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Merge pull request #2297 from akohlmey/more-fix-tests 

Add a few more unit tests for fixes and fix some issues related to it
This commit is contained in:
Axel Kohlmeyer 2020-08-20 20:18:09 -04:00 committed by GitHub
parent a70a5be2d8 cd7ba1d007
commit e7639d4951
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GPG Key ID: 4AEE18F83AFDEB23
53 changed files with 2582 additions and 27 deletions
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31
doc/src/fix_npt_cauchy.rst
View File

@ -13,7 +13,7 @@ Syntax
* ID, group-ID are documented in :doc:`fix <fix>` command
* style_name = *npt/cauchy*
* one or more keyword/value pairs may be appended
* keyword = *temp* or *iso* or *aniso* or *tri* or *x* or *y* or *z* or *xy* or *yz* or *xz* or *couple* or *tchain* or *pchain* or *mtk* or *tloop* or *ploop* or *nreset* or *drag* or *dilate* or *scalexy* or *scaleyz* or *scalexz* or *flip* or *fixedpoint* or *update*
* keyword = *temp* or *iso* or *aniso* or *tri* or *x* or *y* or *z* or *xy* or *yz* or *xz* or *couple* or *tchain* or *pchain* or *mtk* or *tloop* or *ploop* or *nreset* or *drag* or *dilate* or *scalexy* or *scaleyz* or *scalexz* or *flip* or *fixedpoint*
.. parsed-literal::
@ -45,9 +45,8 @@ Syntax
*scaleyz* value = *yes* or *no* = scale yz with lz
*scalexz* value = *yes* or *no* = scale xz with lz
*flip* value = *yes* or *no* = allow or disallow box flips when it becomes highly skewed
*cauchystat* cauchystat values = alpha continue
alpha = strength of Cauchy stress control parameter
continue = *yes* or *no* = whether of not to continue from a previous run
*alpha* value = strength of Cauchy stress control parameter
*continue* value = *yes* or *no* = whether of not to continue from a previous run
*fixedpoint* values = x y z
x,y,z = perform barostat dilation/contraction around this point (distance units)
@ -56,7 +55,7 @@ Examples
.. code-block:: LAMMPS
fix 1 water npt/cauchy temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0
fix 1 water npt/cauchy temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0 alpha 0.001
Description
"""""""""""
@ -573,14 +572,7 @@ can only be used if the second dimension in the keyword is periodic,
and if the tilt factor is not coupled to the barostat via keywords
*tri*\ , *yz*\ , *xz*\ , and *xy*\ .
Without the *cauchystat* keyword, the barostat algorithm
controls the Second-Piola Kirchhoff stress, which is a stress measure
referred to the unmodified (initial) simulation box. If the box
deforms substantially during the equilibration, the difference between
the set values and the final true (Cauchy) stresses can be
considerable.
The *cauchystat* keyword modifies the barostat as per Miller et
The *alpha* keyword modifies the barostat as per Miller et
al. (Miller)_"#nc-Miller" so that the Cauchy stress is controlled.
*alpha* is the non-dimensional parameter, typically set to 0.001 or
0.01 that determines how aggressively the algorithm drives the system
@ -598,13 +590,12 @@ sequence over several fixes.
Setting *alpha* to zero is not permitted. To "turn off" the
cauchystat control and thus restore the equilibrium stress
fluctuations, two subsequent fixes should be used. In the first, the
cauchystat flag is used and the simulation box equilibrates to the
correct shape for the desired stresses. In the second, the *fix*
statement is identical except that the *cauchystat* keyword is removed
(along with related *alpha* and *continue* values). This restores the
original Parrinello-Rahman algorithm, but now with the correct simulation
box shape from the first fix.
fluctuations, two subsequent fixes should be used. In the first, fix
npt/cauchy is used and the simulation box equilibrates to the
correct shape for the desired stresses. In the second,
:doc:`fix npt <fix_nh>` is used instead which uses the
original Parrinello-Rahman algorithm, but now with the corrected
simulation box shape from using fix npt/cauchy.
This fix can be used with dynamic groups as defined by the
:doc:`group <group>` command. Likewise it can be used with groups to

11
doc/src/fix_spring_chunk.rst
View File

@ -50,7 +50,16 @@ atom.
**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 locations of the initial per-chunk center of mass
coordinates 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. Since this fix depends
on an instance of :doc:`compute chunk/atom <compute_chunk_atom>`
it will check when reading the restart if the chunk still exists and
will define the same number of chunks. The restart data is only applied
when the number of chunks matches. Otherwise the center of mass
coordinates are recomputed.
The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
fix to add the energy stored in all the springs to the system's potential

17
doc/src/fix_spring_rg.rst
View File

@ -59,9 +59,20 @@ the time the fix is specified, and that value is used as the target.
**Restart, fix_modify, output, run start/stop, minimize info:**
No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various :doc:`output commands <Howto_output>`.
This fix writes the currently used reference RG (:math:`R_{G0}`) 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.
None of the :doc:`fix_modify <fix_modify>` options
are relevant to this fix.
This fix computes a global scalar which can be accessed by various
:doc:`output commands <Howto_output>`. The scalar is the reference
radius of gyration :math:`R_{G0}` used by the fix. energy change due to
this fix. The scalar value calculated by this fix is "intensive".
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.

