Merge pull request #2284 from akohlmey/fix-tester

Add unit test tool for fixes that do time integration, thermostatting, force manipulations and similar
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Axel Kohlmeyer 2020-08-13 10:23:29 -04:00 committed by GitHub
commit 1c2747739a
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70 changed files with 4066 additions and 75 deletions

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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"

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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;\
)

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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

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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>`

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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

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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

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@ -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]);
}

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@ -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);

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@ -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,

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@ -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);
}
/* ----------------------------------------------------------------------

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@ -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) {

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@ -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");

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@ -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];

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@ -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;
}

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@ -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;

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@ -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;

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@ -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
------------------------------------------------------------------------- */

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@ -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:

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@ -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
------------------------------------------------------------------------- */

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:

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
------------------------------------------------------------------------- */

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:

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));
}
/* ----------------------------------------------------------------------

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];
}

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;

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();

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)

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"););

View File

@ -114,3 +114,16 @@ foreach(TEST ${KSPACE_TESTS})
add_test(NAME ${TNAME} COMMAND test_pair_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()

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}")

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;

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(){};

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);
}
}

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

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);

File diff suppressed because it is too large Load Diff

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;
}
}

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();

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: ! |

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
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...

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: ! |-
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...

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: ! |-
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run_pos: ! |2
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...

View File

@ -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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...

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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
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...

View File

@ -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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...

View File

@ -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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...

View File

@ -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
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...

View File

@ -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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...

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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...

View File

@ -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
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...

View File

@ -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: ! |-
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...

View File

@ -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-
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...

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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: ! |-
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global_scalar: 15.7115214231781
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...

View File

@ -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: ! |-
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global_scalar: 18.3405601674144
run_pos: ! |2
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...

View File

@ -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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global_scalar: 4.53142303857031
run_pos: ! |2
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...

View File

@ -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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...

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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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...

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: ! |-
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...

View File

@ -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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run_pos: ! |2
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...

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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-
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...

View File

@ -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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...

View File

@ -0,0 +1,75 @@
---
lammps_version: 21 Jul 2020
date_generated: Sun Aug 9 14:54:04 202
epsilon: 1e-14
prerequisites: ! |
atom full
fix temp/csld
pre_commands: ! ""
post_commands: ! |
fix all solute nve
fix test solute temp/csld 50.0 ${t_target} 1.0 62823
input_file: in.fourmol
natoms: 29
global_scalar: 150.876840894722
run_pos: ! |2
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run_vel: ! |2
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...

View File

@ -0,0 +1,75 @@
---
lammps_version: 21 Jul 2020
date_generated: Sun Aug 9 14:53:58 202
epsilon: 1e-14
prerequisites: ! |
atom full
fix temp/csvr
pre_commands: ! ""
post_commands: ! |
fix all solute nve
fix test solute temp/csvr 50.0 ${t_target} 1.0 82573
input_file: in.fourmol
natoms: 29
global_scalar: 138.691817964765
run_pos: ! |2
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27 -1.9613581876744359e+00 -4.3556300596085160e+00 2.1101467673534788e+00
28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00
29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00
run_vel: ! |2
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3 -4.6306766915023894e-03 -7.9351414155915453e-03 -2.3497227140117419e-03
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...

