair_style.cpp
View File

@ -1107,8 +1107,7 @@ TEST(PairStyle, single)
(test_config.pair_style.substr(0, 14) == "yukawa/colloid") ||
(test_config.pair_style.substr(0, 3) == "eam") ||
((test_config.pair_style.substr(0, 6) == "hybrid") &&
(test_config.pair_style.find("eam") != std::string::npos))
) {
(test_config.pair_style.find("eam") != std::string::npos))) {
if (!verbose) ::testing::internal::CaptureStdout();
cleanup_lammps(lmp, test_config);
if (!verbose) ::testing::internal::GetCapturedStdout();

2
unittest/force-styles/tests/atomic-pair-edip.yaml
View File

@ -1,7 +1,7 @@
---
lammps_version: 21 Jul 2020
date_generated: Fri Aug 7 16:11:57 202
epsilon: 1e-14
epsilon: 2e-14
prerequisites: ! |
pair edip
pre_commands: ! |

77
unittest/force-styles/tests/fix-timestep-addforce-const.yaml Normal file
View File

@ -0,0 +1,77 @@
---
lammps_version: 21 Jul 2020
date_generated: Tue Aug 11 20:56:35 202
epsilon: 2e-13
prerequisites: ! |
atom full
fix addforce
pre_commands: ! ""
post_commands: ! |
fix move all nve
fix test solute addforce 0.0 -0.1 0.1
input_file: in.fourmol
natoms: 29
global_scalar: 1.48901835738129
global_vector: ! |-
3 0.030822392996626036 0.026014193882019754 -0.017708991389909556
run_pos: ! |2
1 -2.7045575291334861e-01 2.4912098953869757e+00 -1.6695239815574214e-01
2 3.1004076900710170e-01 2.9612149597462425e+00 -8.5464329005027972e-01
3 -7.0398549308743119e-01 1.2305439518786667e+00 -6.2776812583732400e-01
4 -1.5818160726875390e+00 1.4837199951274893e+00 -1.2538503621778578e+00
5 -9.0719748669903200e-01 9.2650033697311973e-01 3.9956266031649879e-01
6 2.4831714249110262e-01 2.8312325631591767e-01 -1.2314165454625041e+00
7 3.4143527198959711e-01 -2.2651747674360529e-02 -2.5292238033565768e+00
8 1.1743553514271237e+00 -4.8863828453992741e-01 -6.3782817835070349e-01
9 1.3800522445502728e+00 -2.5276822789361231e-01 2.8356018210481976e-01
10 2.0510765111429961e+00 -1.4604133270429198e+00 -9.8323043580441027e-01
11 1.7878031588883598e+00 -1.9922071845945071e+00 -1.8890394822792633e+00
12 3.0063007413447411e+00 -4.9014063242955885e-01 -1.6231827019640992e+00
13 4.0515402229636264e+00 -8.9204090546353654e-01 -1.6399797487882732e+00
14 2.6066963018347171e+00 -4.1791325385826189e-01 -2.6633797762015425e+00
15 2.9695287113240152e+00 5.5420546275525007e-01 -1.2341814098635149e+00
16 2.6747030089515893e+00 -2.4124189004358674e+00 -2.3428869709464669e-02
17 2.2153577487661584e+00 -2.0898037210104183e+00 1.1963203850079958e+00
18 2.1369701704121455e+00 3.0158507413641966e+00 -3.5179348337229994e+00
19 1.5355837136088100e+00 2.6255292355377717e+00 -4.2353987779882338e+00
20 2.7727573005679371e+00 3.6923910449611110e+00 -3.9330842459134390e+00
21 4.9040128073204006e+00 -4.0752348172958719e+00 -3.6210314709889815e+00