9
doc/src/fix_temp_rescale.rst
View File

@ -126,7 +126,11 @@ 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>`
@ -136,7 +140,8 @@ this fix and by the compute should be the same.
The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
fix to add the energy change implied by a velocity rescaling to the
system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
system's potential energy as part of :doc:`thermodynamic output
<thermo_style>`.
This fix computes a global scalar which can be accessed by various
:doc:`output commands <Howto_output>`. The scalar is the cumulative

2
src/RIGID/fix_rigid_nh.h
View File

@ -64,7 +64,7 @@ class FixRigidNH : public FixRigid {
double mtk_term1,mtk_term2; // Martyna-Tobias-Klein corrections
double t_current,t_target;
double t_current;
double p_current[3],p_target[3];
char *id_temp,*id_press;

54
src/fix_spring_chunk.cpp
View File

@ -15,6 +15,7 @@
#include <cmath>
#include <cstring>
#include "atom.h"
#include "comm.h"
#include "update.h"
#include "force.h"
#include "respa.h"
@ -37,6 +38,7 @@ FixSpringChunk::FixSpringChunk(LAMMPS *lmp, int narg, char **arg) :
{
if (narg != 6) error->all(FLERR,"Illegal fix spring/chunk command");
restart_global = 1;
scalar_flag = 1;
global_freq = 1;
extscalar = 1;
@ -241,6 +243,58 @@ void FixSpringChunk::min_post_force(int vflag)
post_force(vflag);
}
/* ----------------------------------------------------------------------
writ number of chunks and position of original COM into restart
------------------------------------------------------------------------- */
void FixSpringChunk::write_restart(FILE *fp)
{
double n = nchunk;
if (comm->me == 0) {
int size = (3*n+1) * sizeof(double);
fwrite(&size,sizeof(int),1,fp);
fwrite(&n,sizeof(double),1,fp);
fwrite(&com0[0][0],3*sizeof(double),nchunk,fp);
}
}
/* ----------------------------------------------------------------------
use state info from restart file to restart the Fix
------------------------------------------------------------------------- */
void FixSpringChunk::restart(char *buf)
{
double *list = (double *) buf;
int n = list[0];
memory->destroy(com0);
memory->destroy(fcom);
int icompute = modify->find_compute(idchunk);
if (icompute < 0)
error->all(FLERR,"Chunk/atom compute does not exist for fix spring/chunk");
cchunk = (ComputeChunkAtom *) modify->compute[icompute];
if (strcmp(cchunk->style,"chunk/atom") != 0)
error->all(FLERR,"Fix spring/chunk does not use chunk/atom compute");
nchunk = cchunk->setup_chunks();
cchunk->compute_ichunk();
memory->create(com0,nchunk,3,"spring/chunk:com0");
memory->create(fcom,nchunk,3,"spring/chunk:fcom");
printf("restart chunks:%d computed chunks: %d\n",n,nchunk);
if (n != nchunk) {
if (comm->me == 0)
error->warning(FLERR,"Number of chunks has changed. Cannot use restart");
memory->destroy(com0);
memory->destroy(fcom);
nchunk = 1;
} else {
cchunk->lock(this,update->ntimestep,-1);
memcpy(&com0[0][0],list+1,3*n*sizeof(double));
}
}
/* ----------------------------------------------------------------------
energy of stretched spring
------------------------------------------------------------------------- */

2
src/fix_spring_chunk.h
View File

@ -35,6 +35,8 @@ class FixSpringChunk : public Fix {
void post_force(int);
void post_force_respa(int, int, int);
void min_post_force(int);
void write_restart(FILE *);
void restart(char *);
double compute_scalar();
private:

44
src/fix_spring_rg.cpp
View File

@ -19,6 +19,7 @@
#include "fix_spring_rg.h"
#include <cstring>
#include "atom.h"
#include "comm.h"
#include "update.h"
#include "group.h"
#include "respa.h"
@ -41,6 +42,9 @@ FixSpringRG::FixSpringRG(LAMMPS *lmp, int narg, char **arg) :
if (strcmp(arg[4],"NULL") == 0) rg0_flag = 1;
else rg0 = force->numeric(FLERR,arg[4]);
restart_global = 1;
scalar_flag = 1;
restart_global = 1;
dynamic_group_allow = 1;
respa_level_support = 1;
ilevel_respa = 0;
@ -144,3 +148,43 @@ void FixSpringRG::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == ilevel_respa) post_force(vflag);
}
/* ----------------------------------------------------------------------
pack entire state of Fix into one write
------------------------------------------------------------------------- */
void FixSpringRG::write_restart(FILE *fp)
{
int n = 0;
double list[1];
list[n++] = rg0;
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 FixSpringRG::restart(char *buf)
{
int n = 0;
double *list = (double *) buf;
rg0 = list[n++];
rg0_flag = 0;
}
/* ----------------------------------------------------------------------
return reference radius of gyration
------------------------------------------------------------------------- */
double FixSpringRG::compute_scalar()
{
return rg0;
}