View File

@ -0,0 +1,81 @@
---
lammps_version: 21 Jul 2020
date_generated: Sun Aug 9 16:30:22 202
epsilon: 1e-14
prerequisites: ! |
atom full
fix wall/harmonic
pre_commands: ! |
boundary p f p
post_commands: ! |
fix move all nve
fix test solute wall/harmonic ylo EDGE 100.0 0.0 5.0 yhi EDGE 100.0 0.0 5.0
fix_modify test virial yes
input_file: in.fourmol
natoms: 29
run_stress: ! |2-
0.0000000000000000e+00 7.2422093200265749e+02 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
global_scalar: 42.6997744353244
global_vector: ! |-
2 0.0 161.92409617466126
run_pos: ! |2
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2 3.1037661579862175e-01 2.9347166386691113e+00 -8.5496435221221156e-01
3 -7.0402515865264603e-01 1.2304739304383521e+00 -6.2777422080240730e-01
4 -1.5818156002522876e+00 1.4837443919066966e+00 -1.2538703954644463e+00
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7 3.4143527599853957e-01 -2.2646552136496162e-02 -2.5292291409504188e+00
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29 -1.3126000191357743e+00 -3.5962518039473323e+00 2.2746342468733483e+00
run_vel: ! |2
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6 -3.9677127674597606e-02 4.6816039080495052e-02 3.7148638820894170e-02
7 9.1033730239907995e-04 -1.0128528243740664e-02 -5.1568250829251872e-02
8 7.9064772413549398e-03 -3.3507427942055237e-03 3.4557101116794005e-02
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25 1.3789762510432095e-04 -4.4335895501596183e-03 -8.1808122106665057e-04
26 2.0485904106950122e-03 2.7813358601316666e-03 4.3245727251785618e-03
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29 6.4110631581209361e-04 3.1273432740202512e-03 3.7253671096581808e-03
...

View File

@ -11,6 +11,7 @@ variable bond_style index zero
variable angle_style index zero
variable dihedral_style index zero
variable improper_style index zero
variable t_target index 100.0
atom_style full
atom_modify map array

View File

@ -0,0 +1,155 @@
---
lammps_version: 21 Jul 2020
date_generated: Tue Aug 11 09:00:37 202
epsilon: 5e-13
prerequisites: ! |
pair extep
pre_commands: ! |
variable newton_pair delete
variable newton_pair index on
post_commands: ! ""
input_file: in.manybody
pair_style: extep
pair_coeff: ! |
* * BN.extep B B B B N N N N
extract: ! ""
natoms: 64
init_vdwl: -8.35953889724907
init_coul: 0
init_stress: ! |-
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init_forces: ! |2
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...

View File

@ -0,0 +1,103 @@
---
lammps_version: 21 Jul 2020
date_generated: Tue Aug 11 08:52:27 202
epsilon: 5e-14
prerequisites: ! |
atom full
pair lj/cut/tip4p/cut
pair e3b
pre_commands: ! |
variable newton_pair delete
variable newton_pair index on
post_commands: ! |
pair_modify mix arithmetic
input_file: in.fourmol
pair_style: hybrid/overlay lj/cut/tip4p/cut 5 2 5 1 0.15 10.0 e3b 5
pair_coeff: ! |
1 1 lj/cut/tip4p/cut 0.02 2.5 8
1 2 lj/cut/tip4p/cut 0.01 1.75 8
1 3 lj/cut/tip4p/cut 0.02 2.85 8
1 4 lj/cut/tip4p/cut 0.0173205 2.8 8
1 5 lj/cut/tip4p/cut 0.0173205 2.8 8
2 2 lj/cut/tip4p/cut 0.0 1 8
2 3 lj/cut/tip4p/cut 0.0 2.1 8
2 4 lj/cut/tip4p/cut 0.0 0.5 8
2 5 lj/cut/tip4p/cut 0.0 2.05 8
3 3 lj/cut/tip4p/cut 0.02 3.2 8
3 4 lj/cut/tip4p/cut 0.0173205 3.15 8
3 5 lj/cut/tip4p/cut 0.0173205 3.15 8
4 4 lj/cut/tip4p/cut 0.015 3.1 8
4 5 lj/cut/tip4p/cut 0.015 3.1 8
5 5 lj/cut/tip4p/cut 0.015 3.1 8
* * e3b preset 2015
extract: ! ""
natoms: 29
init_vdwl: 584.671488129934
init_coul: -128.977932168035
init_stress: ! |2-
1.4231803769197056e+03 1.6927616344571190e+03 3.8078398830142301e+03 -1.0764791807445065e+03 -2.0803020422504056e+02 7.2362454225684814e+02
init_forces: ! |2
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2 9.0831848103278351e-02 -3.3313499027414042e+00 -1.2979093715118299e+00
3 -1.4545924445052987e+02 -3.8860032656119461e+02 -1.3922527196173618e+02
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6 -8.3005250913688155e+02 9.6027287048535652e+02 1.1479388267952975e+03
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8 2.2225177792226708e+02 -1.9967109198380381e+01 7.5267413514547968e+02
9 1.6389055151637297e+00 -5.6390633543953870e+00 1.5311382036446766e+00
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29 -3.8831706532739356e+00 -5.2900046950811053e+00 -1.5026494435836046e+00
run_vdwl: 102.202850692313
run_coul: -113.74103929774
run_stress: ! |2-
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run_forces: ! |2
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20 -3.2615898343840461e+00 -5.6090812774873386e+00 4.2429891063539174e+00
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28 8.9221127912602523e+00 -2.5727955175008117e+00 4.4191999926606860e+00
29 -3.6328666974943009e+00 -5.3344846333902503e+00 -1.6032273961495329e+00
...