22 4.3582355554440877e+00 -4.2126119427287128e+00 -4.4612844196313990e+00
23 5.7439382849307599e+00 -3.5821957939275113e+00 -3.8766361295935736e+00
24 2.0689243582419619e+00 3.1513346907267743e+00 3.1550389754827148e+00
25 1.3045351331489012e+00 3.2665125705839713e+00 2.5111855257429738e+00
26 2.5809237402711087e+00 4.0117602605482601e+00 3.2212060529089812e+00
27 -1.9611343130352876e+00 -4.3563411931356626e+00 2.1098293115521889e+00
28 -2.7473562684513193e+00 -4.0200819932379153e+00 1.5830052163433885e+00
29 -1.3126000191359226e+00 -3.5962518039482334e+00 2.2746342468737333e+00
run_vel: ! |2
1 8.1702613218438691e-03 1.6510191351429417e-02 4.7964973237771503e-03
2 5.4511084170875343e-03 5.1590481528437813e-03 -1.4175058774793692e-03
3 -8.2297881733875439e-03 -1.2933678261753652e-02 -4.0910944229037285e-03
4 -3.7701876602396953e-03 -6.5929809185369939e-03 -1.0979051123824390e-03
5 -1.1021655940056645e-02 -9.9111987493572112e-03 -2.8208515585563172e-03
6 -3.9676769272842236e-02 4.6810118626188314e-02 3.7155184099431124e-02
7 9.1033245554758080e-04 -1.0133704610200299e-02 -5.1562858164992204e-02
8 7.9067086761695892e-03 -3.3567238353401636e-03 3.4563427326757518e-02
9 1.5640463507800002e-03 3.7153745906232053e-03 1.5067137863525135e-02
10 2.9201431684716742e-02 -2.9256524162078218e-02 -1.5011015513636336e-02
11 -4.7836707031183607e-03 -3.7689744526784260e-03 -2.3257693833597559e-03
12 2.2697215661243897e-03 -3.5503408953511771e-04 -3.0568221042131718e-03
13 2.7530266001101656e-03 5.7964078805919205e-03 -7.7394765650209171e-04
14 3.5245514557562165e-03 -5.8145427341994562e-03 -3.9275617105511392e-03
15 -1.8548103902428440e-03 -5.8759259808655083e-03 6.3145508812191310e-03
16 1.8681562217261326e-02 -1.3269471066222347e-02 -4.5631826406699355e-02
17 -1.2896316924809444e-02 9.7475788915801498e-03 3.7301887298077194e-02
18 -8.0065794732626385e-04 -8.6270472984577718e-04 -1.4483040728194251e-03
19 1.2452390837669909e-03 -2.5061097114590261e-03 7.2998631002926129e-03
20 3.5930060230919166e-03 3.6938860311325015e-03 3.2322732685912069e-03
21 -1.4689220371368486e-03 -2.7352129777820513e-04 7.0581624254054305e-04
22 -7.0694199254559926e-03 -4.2577148925067674e-03 2.8079117615819173e-04
23 6.0446963117369709e-03 -1.4000131614987045e-03 2.5819754847190117e-03
24 3.1926367840560363e-04 -9.9445664816168633e-04 1.4999996925784762e-04
25 1.3789754450351514e-04 -4.4335894890997355e-03 -8.1808136802931375e-04
26 2.0485904034793470e-03 2.7813358633281375e-03 4.3245727149043870e-03
27 4.5604120382313504e-04 -1.0305523020532397e-03 2.1188058344304351e-04
28 -6.2544520861381259e-03 1.4127711176493136e-03 -1.8429821884921316e-03
29 6.4110631547740983e-04 3.1273432720868841e-03 3.7253671104628787e-03
...