3
src/fix_spring_rg.h
View File

@ -32,6 +32,9 @@ class FixSpringRG : public Fix {
void setup(int);
void post_force(int);
void post_force_respa(int, int, int);
void write_restart(FILE *);
void restart(char *);
double compute_scalar();
private:
int ilevel_respa,rg0_flag;

30
src/fix_temp_rescale.cpp
View File

@ -44,6 +44,7 @@ FixTempRescale::FixTempRescale(LAMMPS *lmp, int narg, char **arg) :
nevery = force->inumeric(FLERR,arg[3]);
if (nevery <= 0) error->all(FLERR,"Illegal fix temp/rescale command");
restart_global = 1;
scalar_flag = 1;
global_freq = nevery;
extscalar = 1;
@ -238,6 +239,35 @@ double FixTempRescale::compute_scalar()
return energy;
}
/* ----------------------------------------------------------------------
pack entire state of Fix into one write
------------------------------------------------------------------------- */
void FixTempRescale::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 FixTempRescale::restart(char *buf)
{
int n = 0;
double *list = (double *) buf;
energy = list[n++];
}
/* ----------------------------------------------------------------------
extract thermostat properties
------------------------------------------------------------------------- */

2
src/fix_temp_rescale.h
View File

@ -34,6 +34,8 @@ class FixTempRescale : 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 &);
protected:

0
unittest/force-styles/tests/fix-timestep-addforce-const.yaml → unittest/force-styles/tests/fix-timestep-addforce_const.yaml
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0
unittest/force-styles/tests/fix-timestep-addforce-variable.yaml → unittest/force-styles/tests/fix-timestep-addforce_variable.yaml
View File

0
unittest/force-styles/tests/fix-timestep-aveforce-const.yaml → unittest/force-styles/tests/fix-timestep-aveforce_const.yaml
View File

0
unittest/force-styles/tests/fix-timestep-aveforce-variable.yaml → unittest/force-styles/tests/fix-timestep-aveforce_variable.yaml
View File