View File

@ -0,0 +1,99 @@
---
lammps_version: 21 Jul 2020
date_generated: Tue Aug 11 08:37:39 202
epsilon: 5e-14
prerequisites: ! |
atom full
pair lj/expand/coul/long
kspace ewald
pre_commands: ! ""
post_commands: ! |
pair_modify mix arithmetic
pair_modify table 0
kspace_style ewald 1.0e-6
kspace_modify gewald 0.3
kspace_modify compute no
input_file: in.fourmol
pair_style: lj/expand/coul/long 8.0
pair_coeff: ! |
1 1 0.02 2.0 0.2
2 2 0.005 0.9 0.05
2 4 0.005 0.5 0.0
3 3 0.02 3.0 0.1
4 4 0.015 2.8 0.2
5 5 0.015 3.0 0.1
extract: ! |
epsilon 2
sigma 2
delta 2
cut_coul 0
natoms: 29
init_vdwl: 869.656344368552
init_coul: 225.821815126925
init_stress: ! |2-
2.5921580595929599e+03 2.4223089648929408e+03 6.9507399765892142e+03 -7.6459626076358222e+02 -1.7918244275053834e+02 1.1183600453689403e+03
init_forces: ! |2
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5 -1.8403216196557828e+00 -1.4631790175600645e+00 6.0818528534738743e+00
6 -9.2216725524164417e+02 1.2287745546964902e+03 2.2653003222879815e+03
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8 1.6813921559524184e+02 -1.4215967591199117e+02 3.8455917372053079e+02
9 9.1633373141575092e+01 9.1135118977716260e+01 3.9972970456422297e+02
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29 1.9071054496393484e+02 2.1815083728566805e+02 4.6871040843718049e+01
run_vdwl: 106.16792769211
run_coul: 232.783864793706
run_stress: ! |2-
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run_forces: ! |2
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3 -2.9508462511221728e+02 1.5540065134595568e+02 1.0032166848378883e+02
4 -4.6990135745775357e+00 1.7664562746630565e+00 -3.4155588447655587e+00
5 -1.6647491427755032e+00 -7.1384505520861741e-01 5.6231908788594200e+00
6 1.9229113379974908e+02 -1.6879183079864617e+02 -1.5821197940587550e+02
7 1.3268776214088212e+00 -3.0212070504821389e+00 -1.3945917603050320e+01
8 -3.0767948041849035e+01 3.3774723064931294e+01 4.1455210291132609e+01
9 1.0981624610986977e+01 3.5815171517217190e+00 4.2835213459206827e+01
10 7.0651343131573768e+01 -7.5364530217274577e+01 -6.2700552936028060e+01
11 -4.6552674358648485e+00 -3.3640968147579642e+00 -1.0071392966729430e+01
12 9.6965594010440821e+00 4.5621471489456713e+00 -2.1188025874175360e+00
13 3.5106358717622150e+00 -1.2472767160147971e+00 -3.8580287143749975e-01
14 -2.8511582585326667e+00 6.3130353605272560e-01 -3.6224095602913993e+00
15 -2.5947961667870077e-02 3.6550638292073843e+00 4.1732465355119469e-01
16 3.1351531521993351e+01 -4.3039259230988741e+01 1.7506976000755010e+01
17 -9.2563379856300898e+00 1.1242483524947740e+01 1.2152716943210445e+01
18 -5.9670106666608946e-01 4.9523970836146356e+00 -6.4763569969688159e+00
19 2.3605537941351202e+00 -1.0192980643878549e+00 5.4296196146473630e+00
20 -2.7295307430735738e+00 -3.9126961062803156e+00 3.4455294221899790e+00
21 -6.6351053993518860e+00 -5.6936051291677838e+00 2.5340192737673494e+01
22 -1.2600719852052331e+01 -3.7030527797125199e+00 -1.9178428988156423e+01
23 1.8521698071959683e+01 1.0087220143578394e+01 -5.2549329175309047e+00
24 8.9245861393053083e+00 -2.1746250247417159e+01 1.5024118744729005e+01
25 -2.1454838578353829e+01 2.4698375849765086e+00 -1.7961262545369252e+01
26 1.1612405148647868e+01 1.8957323157416415e+01 1.9242901272291062e+00
27 8.6191024303209324e-02 -2.3639345894753781e+01 6.2652733477098339e+00
28 -1.5812874994926165e+01 6.0673559816231579e+00 -1.0405039947171305e+01
29 1.6452388975462700e+01 1.7576623833281324e+01 4.0631922647850391e+00
...