82
unittest/force-styles/tests/fix-timestep-addforce-variable.yaml Normal file
View File

@ -0,0 +1,82 @@
---
lammps_version: 21 Jul 2020
date_generated: Tue Aug 11 20:56:35 202
epsilon: 2e-13
prerequisites: ! |
atom full
fix addforce
pre_commands: ! ""
post_commands: ! |
fix init all store/state 0 x y z
variable xforce delete
variable xforce atom f_init[1]
variable zforce delete
variable zforce equal 0.1*step/10.0
fix move all nve
fix test solute addforce v_xforce 0.0 v_zforce
input_file: in.fourmol
natoms: 29
global_scalar: -66.6128081721324
global_vector: ! |-
3 0.030822805860552194 0.026012717110660333 -0.017710664092739137
run_pos: ! |2
1 -2.7047214228789879e-01 2.4912159473897288e+00 -1.6695741351125751e-01
2 3.1010217675350321e-01 2.9612343643897283e+00 -8.5465678502037923e-01
3 -7.0403575539675045e-01 1.2305513713119018e+00 -6.2777371590783770e-01
4 -1.5821400298238728e+00 1.4837402879631465e+00 -1.2538644175974110e+00
5 -9.0738248321725767e-01 9.2652118661051119e-01 3.9954717998547740e-01
6 2.4833938838692704e-01 2.8312848343353764e-01 -1.2314198266861847e+00
7 3.4145305574459789e-01 -2.2646551615904693e-02 -2.5292277033981856e+00
8 1.1744251519295958e+00 -4.8863301930795239e-01 -6.3783420180106931e-01
9 1.3803393322923716e+00 -2.5274719088138620e-01 2.8354262280984910e-01
10 2.0512157806659483e+00 -1.4604034995894550e+00 -9.8323457702970984e-01
11 1.7881766053556223e+00 -1.9921867592459330e+00 -1.8890557966324570e+00
12 3.0065163851107513e+00 -4.9013454995145816e-01 -1.6231872062008903e+00
13 4.0523716162518593e+00 -8.9201902994109461e-01 -1.6399944550397565e+00
14 2.6072370808739733e+00 -4.1789116991871833e-01 -2.6633963232657543e+00
15 2.9701454639399292e+00 5.5422639267898544e-01 -1.2341975484787577e+00
16 2.6748871049483789e+00 -2.4124111330493521e+00 -2.3431784517031026e-02
17 2.2154747990656891e+00 -2.0897989887607591e+00 1.1963148502274976e+00
18 2.1369701704176829e+00 3.0158507413681335e+00 -3.5179348337252407e+00
19 1.5355837136089958e+00 2.6255292355383033e+00 -4.2353987779886255e+00
20 2.7727573005681436e+00 3.6923910449611030e+00 -3.9330842459134483e+00
21 4.9040128073163958e+00 -4.0752348172839117e+00 -3.6210314709779454e+00
22 4.3582355554441445e+00 -4.2126119427283166e+00 -4.4612844196308510e+00
23 5.7439382849302527e+00 -3.5821957939267821e+00 -3.8766361295928178e+00
24 2.0689243582437542e+00 3.1513346907275186e+00 3.1550389754841301e+00
25 1.3045351331496602e+00 3.2665125705847990e+00 2.5111855257446942e+00
26 2.5809237402712069e+00 4.0117602605483258e+00 3.2212060529090598e+00
27 -1.9611343130422572e+00 -4.3563411931406684e+00 2.1098293115555511e+00
28 -2.7473562684515755e+00 -4.0200819932380565e+00 1.5830052163434851e+00
29 -1.3126000191366660e+00 -3.5962518039487934e+00 2.2746342468743648e+00
run_vel: ! |2
1 8.1542005804048114e-03 1.6516352657195144e-02 4.7916994861873716e-03
2 5.5108616996518527e-03 5.1769592855304752e-03 -1.4262044196006701e-03
3 -8.2819560524694975e-03 -1.2925874484803790e-02 -4.0962172584282129e-03
4 -4.0886380039043026e-03 -6.5733036630979845e-03 -1.1077208107759873e-03
5 -1.1204698339013554e-02 -9.8903762469767197e-03 -2.8335724171420786e-03
6 -3.9653324695987140e-02 4.6814090441761887e-02 3.7154219827738325e-02
7 9.2811228899244145e-04 -1.0128521447666933e-02 -5.1566014310509153e-02
8 7.9768414397017682e-03 -3.3521215541620886e-03 3.4557180732453542e-02
9 1.8506084396989573e-03 3.7365307043657862e-03 1.5049937691527137e-02
10 2.9339781785645530e-02 -2.9244335397845489e-02 -1.5013285041501756e-02
11 -4.4111732898708574e-03 -3.7490441708152595e-03 -2.3402341830182269e-03
12 2.4919774686993339e-03 -3.4986602016114646e-04 -3.0596868750942985e-03
13 3.5708757570142549e-03 5.8192695094192127e-03 -7.8509643584213180e-04
14 4.0624997491302594e-03 -5.7912127152414828e-03 -3.9424433676611033e-03
15 -1.2427000878928462e-03 -5.8549223934944352e-03 6.3005021988472203e-03
16 1.8865114672276220e-02 -1.3261139374878017e-02 -4.5632510336419303e-02
17 -1.2778996290317002e-02 9.7520044246185329e-03 3.7296098445722708e-02
18 -8.0065793587999099e-04 -8.6270472146121331e-04 -1.4483040775306573e-03
19 1.2452390841875935e-03 -2.5061097103150493e-03 7.2998630994791933e-03
20 3.5930060235755922e-03 3.6938860311851785e-03 3.2322732685174278e-03
21 -1.4689220453590402e-03 -2.7352127317486851e-04 7.0581626525379880e-04
22 -7.0694199252635138e-03 -4.2577148916858000e-03 2.8079117743316296e-04
23 6.0446963107027478e-03 -1.4000131600045436e-03 2.5819754862959378e-03
24 3.1926368204184148e-04 -9.9445664667548433e-04 1.4999997209784617e-04
25 1.3789754604908935e-04 -4.4335894874218615e-03 -8.1808136451897351e-04
26 2.0485904036966728e-03 2.7813358634892773e-03 4.3245727150655168e-03
27 4.5604118959923195e-04 -1.0305523122762120e-03 2.1188059030274769e-04
28 -6.2544520866959210e-03 1.4127711173635808e-03 -1.8429821883176730e-03
29 6.4110631389697711e-04 3.1273432708352981e-03 3.7253671117315453e-03
...