76
unittest/force-styles/tests/fix-timestep-drag.yaml Normal file
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@ -0,0 +1,76 @@
---
lammps_version: 21 Jul 2020
date_generated: Thu Aug 20 10:19:50 202
epsilon: 1e-14
prerequisites: ! |
atom full
fix drag
pre_commands: ! ""
post_commands: ! |
fix move all nve
fix test solute drag 2.4 -1.0 -1.0 10.0 0.6
input_file: in.fourmol
natoms: 29
global_vector: ! |-
3 49.37386569186292 -47.91054585938017 2.7675838589028423
run_pos: ! |2
1 -2.7009921016892235e-01 2.4907528197219242e+00 -1.6706714742004872e-01
2 3.1102754907763769e-01 2.9594027135767238e+00 -8.5473698877862359e-01
3 -7.0341245968566879e-01 1.2301368186713786e+00 -6.2784532277539096e-01
4 -1.5800754141862727e+00 1.4826400216615525e+00 -1.2537661019410140e+00
5 -9.0551985520028100e-01 9.2552850343442328e-01 3.9883606607154776e-01
6 2.4889979318182220e-01 2.8279798387704186e-01 -1.2313288119237860e+00
7 3.4183130472378914e-01 -2.2840316788830771e-02 -2.5289657703463995e+00
8 1.1748766924664271e+00 -4.8884547615224400e-01 -6.3798037333935742e-01
9 1.3812557384528446e+00 -2.5359438142640300e-01 2.8212931861687268e-01
10 2.0511008425571324e+00 -1.4604295217499343e+00 -9.8323768143111301e-01
11 1.7886612283034122e+00 -1.9907964477021713e+00 -1.8878280028824912e+00
12 3.0058773477814476e+00 -4.9049281496219399e-01 -1.6227540908579672e+00
13 4.0496284046487334e+00 -8.9214812510857799e-01 -1.6392496185507874e+00
14 2.6064486577696244e+00 -4.1858286397784850e-01 -2.6614777350069176e+00
15 2.9688187183894881e+00 5.5231783710810345e-01 -1.2338930341849850e+00
16 2.6746089785699212e+00 -2.4118620888291584e+00 -2.3855010361450477e-02
17 2.2153906337644615e+00 -2.0895596496269095e+00 1.1958621828113769e+00
18 2.1369701704069621e+00 3.0158507413473430e+00 -3.5179348336963914e+00
19 1.5355837136075170e+00 2.6255292355385769e+00 -4.2353987779863020e+00
20 2.7727573005671085e+00 3.6923910449616164e+00 -3.9330842459130770e+00
21 4.9040128073079865e+00 -4.0752348172925501e+00 -3.6210314709803710e+00
22 4.3582355554437813e+00 -4.2126119427287394e+00 -4.4612844196310357e+00
23 5.7439382849306133e+00 -3.5821957939284732e+00 -3.8766361295936838e+00
24 2.0689243582545647e+00 3.1513346907116913e+00 3.1550389754738388e+00
25 1.3045351331613000e+00 3.2665125705751850e+00 2.5111855257457640e+00
26 2.5809237402717207e+00 4.0117602605475788e+00 3.2212060529089568e+00
27 -1.9611343130483321e+00 -4.3563411931417928e+00 2.1098293115519544e+00
28 -2.7473562684516057e+00 -4.0200819932381568e+00 1.5830052163434070e+00
29 -1.3126000191368539e+00 -3.5962518039489728e+00 2.2746342468742613e+00
run_vel: ! |2
1 8.5245692419034496e-03 1.6054359615288082e-02 4.6835706342010699e-03
2 6.4469181534162982e-03 3.3572509925720315e-03 -1.5167252018059632e-03
3 -7.6446099104923171e-03 -1.3347273672018593e-02 -4.1697832271252889e-03
4 -2.0567476876389777e-03 -7.6669151224523120e-03 -1.0198053461907023e-03
5 -9.3569552193218820e-03 -1.0882851843050193e-02 -3.5334700439280074e-03
6 -3.9106465978160643e-02 4.6496857496481636e-02 3.7247257153434250e-02
7 1.3059086080740997e-03 -1.0323892210522569e-02 -5.1314637706566767e-02
8 8.4142216534211708e-03 -3.5565684772021233e-03 3.4400630540566565e-02
9 2.7821506314630175e-03 2.9127766895719028e-03 1.3711312410369396e-02
10 2.9245154884128457e-02 -2.9289778535465768e-02 -1.5017110420116284e-02
11 -3.9376008935933897e-03 -2.3830258447108204e-03 -1.1504378141809892e-03
12 1.8415493135460349e-03 -7.1221479538782968e-04 -2.6222068799362790e-03
13 8.7397591637950823e-04 5.6786568476995458e-03 -4.6959188559560803e-05
14 3.2686129061490826e-03 -6.4777672751304824e-03 -2.0572626109492988e-03
15 -2.5621680789948958e-03 -7.7318113961355357e-03 6.6113139508743373e-03
16 1.8591880620408622e-02 -1.2716970618980200e-02 -4.6060427771778933e-02
17 -1.2865567938515562e-02 9.9920280977181166e-03 3.6850337974210626e-02
18 -8.0065795856943756e-04 -8.6270476392988284e-04 -1.4483040184797788e-03
19 1.2452390810585108e-03 -2.5061097098477390e-03 7.2998631044990988e-03
20 3.5930060212105096e-03 3.6938860319506088e-03 3.2322732695887410e-03
21 -1.4689220629138253e-03 -2.7352129045937475e-04 7.0581626051508884e-04
22 -7.0694199261113391e-03 -4.2577148925603400e-03 2.8079117696165005e-04
23 6.0446963112475265e-03 -1.4000131635613822e-03 2.5819754846041587e-03
24 3.1926370424225161e-04 -9.9445667906353295e-04 1.4999995101417848e-04
25 1.3789756975914627e-04 -4.4335895072924450e-03 -8.1808136260541489e-04
26 2.0485904046666191e-03 2.7813358617992980e-03 4.3245727148598393e-03
27 4.5604117722843052e-04 -1.0305523146029992e-03 2.1188058296474420e-04
28 -6.2544520868644485e-03 1.4127711171995772e-03 -1.8429821885457452e-03
29 6.4110631343027393e-04 3.1273432703629624e-03 3.7253671115222839e-03
...

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

@ -0,0 +1,77 @@
---
lammps_version: 21 Jul 2020
date_generated: Thu Aug 20 10:58:24 202
epsilon: 2e-13
prerequisites: ! |
atom full
fix efield
pre_commands: ! ""
post_commands: ! |
fix move all nve
fix test solute efield 0.0 -0.1 0.1
input_file: in.fourmol
natoms: 29
global_scalar: -0.0309186331146529
global_vector: ! |-
3 0.0 -2.220446049250313e-16 2.220446049250313e-16
run_pos: ! |2
1 -2.7045797446143222e-01 2.4912780824342802e+00 -1.6702148063946790e-01
2 3.1004707684044314e-01 2.9610914097014920e+00 -8.5452223796947857e-01
3 -7.0398484421621654e-01 1.2305550653443955e+00 -6.2777724227837073e-01
4 -1.5818164098199170e+00 1.4836974500211317e+00 -1.2538283730077453e+00
5 -9.0719712315200163e-01 9.2647873125900360e-01 3.9958448834208099e-01
6 2.4830742687969690e-01 2.8305198679565441e-01 -1.2313591589315209e+00
7 3.4143491049380226e-01 -2.2582293531425542e-02 -2.5292818547848865e+00
8 1.1743661795764639e+00 -4.8857450097191185e-01 -6.3789242029446702e-01
9 1.3800498496144755e+00 -2.5289843545236201e-01 2.8368125556402707e-01
10 2.0510752375373285e+00 -1.4604162356321775e+00 -9.8322531981896188e-01
11 1.7878031719933214e+00 -1.9922296675363795e+00 -1.8890171495010866e+00
12 3.0063007792511223e+00 -4.9009151024452913e-01 -1.6232320206418513e+00
13 4.0515398657564985e+00 -8.9206282760570232e-01 -1.6399577186750036e+00
14 2.6066960676892901e+00 -4.1793489312186022e-01 -2.6633588373115313e+00
15 2.9695286672861796e+00 5.5418409834628024e-01 -1.2341593925963330e+00
16 2.6747058904109253e+00 -2.4124963123525687e+00 -2.3362361147189377e-02
17 2.2153553155630221e+00 -2.0897346921363296e+00 1.1962597568420426e+00
18 2.1369701704188535e+00 3.0158507413726054e+00 -3.5179348337219212e+00
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...