View File

@ -0,0 +1,99 @@
---
lammps_version: 21 Jul 2020
date_generated: Tue Aug 11 08:37:46 202
epsilon: 2e-13
prerequisites: ! |
atom full
pair lj/expand/coul/long
kspace ewald
pre_commands: ! ""
post_commands: ! |
pair_modify mix arithmetic
pair_modify table 16
kspace_style ewald 1.0e-6
kspace_modify gewald 0.3
kspace_modify compute no
input_file: in.fourmol
pair_style: lj/expand/coul/long 8.0
pair_coeff: ! |
1 1 0.02 2.0 0.2
2 2 0.005 0.9 0.05
2 4 0.005 0.5 0.0
3 3 0.02 3.0 0.1
4 4 0.015 2.8 0.2
5 5 0.015 3.0 0.1
extract: ! |
epsilon 2
sigma 2
delta 2
cut_coul 0
natoms: 29
init_vdwl: 869.656344368552
init_coul: 225.821851347828
init_stress: ! |2-
2.5921580798556824e+03 2.4223089706490100e+03 6.9507399900138435e+03 -7.6459625746898860e+02 -1.7918243325539206e+02 1.1183600494596001e+03
init_forces: ! |2
1 -4.7163196497192146e+01 2.2834247625360311e+02 3.4399686846972884e+02
2 1.7562443791586878e+02 1.4182973406537658e+02 -2.0831292012253465e+02
3 -1.2508615412049755e+02 -3.6798478260953948e+02 -1.3720477930247748e+02
4 -3.9145743494796221e+00 1.0488899572714241e+00 -2.9680203360986748e+00
5 -1.8403214518471285e+00 -1.4631780700724715e+00 6.0818530886023696e+00
6 -9.2216725569750508e+02 1.2287745556395873e+03 2.2653003204922916e+03
7 1.0275707715277815e+02 -5.6390694237167190e+02 -2.8553236443303790e+03
8 1.6813921486566832e+02 -1.4215967617670751e+02 3.8455917576207537e+02
9 9.1633374940159385e+01 9.1135118386813176e+01 3.9972970646304736e+02
10 5.5213457218623114e+02 -6.1976136770574067e+02 -1.8860732949551110e+02
11 -2.0653676548734623e+00 -1.9067206261734890e+00 -5.3629739888026009e+00
12 1.0622339925344464e+01 3.7670291242792402e+00 -1.8951382266525523e+00
13 3.7979474711116428e+00 -1.5435841677028326e+00 -2.4862374988427219e-01
14 -2.6935753079358653e+00 6.8698435600643282e-01 -4.3199667618308677e+00
15 2.5305888243541896e-01 3.8734446145889341e+00 4.3728358791332234e-01
16 7.2257309763088028e+02 -5.0816302227466247e+02 -1.9004596843358918e+03
17 -7.2145162977104178e+02 5.0721299303460768e+02 1.9029446585142175e+03
18 3.5593760651461531e-01 4.7720712851654818e+00 -7.8585043264622421e+00
19 1.9901790463157074e+00 -7.2114219691675963e-01 5.5216951671183532e+00
20 -2.9133073882620311e+00 -3.9873665785059766e+00 4.1253505922291556e+00
21 -1.0687319963014248e+02 -1.1890793903453265e+02 3.3030668864705302e+02
22 -1.6028118611248254e+02 -3.9850735525595468e+01 -2.4839117530412136e+02
23 2.6673946951865724e+02 1.5917281609743972e+02 -8.1412459717501179e+01
24 5.1622158847869976e+01 -3.1012002774355045e+02 1.6256339581267164e+02
25 -2.1901544635946527e+02 3.2814415857796341e+01 -1.8327904858335660e+02