76
unittest/force-styles/tests/fix-timestep-aveforce-const.yaml Normal file
View File

@ -0,0 +1,76 @@
---
lammps_version: 21 Jul 2020
date_generated: Tue Aug 11 20:59:48 202
epsilon: 2e-13
prerequisites: ! |
atom full
fix aveforce
pre_commands: ! ""
post_commands: ! |
fix move all nve
fix test solute aveforce 0.0 -0.1 0.1
input_file: in.fourmol
natoms: 29
global_vector: ! |-
3 0.030693239277496787 0.026836713504508225 -0.017872771454378267
run_pos: ! |2
1 -2.7837937276378577e-01 2.4738323337395633e+00 -1.7244628118937513e-01
2 3.0739712238693778e-01 2.9607606438663985e+00 -8.4971558628080046e-01
3 -6.9690101126084858e-01 1.2472621905952943e+00 -6.2300348438124675e-01
4 -1.5790176115308630e+00 1.4890051885382072e+00 -1.2569330199852327e+00
5 -8.9737740636582297e-01 9.3716922702553496e-01 4.0243602458027911e-01
6 2.9350792503004042e-01 2.2973704675580464e-01 -1.2827110266930783e+00
7 3.3997804713002810e-01 -1.0668179410931006e-02 -2.4648504997159280e+00
8 1.1649000306414594e+00 -4.8538782401639990e-01 -6.7628963324595071e-01
9 1.3802414668448064e+00 -2.5900562603021171e-01 2.7102062739419147e-01
10 2.0194286609797985e+00 -1.4274129376624451e+00 -9.6779510337284758e-01
11 1.7922388743932793e+00 -1.9901831169119615e+00 -1.8898772827854291e+00
12 3.0051950803427370e+00 -4.9053937459745156e-01 -1.6214531896525444e+00
13 4.0528786674689306e+00 -8.9433183344016831e-01 -1.6399905570763349e+00
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19 1.5355837134891335e+00 2.6255292349555996e+00 -4.2353987775907820e+00
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21 4.9040128097611282e+00 -4.0752348192998742e+00 -3.6210314741040888e+00
22 4.3582355555035486e+00 -4.2126119428105140e+00 -4.4612844198387114e+00
23 5.7439382850855170e+00 -3.5821957939653362e+00 -3.8766361297558971e+00
24 2.0689243589260014e+00 3.1513346914908205e+00 3.1550389767665203e+00
25 1.3045351340666116e+00 3.2665125708708889e+00 2.5111855275754800e+00
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27 -1.9611343134182779e+00 -4.3563411935660996e+00 2.1098293111593480e+00
28 -2.7473562684449138e+00 -4.0200819932443128e+00 1.5830052163349162e+00
29 -1.3126000190352287e+00 -3.5962518039727378e+00 2.2746342468394127e+00
run_vel: ! |2
1 7.7878588734526198e-04 5.8382345680427130e-04 -2.1588360870901697e-04
2 2.7133298635754447e-03 4.6080941432587817e-03 3.6012143490662431e-03
3 -1.2735533433080959e-03 1.6040104178824128e-03 -3.2928787663304100e-04
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6 -3.0901428918666851e-04 1.2686815717087763e-03 8.0263701588449308e-04
7 -1.1028454231743601e-04 -7.7279598321444340e-04 -7.6700101339104750e-04
8 3.9071065119356116e-04 -8.2032217860919109e-04 1.5725797910453806e-04
9 1.2479299632287711e-03 -2.6813940130008974e-03 1.1324196703928796e-03
10 4.5021559737281377e-04 4.8844497171634344e-04 -2.2646836122846916e-04
11 -3.6939982362589797e-04 -1.5494557630536987e-03 -2.8969796085021034e-03
12 1.0852092126307005e-03 -6.5651598379105566e-04 -1.2902212798795269e-03
13 4.0758327867858645e-03 3.4838016716369673e-03 -7.6258549719693985e-04
14 -1.3799533732466697e-04 -4.0861534316170862e-03 -3.9126867377128425e-03
15 -4.3297938711093853e-03 -3.2008147343211384e-03 3.2244512840176650e-03
16 -9.6589991406029584e-05 -5.0702273154864109e-04 1.5014598698974305e-03
17 6.5701621273287663e-04 3.6121026772938211e-04 8.4012943587149819e-04
18 -8.0066194144632968e-04 -8.6271665406919022e-04 -1.4482973852517659e-03
19 1.2452388413347042e-03 -2.5061108560376941e-03 7.2998638677115694e-03
20 3.5930058301559932e-03 3.6938856643002412e-03 3.2322734436995241e-03
21 -1.4689171694767468e-03 -2.7352531122827996e-04 7.0581004752321775e-04
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...