78
unittest/force-styles/tests/fix-timestep-efield_region.yaml Normal file
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@ -0,0 +1,78 @@
---
lammps_version: 21 Jul 2020
date_generated: Thu Aug 20 10:58:24 202
epsilon: 2e-13
prerequisites: ! |
atom full
fix efield
pre_commands: ! ""
post_commands: ! |
region half block 0 EDGE EDGE EDGE EDGE EDGE
fix move all nve
fix test solute efield 0.1 0.1 0.1 region half
input_file: in.fourmol
natoms: 29
global_scalar: -2.82714020161747
global_vector: ! |-
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run_pos: ! |2
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...

82
unittest/force-styles/tests/fix-timestep-efield_variable.yaml Normal file
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@ -0,0 +1,82 @@
---
lammps_version: 21 Jul 2020
date_generated: Thu Aug 20 10:58:24 202
epsilon: 2e-13
prerequisites: ! |
atom full
fix efield
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 efield v_xforce 0.0 v_zforce
input_file: in.fourmol
natoms: 29
global_scalar: 0
global_vector: ! |-
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run_pos: ! |2
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...

75
unittest/force-styles/tests/fix-timestep-heat.yaml Normal file
View File

@ -0,0 +1,75 @@
---
lammps_version: 21 Jul 2020
date_generated: Thu Aug 20 11:33:32 202
epsilon: 1e-14
prerequisites: ! |
atom full
fix heat
pre_commands: ! ""
post_commands: ! |
fix move all nve
fix test solute heat 1 1.0
input_file: in.fourmol
natoms: 29
global_scalar: 1.00047909696244
run_pos: ! |2
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...

76
unittest/force-styles/tests/fix-timestep-heat_region.yaml Normal file
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@ -0,0 +1,76 @@
---
lammps_version: 21 Jul 2020
date_generated: Thu Aug 20 11:33:32 202
epsilon: 2e-13
prerequisites: ! |
atom full
fix heat
pre_commands: ! ""
post_commands: ! |
region half block 0 EDGE EDGE EDGE EDGE EDGE
fix move all nve
fix test solute heat 1 1.0 region half
input_file: in.fourmol
natoms: 29
global_scalar: 1.00050043255327
run_pos: ! |2
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...

75
unittest/force-styles/tests/fix-timestep-oneway.yaml Normal file
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@ -0,0 +1,75 @@
---
lammps_version: 21 Jul 2020
date_generated: Thu Aug 20 11:37:30 202
epsilon: 2e-14
prerequisites: ! |
atom full
fix oneway
pre_commands: ! ""
post_commands: ! |
region half block 0 EDGE EDGE EDGE EDGE EDGE
fix move all nve
fix test solute oneway 2 half -y
input_file: in.fourmol
natoms: 29
run_pos: ! |2
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...

0
unittest/force-styles/tests/fix-timestep-rigid-group.yaml → unittest/force-styles/tests/fix-timestep-rigid_group.yaml
View File

0
unittest/force-styles/tests/fix-timestep-rigid-molecule.yaml → unittest/force-styles/tests/fix-timestep-rigid_molecule.yaml
View File

79
unittest/force-styles/tests/fix-timestep-rigid_molecule_tri.yaml Normal file
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@ -0,0 +1,79 @@
---
lammps_version: 21 Jul 2020
date_generated: Thu Aug 20 09:36:31 202
epsilon: 5e-12
prerequisites: ! |
atom full
fix rigid
pre_commands: ! ""
post_commands: ! |
change_box all triclinic
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: 18.3405601674143
run_pos: ! |2
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...

78
unittest/force-styles/tests/fix-timestep-rigid_nph.yaml Normal file
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@ -0,0 +1,78 @@
---
lammps_version: 21 Jul 2020
date_generated: Thu Aug 20 10:02:05 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
fix rigid/nph
pre_commands: ! ""
post_commands: ! |
variable t_target delete
fix test solvent rigid/nph molecule iso 1.0 1.0 100.0
fix_modify test virial yes
input_file: in.fourmol
natoms: 29
run_stress: ! |2-
4.3578059170174832e+01 1.7275105168494740e+01 6.7372361278298868e+01 5.1985075051780690e+01 -2.0990677390560389e+01 -7.5321398094463152e+00
global_scalar: 29.0236364415722
run_pos: ! |2
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...