26 1.6682970674933870e+02 2.7704983923248733e+02 2.0098821433126425e+01
27 7.8770042449054543e+01 -3.3142512528162013e+02 1.3455926006838362e+02
28 -2.6908794843481189e+02 1.1327040466303316e+02 -1.8145185186649925e+02
29 1.9071054758730884e+02 2.1815083779493665e+02 4.6871042349543053e+01
run_vdwl: 106.167927306934
run_coul: 232.783872560844
run_stress: ! |2-
5.4033889185122246e+02 5.4892479679809765e+02 2.8955268188032755e+02 -3.1667993134714584e+02 -5.9418514448016722e+01 1.4135196542323126e+02
run_forces: ! |2
1 1.5042191731528032e+01 7.0524187035940841e+01 5.3102809100251832e+01
2 1.6025095744488677e+01 1.0007002564822953e+01 -2.1158887488756886e+01
3 -2.9508462401688416e+02 1.5540064992154834e+02 1.0032166792537170e+02
4 -4.6990139078806985e+00 1.7664569920998929e+00 -3.4155586861921678e+00
5 -1.6647490390909379e+00 -7.1384403123709927e-01 5.6231913002355691e+00
6 1.9229113649576860e+02 -1.6879183322567181e+02 -1.5821198229106906e+02
7 1.3268779483228397e+00 -3.0212055830968931e+00 -1.3945914850434395e+01
8 -3.0767951196938704e+01 3.3774724457681103e+01 4.1455210935792906e+01
9 1.0981625491800322e+01 3.5815167138957573e+00 4.2835213672255946e+01
10 7.0651342880628548e+01 -7.5364529395568468e+01 -6.2700552629269403e+01
11 -4.6552675714512306e+00 -3.3640962703239836e+00 -1.0071392993905647e+01
12 9.6965597982755973e+00 4.5621468027776313e+00 -2.1188034676686951e+00
13 3.5106360312289651e+00 -1.2472769016775080e+00 -3.8580273777294372e-01
14 -2.8511586869301606e+00 6.3130344465834132e-01 -3.6224094710691888e+00
15 -2.5948083380200986e-02 3.6550635613088232e+00 4.1732526656150110e-01
16 3.1351530288856495e+01 -4.3039257792019207e+01 1.7506979549615181e+01
17 -9.2563361597161808e+00 1.1242483077205343e+01 1.2152712647114377e+01
18 -5.9670063451193034e-01 4.9523968092195076e+00 -6.4763579876532082e+00
19 2.3605517380981142e+00 -1.0192995004118002e+00 5.4296195197490729e+00
20 -2.7295289246110710e+00 -3.9126947888476593e+00 3.4455303030875251e+00
21 -6.6351057460657072e+00 -5.6936042652828442e+00 2.5340192741066605e+01
22 -1.2600721158161978e+01 -3.7030538274119085e+00 -1.9178429616278798e+01
23 1.8521699843022176e+01 1.0087220490406569e+01 -5.2549324889294233e+00
24 8.9245858291795237e+00 -2.1746249717816461e+01 1.5024117239152851e+01
25 -2.1454839054527017e+01 2.4698362443277517e+00 -1.7961262718374137e+01
26 1.1612406206864165e+01 1.8957323737221003e+01 1.9242912492915349e+00
27 8.6190447470516060e-02 -2.3639345383014803e+01 6.2652730906494423e+00
28 -1.5812876277619852e+01 6.0673551856385073e+00 -1.0405040442005870e+01
29 1.6452389982237243e+01 1.7576623643628043e+01 4.0631933291837985e+00
...