81
unittest/force-styles/tests/fix-timestep-aveforce-variable.yaml Normal file
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@ -0,0 +1,81 @@
---
lammps_version: 21 Jul 2020
date_generated: Tue Aug 11 20:59:48 202
epsilon: 2e-13
prerequisites: ! |
atom full
fix aveforce
pre_commands: ! ""
post_commands: ! |
fix init all store/state 0 x y z
variable xforce delete
# variable xforce atom f_init[1]
variable zforce delete
variable zforce equal 0.1*step/10.0
fix move all nve
fix test solute aveforce 0.0 0.0 v_zforce
input_file: in.fourmol
natoms: 29
global_vector: ! |-
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run_pos: ! |2
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...

76
unittest/force-styles/tests/fix-timestep-nph.yaml Normal file
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@ -0,0 +1,76 @@
---
lammps_version: 21 Jul 2020
date_generated: Sun Aug 9 07:12:15 202
epsilon: 2e-13
prerequisites: ! |
atom full
fix nph
pre_commands: ! ""
post_commands: ! |
fix test solute nph aniso 1.0 1.0 100.0 ptemp ${t_target} fixedpoint 0.0 0.0 0.0 couple xy
input_file: in.fourmol
natoms: 29
global_scalar: 157.324342558061
global_vector: ! |-
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run_pos: ! |2
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...

76
unittest/force-styles/tests/fix-timestep-npt_aniso.yaml Normal file
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@ -0,0 +1,76 @@
---
lammps_version: 21 Jul 2020
date_generated: Sun Aug 9 07:12:15 202
epsilon: 2e-12
prerequisites: ! |
atom full
fix npt
pre_commands: ! ""
post_commands: ! |
fix test solute npt temp 50.0 ${t_target} 1.0 aniso 1.0 1.0 100.0 drag 0.01 flip no
input_file: in.fourmol
natoms: 29
global_scalar: 343.095604765377
global_vector: ! |-
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...

76
unittest/force-styles/tests/fix-timestep-npt_iso.yaml Normal file
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@ -0,0 +1,76 @@
---
lammps_version: 21 Jul 2020
date_generated: Sun Aug 9 07:12:15 202
epsilon: 5e-13
prerequisites: ! |
atom full
fix npt
pre_commands: ! ""
post_commands: ! |
fix test solute npt temp 50.0 ${t_target} 1.0 iso 1.0 1.0 100.0 dilate solute
input_file: in.fourmol
natoms: 29
global_scalar: 394.052580100464
global_vector: ! |-
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...

77
unittest/force-styles/tests/fix-timestep-npt_tri.yaml Normal file
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@ -0,0 +1,77 @@
---
lammps_version: 21 Jul 2020
date_generated: Sun Aug 9 07:12:15 202
epsilon: 5e-12
prerequisites: ! |
atom full
fix npt
pre_commands: ! ""
post_commands: ! |
change_box all triclinic
fix test solute npt temp 50.0 ${t_target} 1.0 tri 1.0 1.0 100.0 nreset 2
input_file: in.fourmol
natoms: 29
global_scalar: 354.174797856098
global_vector: ! |-
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...