78
unittest/force-styles/tests/fix-timestep-rigid_nph_small.yaml Normal file
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@ -0,0 +1,78 @@
---
lammps_version: 21 Jul 2020
date_generated: Thu Aug 20 10:08:29 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
fix rigid/nph/small
pre_commands: ! ""
post_commands: ! |
variable t_target delete
fix test solvent rigid/nph/small molecule aniso 1.0 1.0 100.0
fix_modify test virial yes
input_file: in.fourmol
natoms: 29
run_stress: ! |2-
2.7340318969496678e+01 4.7963870140135469e+00 6.8884396850629400e+01 2.9853310008504316e+01 -1.0857139901179401e+01 -5.1889756547613537e+00
global_scalar: 9.77678786322453
run_pos: ! |2
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29 -1.6779316575994772e+00 -4.0348635219032660e+00 3.1144975929061580e+00
run_vel: ! |2
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29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03
...

77
unittest/force-styles/tests/fix-timestep-rigid_npt.yaml Normal file
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@ -0,0 +1,77 @@
---
lammps_version: 21 Jul 2020
date_generated: Thu Aug 20 09:48:20 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
fix rigid/npt
pre_commands: ! ""
post_commands: ! |
fix test all rigid/npt group 2 solute solvent aniso 1.0 1.0 100.0 temp 50.0 ${t_target} 1.0
fix_modify test virial yes
input_file: in.fourmol
natoms: 29
run_stress: ! |-
-1.6326314448657713e+03 -1.4727331978534244e+03 -3.8557370515929333e+03 5.5052891601613476e+02 4.7346742977275369e+02 -6.2035591882215908e+02
global_scalar: 106.866830724743
run_pos: ! |2
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run_vel: ! |2
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...

77
unittest/force-styles/tests/fix-timestep-rigid_npt_small.yaml Normal file
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@ -0,0 +1,77 @@
---
lammps_version: 21 Jul 2020
date_generated: Thu Aug 20 10:08:15 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
fix rigid/npt/small
pre_commands: ! ""
post_commands: ! |
fix test solvent rigid/npt/small molecule iso 1.0 1.0 100.0 temp 50.0 ${t_target} 1.0
fix_modify test virial yes
input_file: in.fourmol
natoms: 29
run_stress: ! |-
-8.7531774792845880e+01 5.5811525713967427e+00 -5.5468297751741936e+01 -1.5316306340330462e+02 1.4641268099032845e+02 1.7263710124990443e+01
global_scalar: 77.7898343033466
run_pos: ! |2
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...

78
unittest/force-styles/tests/fix-timestep-rigid_nve_group.yaml Normal file
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@ -0,0 +1,78 @@
---
lammps_version: 21 Jul 2020
date_generated: Thu Aug 20 09:29:53 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
fix rigid/nve
pre_commands: ! ""
post_commands: ! |
variable t_target delete
fix test all rigid/nve group 2 solute solvent
fix_modify test virial yes
input_file: in.fourmol
natoms: 29
run_stress: ! |-
-1.4245356938010630e+03 -1.4496493316651863e+03 -3.6144360982531375e+03 8.4840626794791422e+02 2.0318336802435149e+02 -6.0622397695991776e+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_nve_molecule.yaml Normal file
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@ -0,0 +1,78 @@
---
lammps_version: 21 Jul 2020
date_generated: Thu Aug 20 09:29:53 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
fix rigid/nve
pre_commands: ! ""
post_commands: ! |
variable t_target delete
fix test solvent rigid/nve molecule
fix_modify test virial yes
input_file: in.fourmol
natoms: 29
run_stress: ! |-
-4.9200114783104425e+01 -2.6907707681632978e+01 -6.0080872466970643e+00 -2.5620425754068116e+01 -1.3450222537284642e+01 -1.4947348675137455e+00
global_scalar: 18.3405601681427
run_pos: ! |2
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...

78
unittest/force-styles/tests/fix-timestep-rigid_nve_single.yaml Normal file
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@ -0,0 +1,78 @@
---
lammps_version: 21 Jul 2020
date_generated: Thu Aug 20 09:29:53 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
fix rigid/nve
pre_commands: ! ""
post_commands: ! |
variable t_target delete
fix test solute rigid/nve single
fix_modify test virial yes
input_file: in.fourmol
natoms: 29
run_stress: ! |-
-1.3754817467882001e+03 -1.4228425246443051e+03 -3.6087196200592211e+03 8.7407043142561224e+02 2.1665316510417915e+02 -6.0480791467760923e+02
global_scalar: 4.53142303857025
run_pos: ! |2
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...

78
unittest/force-styles/tests/fix-timestep-rigid_nve_small.yaml Normal file
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@ -0,0 +1,78 @@
---
lammps_version: 21 Jul 2020
date_generated: Thu Aug 20 09:37:07 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
fix rigid/nve/small
pre_commands: ! ""
post_commands: ! |
variable t_target delete
fix test solvent rigid/nve/small molecule
fix_modify test virial yes
input_file: in.fourmol
natoms: 29
run_stress: ! |-
-4.9200114783104425e+01 -2.6907707681632978e+01 -6.0080872466970643e+00 -2.5620425754068116e+01 -1.3450222537284642e+01 -1.4947348675137455e+00
global_scalar: 0.500731871980239
run_pos: ! |2
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...

