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Merge pull request #2685 from akohlmey/collected-small-changes 

Collected small changes and fixes
This commit is contained in:
Axel Kohlmeyer 2021-04-02 19:42:04 -04:00 committed by GitHub
parent b976c2d13c 66e885b6e5
commit 9da49d9c6f
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GPG Key ID: 4AEE18F83AFDEB23
169 changed files with 1339 additions and 744 deletions
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2
doc/src/Build_basics.rst
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@ -1,7 +1,7 @@
Basic build options
===================
The following topics are covered on this page, for building both with
The following topics are covered on this page, for building with both
CMake and make:
* :ref:`Serial vs parallel build <serial>`

10
doc/src/Howto_granular.rst
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@ -18,12 +18,13 @@ This compute
calculates rotational kinetic energy which can be :doc:`output with thermodynamic info <Howto_output>`.
Use one of these 3 pair potentials, which compute forces and torques
Use one of these 4 pair potentials, which compute forces and torques
between interacting pairs of particles:
* :doc:`pair_style <pair_style>` gran/history
* :doc:`pair_style <pair_style>` gran/no_history
* :doc:`pair_style <pair_style>` gran/hertzian
* :doc:`pair_style gran/history <pair_gran>`
* :doc:`pair_style gran/no_history <pair_gran>`
* :doc:`pair_style gran/hertzian <pair_gran>`
* :doc:`pair_style granular <pair_granular>`
These commands implement fix options specific to granular systems:
@ -31,6 +32,7 @@ These commands implement fix options specific to granular systems:
* :doc:`fix pour <fix_pour>`
* :doc:`fix viscous <fix_viscous>`
* :doc:`fix wall/gran <fix_wall_gran>`
* :doc:`fix wall/gran/region <fix_wall_gran_region>`
The fix style *freeze* zeroes both the force and torque of frozen
atoms, and should be used for granular system instead of the fix style

70
doc/src/Install_git.rst
View File

@ -86,33 +86,59 @@ check out any other desired branch) first.
Once you have updated your local files with a ``git pull`` (or ``git
checkout``), you still need to re-build LAMMPS if any source files have
changed. To do this, you should cd to the src directory and type:
changed. How to do this depends on the build system you are using.
.. code-block:: bash
.. tabs::
$ make purge # remove any deprecated src files
$ make package-update # sync package files with src files
$ make foo # re-build for your machine (mpi, serial, etc)
.. tab:: CMake build
just as described on the :doc:`Apply patch <Install_patch>` page,
after a patch has been installed.
Change to your build folder and type:
.. warning::
.. code-block:: bash
If you wish to edit/change a src file that is from a
package, you should edit the version of the file inside the package
sub-directory with src, then re-install the package. The version in
the source directory is merely a copy and will be wiped out if you type "make
package-update".
cmake . --build
.. warning::
CMake should auto-detect whether it needs to re-run the CMake
configuration step and otherwise redo the build for all files
that have been changed or files that depend on changed files.
In case some build options have been changed or renamed, you
may have to update those by running:
The GitHub servers support both the "git://" and
"https://" access protocols for anonymous read-only access. If you
have a correspondingly configured GitHub account, you may also use
SSH access with the URL "git@github.com:lammps/lammps.git".
.. code-block:: bash
The LAMMPS GitHub project is managed by Christoph Junghans (LANL,
junghans at lanl.gov), Axel Kohlmeyer (Temple U, akohlmey at
gmail.com) and Richard Berger (Temple U, richard.berger at
temple.edu).
cmake .
and then rebuild.
.. tab:: Traditional make
Switch to the src directory and type:
.. code-block:: bash
$ make purge # remove any deprecated src files
$ make package-update # sync package files with src files
$ make foo # re-build for your machine (mpi, serial, etc)
Just as described on the :doc:`Apply patch <Install_patch>` page,
after a patch has been installed.
.. warning::
If you wish to edit/change a src file that is from a package,
you should edit the version of the file inside the package
sub-directory with src, then re-install the package. The
version in the source directory is merely a copy and will be
wiped out if you type "make package-update".
.. admonition:: Git protocols
:class: note
The servers at github.com support the "git://" and "https://" access
protocols for anonymous, read-only access. If you have a suitably
configured GitHub account, you may also use SSH protocol with the
URL "git@github.com:lammps/lammps.git".
The LAMMPS GitHub project is currently managed by Axel Kohlmeyer
(Temple U, akohlmey at gmail.com) and Richard Berger (Temple U,
richard.berger at temple.edu).

62
doc/src/Install_patch.rst
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@ -43,24 +43,54 @@ up to date.
* A list of updated files print out to the screen. The -b switch
creates backup files of your originals (e.g. src/force.cpp.orig), so
you can manually undo the patch if something goes wrong.
* Type the following from the src directory, to enforce consistency
between the src and package directories. This is OK to do even if you
don't use one or more packages. If you are applying several patches
successively, you only need to type this once at the end. The purge
command removes deprecated src files if any were removed by the patch
from package sub-directories.
.. code-block:: bash
* Once you have updated your local files you need to re-build LAMMPS.
If you are applying several patches successively, you only need to
do the rebuild once at the end. How to do it depends on the build
system you are using.
$ make purge
$ make package-update
.. tabs::
* Re-build LAMMPS via the "make" command.
.. tab:: CMake build
.. warning::
Change to your build folder and type:
If you wish to edit/change a source file that is part of a package,
you should edit the version of the file inside the package folder in
src, and then re-install or update the package. The version in the
src directory is merely a copy and will be wiped out when you type
"make package-update".
.. code-block:: bash
cmake . --build
CMake should auto-detect whether it needs to re-run the CMake
configuration step and otherwise redo the build for all files
that have been changed or files that depend on changed files.
In case some build options have been changed or renamed, you
may have to update those by running:
.. code-block:: bash
cmake .
and then rebuild.
.. tab:: Traditional make
Switch to the src directory and type:
.. code-block:: bash
$ make purge # remove any deprecated src files
$ make package-update # sync package files with src files
$ make foo # re-build for your machine (mpi, serial, etc)
to enforce consistency of the source between the src folder
and package directories. This is OK to do even if you don't
use any packages. The "make purge" command removes any deprecated
src files if they were removed by the patch from a package
sub-directory.
.. warning::
If you wish to edit/change a src file that is from a package,
you should edit the version of the file inside the package
sub-directory with src, then re-install the package. The
version in the source directory is merely a copy and will be
wiped out if you type "make package-update".