73
unittest/force-styles/tests/fix-timestep-nve.yaml Normal file
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@ -0,0 +1,73 @@
---
lammps_version: 21 Jul 2020
date_generated: Sun Aug 9 07:12:15 202
epsilon: 1e-14
prerequisites: ! |
atom full
fix nve
pre_commands: ! ""
post_commands: ! |
fix test solute nve
input_file: in.fourmol
natoms: 29
run_pos: ! |2
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...

76
unittest/force-styles/tests/fix-timestep-nvt.yaml Normal file
View File

@ -0,0 +1,76 @@
---
lammps_version: 21 Jul 2020
date_generated: Sun Aug 9 07:12:15 202
epsilon: 5e-14
prerequisites: ! |
atom full
fix nvt
pre_commands: ! ""
post_commands: ! |
fix test solute nvt temp 50.0 ${t_target} 1.0 mtk no tchain 1
input_file: in.fourmol
natoms: 29
global_scalar: 161.082193606418
global_vector: ! |-
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run_pos: ! |2
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...

74
unittest/force-styles/tests/fix-timestep-press_berendsen_iso.yaml Normal file
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@ -0,0 +1,74 @@
---
lammps_version: 21 Jul 2020
date_generated: Sun Aug 9 16:44:09 202
epsilon: 2e-13
prerequisites: ! |
atom full
fix press/berendsen
pre_commands: ! ""
post_commands: ! |
fix all solute nve
fix test solute press/berendsen iso 5000.0 5000.0 10000.0
input_file: in.fourmol
natoms: 29
run_pos: ! |2
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...

77
unittest/force-styles/tests/fix-timestep-rattle_angle.yaml Normal file
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@ -0,0 +1,77 @@
---
lammps_version: 21 Jul 2020
date_generated: Sun Aug 9 16:30:21 202
epsilon: 2e-13
prerequisites: ! |
atom full
fix rattle
pre_commands: ! ""
post_commands: ! |
fix move all nve
fix test solvent rattle 1.0e-5 20 4 b 5 a 1
fix_modify test virial yes
input_file: in.fourmol
natoms: 29
run_stress: ! |-
-6.7489444076122581e+01 -3.6466857275816793e+01 -4.1453650662488030e+01 -3.0881715538687999e+01 -2.8271646386126275e+01 1.8512924155867125e-01
run_pos: ! |2
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...

77
unittest/force-styles/tests/fix-timestep-rattle_bond.yaml Normal file
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@ -0,0 +1,77 @@
---
lammps_version: 21 Jul 2020
date_generated: Sun Aug 9 16:30:21 202
epsilon: 2e-13
prerequisites: ! |
atom full
fix rattle
pre_commands: ! ""
post_commands: ! |
fix move all nve
fix test solute rattle 1.0e-5 20 4 m 4.00794
fix_modify test virial yes
input_file: in.fourmol
natoms: 29
run_stress: ! |2-
3.9891557115890999e+00 3.7983351717152480e+00 7.6152694943743228e+01 5.7163462651523300e-01 3.0839737670745507e+01 3.0066936263232019e+01
run_pos: ! |2
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...

78
unittest/force-styles/tests/fix-timestep-rigid-group.yaml Normal file
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@ -0,0 +1,78 @@
---
lammps_version: 21 Jul 2020
date_generated: Sun Aug 9 16:30:21 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
fix rigid
pre_commands: ! ""
post_commands: ! |
variable t_target delete
fix test all rigid group 2 solute solvent
fix_modify test virial yes
input_file: in.fourmol
natoms: 29
run_stress: ! |-
-1.4245356937318927e+03 -1.4496493315649675e+03 -3.6144360984224963e+03 8.4840626828643849e+02 2.0318336761611764e+02 -6.0622397707969685e+02
global_scalar: 15.7115214231781
run_pos: ! |2
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run_vel: ! |2
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...

78
unittest/force-styles/tests/fix-timestep-rigid-molecule.yaml Normal file
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@ -0,0 +1,78 @@
---
lammps_version: 21 Jul 2020
date_generated: Sun Aug 9 16:30:21 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
fix rigid
pre_commands: ! ""
post_commands: ! |
variable t_target delete
fix test solvent rigid molecule
fix_modify test virial yes
input_file: in.fourmol
natoms: 29
run_stress: ! |-
-4.9200116134790363e+01 -2.6907707565987732e+01 -6.0080860422282560e+00 -2.5620423972101747e+01 -1.3450224059984075e+01 -1.4947288487004844e+00
global_scalar: 18.3405601674144
run_pos: ! |2
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...