77
unittest/force-styles/tests/fix-timestep-rigid_nvt.yaml Normal file
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@ -0,0 +1,77 @@
---
lammps_version: 21 Jul 2020
date_generated: Thu Aug 20 09:48:20 202
epsilon: 5e-13
prerequisites: ! |
atom full
fix rigid/nvt
pre_commands: ! ""
post_commands: ! |
fix test solute rigid/nvt single temp 50.0 ${t_target} 1.0
fix_modify test virial yes
input_file: in.fourmol
natoms: 29
run_stress: ! |-
-1.3123962047751329e+03 -1.3675423591737690e+03 -3.5468492999580276e+03 7.8271738572462300e+02 2.6480486115425720e+02 -7.6950536863901277e+02
global_scalar: 68.0865964742217
run_pos: ! |2
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...

77
unittest/force-styles/tests/fix-timestep-rigid_nvt_small.yaml Normal file
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@ -0,0 +1,77 @@
---
lammps_version: 21 Jul 2020
date_generated: Thu Aug 20 10:08:25 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
fix rigid/nvt/small
pre_commands: ! ""
post_commands: ! |
fix test solvent rigid/nvt/small molecule temp 50.0 ${t_target} 1.0
fix_modify test virial yes
input_file: in.fourmol
natoms: 29
run_stress: ! |-
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global_scalar: 0.953260955609303
run_pos: ! |2
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...

0
unittest/force-styles/tests/fix-timestep-rigid-single.yaml → unittest/force-styles/tests/fix-timestep-rigid_single.yaml
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78
unittest/force-styles/tests/fix-timestep-rigid_small.yaml Normal file
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@ -0,0 +1,78 @@
---
lammps_version: 21 Jul 2020
date_generated: Thu Aug 20 09:37:07 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
fix rigid/small
pre_commands: ! ""
post_commands: ! |
variable t_target delete
fix test solvent rigid/small 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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...

0
unittest/force-styles/tests/fix-timestep-setforce-const.yaml → unittest/force-styles/tests/fix-timestep-setforce_const.yaml
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0
unittest/force-styles/tests/fix-timestep-setforce-region.yaml → unittest/force-styles/tests/fix-timestep-setforce_region.yaml
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0
unittest/force-styles/tests/fix-timestep-setforce-variable.yaml → unittest/force-styles/tests/fix-timestep-setforce_variable.yaml
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76
unittest/force-styles/tests/fix-timestep-smd_couple.yaml Normal file
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@ -0,0 +1,76 @@
---
lammps_version: 21 Jul 2020
date_generated: Thu Aug 20 15:09:24 202
epsilon: 2e-14
prerequisites: ! |
atom full
fix smd
pre_commands: ! ""
post_commands: ! |
fix move all nve
fix test solute smd cvel 10.0 0.1 couple solvent 10.0 1.0 1.0 1.0 2.0
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-smd_tether.yaml Normal file
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@ -0,0 +1,76 @@
---
lammps_version: 21 Jul 2020
date_generated: Thu Aug 20 15:09:24 202
epsilon: 2e-14
prerequisites: ! |
atom full
fix smd
pre_commands: ! ""
post_commands: ! |
fix move all nve
fix test solute smd cfor 5.0 tether 2.0 -1.0 -1.0 0.1
input_file: in.fourmol
natoms: 29
global_vector: ! |-
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...

77
unittest/force-styles/tests/fix-timestep-spring_chunk.yaml Normal file
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@ -0,0 +1,77 @@
---
lammps_version: 21 Jul 2020
date_generated: Thu Aug 20 14:12:59 202
epsilon: 2e-14
prerequisites: ! |
atom full
fix spring/chunk
pre_commands: ! ""
post_commands: ! |
compute mol all chunk/atom molecule
compute com all com/chunk mol
fix move all nve
fix test solute spring/chunk 10.0 mol com
input_file: in.fourmol
natoms: 29
global_scalar: 0.00150643062337391
run_pos: ! |2
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...

77
unittest/force-styles/tests/fix-timestep-spring_couple.yaml Normal file
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@ -0,0 +1,77 @@
---
lammps_version: 21 Jul 2020
date_generated: Thu Aug 20 12:11:24 202
epsilon: 2e-14
prerequisites: ! |
atom full
fix spring
pre_commands: ! ""
post_commands: ! |
fix move all nve
fix test solute spring couple solvent 10.0 1.0 1.0 1.0 2.0
input_file: in.fourmol
natoms: 29
global_scalar: 0.0745600021880662
global_vector: ! |-
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run_pos: ! |2
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...

75
unittest/force-styles/tests/fix-timestep-spring_rg.yaml Normal file
View File

@ -0,0 +1,75 @@
---
lammps_version: 21 Jul 2020
date_generated: Thu Aug 20 15:28:29 202
epsilon: 2e-14
prerequisites: ! |
atom full
fix spring/rg
pre_commands: ! ""
post_commands: ! |
fix move all nve
fix test solute spring/rg 10.0 NULL
input_file: in.fourmol
natoms: 29
global_scalar: 2.28284405113276
run_pos: ! |2
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...