View File

@ -0,0 +1,96 @@
---
lammps_version: 21 Jul 2020
date_generated: Tue Aug 11 09:15:04 202
epsilon: 5e-14
prerequisites: ! |
atom full
pair morse/smooth/linear
pre_commands: ! ""
post_commands: ! ""
input_file: in.fourmol
pair_style: morse/smooth/linear 8.0
pair_coeff: ! "1 1 0.0202798941614106 2.78203488021395 2.725417159299 \n1 2 0.0101167811264648
3.9793050302425 1.90749569018897 \n1 3 0.0202934330695928 2.43948720203264 3.10711749999622
\n1 4 0.0175731334238374 2.48316585521317 3.05258880102438 \n1 5 0.0175731334238374
2.48316585521317 3.05258880102438 \n2 2 0.00503064360487288 6.98433077606902 1.08960295117864
\n2 3 0.0101296013842819 3.31380153807866 2.28919067558352 \n2 4 0.00497405122588691
14.0508902925745 0.544416409093563 \n2 5 0.00877114211614446 3.39491256196178 2.23466262511073
\n3 3 0.0203039874239943 2.17204344301477 3.48881895084762 \n3 4 0.0175825321440736
2.20660439192238 3.43428999287994 \n3 5 0.0175825321440736 2.20660439192238 3.43428999287994
\n4 4 0.0152259201379927 2.24227873774009 3.37976131582396 \n4 5 0.0152259201379927
2.24227873774009 3.37976131582396 \n5 5 0.0152259201379927 2.24227873774009 3.37976131582396
\n"
extract: ! |
d0 2
r0 2
alpha 2
natoms: 29
init_vdwl: 110.576455574558
init_coul: 0
init_stress: ! |2-
2.0965672593667708e+02 2.1015032692452459e+02 3.3202360755330801e+02 -3.7942655658588343e+01 2.3588817932865467e+01 3.0835767484464419e+01
init_forces: ! |2
1 -3.0480780002327008e+00 2.7921984122028618e+01 3.5405528010927227e+01
2 1.7192246011451811e+01 1.4143557582376275e+01 -2.0236514220183114e+01
3 -1.4198382794249000e+01 -3.5992270842783007e+01 -1.4439948386213564e+01
4 -3.5571543955166662e+00 9.2208514241020678e-01 -2.5349681982497936e+00
5 -1.1301072607183411e+00 -1.9175172427659009e+00 5.0830194514203129e+00
6 -4.9081806263588575e+01 5.2933354037517596e+01 4.4324760767644200e+01
7 -6.5864013709165958e-01 -1.4367994435644658e+01 -9.1085601115349490e+01
8 1.1150805850946377e+00 -4.4339866650423687e+00 2.5401312718266635e+01
9 7.4783930937568188e+00 8.0676720298458289e+00 3.3115612041353316e+01
10 3.3188057609406087e+01 -4.4107423530419425e+01 -1.2533250685202610e+01
11 -9.8644754274471402e-01 -2.5309184692840789e+00 -4.1172191247102985e+00
12 7.4159396774726947e+00 3.1970602905033090e+00 -3.0999793772095403e+00
13 3.7535455067051284e+00 -1.4897927833271114e+00 -6.7477453438214360e-02
14 -1.5383546569690458e+00 3.0912292765196109e-01 -3.9556251540727660e+00
15 -8.5848623703835225e-02 3.9007406258082198e+00 1.3813013508321210e+00
16 2.9105971441820422e+01 -2.3344118296546768e+01 -6.1783781738583087e+01
17 -2.4933886705568032e+01 1.6819227323062634e+01 6.9127586364919054e+01
18 -2.0463150235275587e-02 -3.1682923586303320e-02 2.7190932368002206e-02
19 2.4436300234190135e-04 2.0012946485199428e-04 1.5669609108697242e-04
20 -2.8081912468459465e-04 -2.4223792822233381e-04 -4.8875919887793612e-05
21 -7.8515953056435253e+00 -9.3116035968764841e+00 2.6685440056459196e+01