78
unittest/force-styles/tests/fix-timestep-rigid-single.yaml Normal file
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@ -0,0 +1,78 @@
---
lammps_version: 21 Jul 2020
date_generated: Sun Aug 9 16:30:21 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
fix rigid
pre_commands: ! ""
post_commands: ! |
variable t_target delete
fix test solute rigid single
fix_modify test virial yes
input_file: in.fourmol
natoms: 29
run_stress: ! |-
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...

76
unittest/force-styles/tests/fix-timestep-setforce-const.yaml Normal file
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@ -0,0 +1,76 @@
---
lammps_version: 21 Jul 2020
date_generated: Sun Aug 9 07:12:16 202
epsilon: 2e-13
prerequisites: ! |
atom full
fix setforce
pre_commands: ! ""
post_commands: ! |
fix move all nve
fix test solute setforce 0.0 NULL 0.1
input_file: in.fourmol
natoms: 29
global_vector: ! |-
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run_pos: ! |2
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...

77
unittest/force-styles/tests/fix-timestep-setforce-region.yaml Normal file
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@ -0,0 +1,77 @@
---
lammps_version: 21 Jul 2020
date_generated: Sun Aug 9 15:15:21 202
epsilon: 2e-13
prerequisites: ! |
atom full
fix setforce
pre_commands: ! ""
post_commands: ! |
region half block 0 EDGE EDGE EDGE EDGE EDGE
fix move all nve
fix test solute setforce 0.0 0.0 0.0 region half
input_file: in.fourmol
natoms: 29
global_vector: ! |-
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run_pos: ! |2
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...

81
unittest/force-styles/tests/fix-timestep-setforce-variable.yaml Normal file
View File

@ -0,0 +1,81 @@
---
lammps_version: 21 Jul 2020
date_generated: Sun Aug 9 07:31:40 202
epsilon: 2e-13
prerequisites: ! |
atom full
fix setforce
pre_commands: ! ""
post_commands: ! |
fix init all store/state 0 x y z
variable xforce delete
variable xforce atom f_init[1]
variable zforce delete
variable zforce equal 0.1*step/10.0
fix move all nve
fix test solute setforce v_xforce NULL v_zforce
input_file: in.fourmol
natoms: 29
global_vector: ! |-
3 0.031197043446070438 0.027174896355546707 -0.0182497728803952
run_pos: ! |2
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...

77
unittest/force-styles/tests/fix-timestep-shake_angle.yaml Normal file
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@ -0,0 +1,77 @@
---
lammps_version: 21 Jul 2020
date_generated: Sun Aug 9 16:30:22 202
epsilon: 2e-12
prerequisites: ! |
atom full
fix shake
pre_commands: ! ""
post_commands: ! |
fix move all nve
fix test solvent shake 1.0e-5 20 4 b 5 a 1
fix_modify test virial yes
input_file: in.fourmol
natoms: 29
run_stress: ! |-
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...

77
unittest/force-styles/tests/fix-timestep-shake_bond.yaml Normal file
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@ -0,0 +1,77 @@
---
lammps_version: 21 Jul 2020
date_generated: Sun Aug 9 16:30:22 202
epsilon: 2e-12
prerequisites: ! |
atom full
fix shake
pre_commands: ! ""
post_commands: ! |
fix move all nve
fix test solute shake 1.0e-5 20 4 m 4.00794
fix_modify test virial yes
input_file: in.fourmol
natoms: 29
run_stress: ! |2-
4.1327164284089424e+00 4.1298776885725212e+00 7.7065049821613400e+01 7.3427739401911385e-01 3.1021321349896283e+01 3.0482918118325731e+01
run_pos: ! |2
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...

75
unittest/force-styles/tests/fix-timestep-temp_berendsen.yaml Normal file
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@ -0,0 +1,75 @@
---
lammps_version: 21 Jul 2020
date_generated: Sun Aug 9 07:12:16 202
epsilon: 1e-14
prerequisites: ! |
atom full
fix temp/berendsen
pre_commands: ! ""
post_commands: ! |
fix all solute nve
fix test solute temp/berendsen 50.0 ${t_target} 1.0
input_file: in.fourmol
natoms: 29
global_scalar: 140.500399901528
run_pos: ! |2
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run_vel: ! |2
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...

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