75
unittest/force-styles/tests/fix-timestep-spring_self.yaml Normal file
View File

@ -0,0 +1,75 @@
---
lammps_version: 21 Jul 2020
date_generated: Thu Aug 20 13:49:05 202
epsilon: 2e-14
prerequisites: ! |
atom full
fix spring/self
pre_commands: ! ""
post_commands: ! |
fix move all nve
fix test solute spring/self 10.0 xyz
input_file: in.fourmol
natoms: 29
global_scalar: 0.126237053707504
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...

77
unittest/force-styles/tests/fix-timestep-spring_tether.yaml Normal file
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@ -0,0 +1,77 @@
---
lammps_version: 21 Jul 2020
date_generated: Thu Aug 20 12:11:25 202
epsilon: 2e-14
prerequisites: ! |
atom full
fix spring
pre_commands: ! ""
post_commands: ! |
fix move all nve
fix test solute spring tether 10.0 2.4 -1.0 -1.0 0.1
input_file: in.fourmol
natoms: 29
global_scalar: 9.11717430556703
global_vector: ! |-
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...

75
unittest/force-styles/tests/fix-timestep-temp_rescale.yaml Normal file
View File

@ -0,0 +1,75 @@
---
lammps_version: 21 Jul 2020
date_generated: Thu Aug 20 12:17:59 202
epsilon: 1e-14
prerequisites: ! |
atom full
fix temp/rescale
pre_commands: ! ""
post_commands: ! |
fix all solute nve
fix test solute temp/rescale 1 50.0 ${t_target} 20.0 1.0
input_file: in.fourmol
natoms: 29
global_scalar: 111.985962801373
run_pos: ! |2
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...

0
unittest/force-styles/tests/fix-timestep-wall-harmonic_const.yaml → unittest/force-styles/tests/fix-timestep-wall_harmonic_const.yaml
View File

81
unittest/force-styles/tests/fix-timestep-wall_lj1043_const.yaml Normal file
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@ -0,0 +1,81 @@
---
lammps_version: 21 Jul 2020
date_generated: Thu Aug 20 15:39:07 202
epsilon: 1e-14
prerequisites: ! |
atom full
fix wall/lj1043
pre_commands: ! |
boundary p f p
post_commands: ! |
fix move all nve
fix test solute wall/lj1043 ylo EDGE 100.0 2.0 5.0 yhi EDGE 100.0 2.0 5.0
fix_modify test virial yes
input_file: in.fourmol
natoms: 29
run_stress: ! |2-
0.0000000000000000e+00 -2.6193298572154652e+02 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
global_scalar: -21.0862098649006
global_vector: ! |-
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run_pos: ! |2
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run_vel: ! |2
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...

81
unittest/force-styles/tests/fix-timestep-wall_lj126_const.yaml Normal file
View File

@ -0,0 +1,81 @@
---
lammps_version: 21 Jul 2020
date_generated: Thu Aug 20 15:37:32 202
epsilon: 1e-14
prerequisites: ! |
atom full
fix wall/lj126
pre_commands: ! |
boundary p f p
post_commands: ! |
fix move all nve
fix test solute wall/lj126 ylo EDGE 100.0 2.0 5.0 yhi EDGE 100.0 2.0 5.0
fix_modify test virial yes
input_file: in.fourmol
natoms: 29
run_stress: ! |2-
0.0000000000000000e+00 -3.4585143439781433e+01 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
global_scalar: -2.5475438051924
global_vector: ! |-
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run_pos: ! |2
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...

81
unittest/force-styles/tests/fix-timestep-wall_lj93_const.yaml Normal file
View File

@ -0,0 +1,81 @@
---
lammps_version: 21 Jul 2020
date_generated: Thu Aug 20 15:36:00 202
epsilon: 1e-14
prerequisites: ! |
atom full
fix wall/lj93
pre_commands: ! |
boundary p f p
post_commands: ! |
fix move all nve
fix test solute wall/lj93 ylo EDGE 100.0 2.0 5.0 yhi EDGE 100.0 2.0 5.0
fix_modify test virial yes
input_file: in.fourmol
natoms: 29
run_stress: ! |2-
0.0000000000000000e+00 -5.0602303343219951e+01 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
global_scalar: -4.10898799728224
global_vector: ! |-
2 0.0 -11.164431050504302
run_pos: ! |2
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...

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

@ -0,0 +1,81 @@
---
lammps_version: 21 Jul 2020
date_generated: Thu Aug 20 15:41:18 202
epsilon: 1e-14
prerequisites: ! |
atom full
fix wall/morse
pre_commands: ! |
boundary p f p
post_commands: ! |
fix move all nve
fix test solute wall/morse ylo EDGE 6000.0 0.3 1.1 5.0 yhi EDGE 6000.0 0.3 1.1 5.0
fix_modify test virial yes
input_file: in.fourmol
natoms: 29
run_stress: ! |2-
0.0000000000000000e+00 -1.6447328969000660e+03 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
global_scalar: -715.415406257395
global_vector: ! |-
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run_pos: ! |2
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...