22 -1.2867736365314238e+01 -3.1182930701545755e+00 -2.0188464470088331e+01
23 2.0716179059819009e+01 1.2433662272735450e+01 -6.4932678015133840e+00
24 5.1337007408372548e+00 -2.4468533130324765e+01 1.3657847418029165e+01
25 -1.7989393885078467e+01 2.8952531925571088e+00 -1.5124698757200122e+01
26 1.2846154844554052e+01 2.1568770430924985e+01 1.4520235362983340e+00
27 4.7651727706625060e+00 -2.6604514922840195e+01 9.9133238206128400e+00
28 -2.0185283324769507e+01 8.6749457166585184e+00 -1.3657622291951469e+01
29 1.5422773525965512e+01 1.7931256323978314e+01 3.7433644846642018e+00
run_vdwl: 98.417588075604
run_coul: 0
run_stress: ! |2-
1.9601417183585471e+02 1.9700368853406772e+02 2.9154296827992243e+02 -3.7890872102168025e+01 2.2194690018415880e+01 2.9595931426759432e+01
run_forces: ! |2
1 -1.2307305201683669e+00 2.6447509305163727e+01 3.0470800924098523e+01
2 1.4299083308853650e+01 1.1826264766972807e+01 -1.6429998389881643e+01
3 -1.4157389063933350e+01 -3.1600856808471050e+01 -1.2693607969343061e+01
4 -3.3658701307181786e+00 8.8274427277102663e-01 -2.4548191756434177e+00
5 -1.0445920630425243e+00 -1.7759542240829833e+00 4.8041006652309290e+00
6 -4.3663249501195480e+01 4.6750257951934081e+01 3.2568897712249886e+01
7 -1.1941996581070721e-01 -1.2508303885030813e+01 -7.4567467003068529e+01
8 -2.8365183621696771e-01 -2.4283998406502945e+00 2.4825225007617721e+01
9 6.4234184377526304e+00 6.6360503245786022e+00 2.7951975394615243e+01
10 3.0610663078987621e+01 -4.1069619835647295e+01 -1.2566492949739969e+01
11 -9.5038761789038062e-01 -2.2898897341045954e+00 -3.7835192708263246e+00
12 7.2054253435572519e+00 3.1352360891284623e+00 -3.4732368787593755e+00
13 3.5724626043568888e+00 -1.3512903581673283e+00 -5.3544979313710710e-02
14 -1.3844723456086208e+00 2.2392513651771506e-01 -3.5288110784726916e+00
15 -1.6704585605001740e-01 3.8585136513780287e+00 1.4472031447069291e+00
16 2.5395501554353512e+01 -2.1203014586738636e+01 -5.1476843446578606e+01
17 -2.1108999005587926e+01 1.4497424828459637e+01 5.8945089304411582e+01
18 -2.0407885139876018e-02 -3.1613478806902184e-02 2.7095801901916405e-02
19 1.8505535479816727e-04 1.5148781843684435e-04 1.4466565142221593e-04
20 -2.1725919415478855e-04 -1.8964914225522977e-04 -3.4850592786958239e-05
21 -7.1560574272745390e+00 -7.8117417587142493e+00 2.3472474332002371e+01
22 -1.1620561455492469e+01 -2.9918169870657452e+00 -1.7768473787797753e+01
23 1.8773358904345674e+01 1.0807449396958578e+01 -5.7001611321217229e+00
24 5.8670774694819343e+00 -2.2854064241583384e+01 1.3389367814003592e+01
25 -1.7841968739230779e+01 2.5813803672129412e+00 -1.5089203819513493e+01
26 1.1965180636297607e+01 2.0268154831625505e+01 1.6847640847945964e+00
27 4.4982185784244653e+00 -2.3705161804550581e+01 8.3847128455906059e+00
28 -1.7971511747703875e+01 7.7287341777176994e+00 -1.1947618548178538e+01
29 1.3475957448492176e+01 1.5978120604518875e+01 3.5619815829562675e+00
...