6
doc/src/angle_cosine_periodic.rst
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@ -71,9 +71,3 @@ Default
none
----------
.. _cosine-Mayo:
**(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990).

4
doc/src/dihedral_table.rst
View File

@ -15,10 +15,10 @@ Syntax
.. code-block:: LAMMPS
dihedral_style style interp Ntable
dihedral_style style interpolation Ntable
* style = *table* or *table/cut*
* interp = *linear* or *spline* = method of interpolation
* interpolation = *linear* or *spline* = method of interpolation
* Ntable = size of the internal lookup table
Examples

2
doc/src/dump.rst
View File

@ -349,7 +349,7 @@ the box size stored with the snapshot.
The *xtc* style writes XTC files, a compressed trajectory format used
by the GROMACS molecular dynamics package, and described
`here <http://manual.gromacs.org/current/online/xtc.html>`_.
`here <https://manual.gromacs.org/current/reference-manual/file-formats.html#xtc>`_.
The precision used in XTC files can be adjusted via the
:doc:`dump_modify <dump_modify>` command. The default value of 1000
means that coordinates are stored to 1/1000 nanometer accuracy. XTC

4
doc/src/fix_ave_chunk.rst
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@ -307,7 +307,9 @@ atoms in the chunk. The averaged output value for the chunk on the
average over atoms across the entire *Nfreq* timescale. For the
*density/number* and *density/mass* values, the volume (bin volume or
system volume) used in the final normalization will be the volume at
the final *Nfreq* timestep.
the final *Nfreq* timestep. For the *temp* values, degrees of freedom and
kinetic energy are summed separately across the entire *Nfreq* timescale, and
the output value is calculated by dividing those two sums.
If the *norm* setting is *sample*\ , the chunk value is summed over
atoms for each sample, as is the count, and an "average sample value"

5
doc/src/fix_cmap.rst
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@ -127,6 +127,11 @@ the :doc:`run <run>` command.
The forces due to this fix are imposed during an energy minimization,
invoked by the :doc:`minimize <minimize>` command.
The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
fix. This allows to set at which level of the :doc:`r-RESPA
<run_style>` integrator the fix is adding its forces. Default is the
outermost level.
.. note::
If you want the potential energy associated with the CMAP terms

2
doc/src/pair_dpd.rst
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@ -150,7 +150,7 @@ shifted to be 0.0 at the cutoff distance Rc.
The :doc:`pair_modify <pair_modify>` table option is not relevant
for these pair styles.
These pair style do not support the :doc:`pair_modify <pair_modify>`
These pair styles do not support the :doc:`pair_modify <pair_modify>`
tail option for adding long-range tail corrections to energy and
pressure.

2
doc/src/pair_fep_soft.rst
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@ -363,7 +363,7 @@ Mixing, shift, table, tail correction, restart, rRESPA info
The different versions of the *lj/cut/soft* pair styles support mixing. For
atom type pairs I,J and I != J, the :math:`\epsilon` and :math:`\sigma`
coefficients and cutoff distance for these pair style can be mixed. The default
coefficients and cutoff distance for these pair styles can be mixed. The default
mix value is *geometric* for 12-6 styles.
The mixing rule for epsilon and sigma for *lj/class2/soft* 9-6 potentials is to

2
doc/src/pair_gayberne.rst
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@ -188,7 +188,7 @@ Restrictions
The *gayberne* style is part of the ASPHERE package. It is only
enabled if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
These pair style require that atoms store torque and a quaternion to
These pair styles require that atoms store torque and a quaternion to
represent their orientation, as defined by the
:doc:`atom_style <atom_style>`. It also require they store a per-type
:doc:`shape <set>`. The particles cannot store a per-particle

2
doc/src/pair_vashishta.rst
View File

@ -217,7 +217,7 @@ This pair style can only be used via the *pair* keyword of the
Restrictions
""""""""""""
These pair style are part of the MANYBODY package. They is only
These pair styles are part of the MANYBODY package. They are only
enabled if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
These pair styles requires the :doc:`newton <newton>` setting to be "on"

56
examples/deposit/in.deposit.molecule.rigid-small Normal file
View File

@ -0,0 +1,56 @@
# sample surface deposition script for molecules
units lj
atom_style bond
boundary p p f
lattice fcc 1.0
region box block 0 5 0 5 0 10
create_box 3 box bond/types 1 extra/bond/per/atom 1
region substrate block INF INF INF INF INF 3
create_atoms 1 region substrate
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0
pair_coeff 1 2 1.0 1.0 5.0
mass * 1.0
bond_style harmonic
bond_coeff 1 5.0 1.0
neigh_modify delay 0
molecule dimer molecule.dimer
region slab block 0 5 0 5 8 9
group addatoms empty
region mobile block 0 5 0 5 2 INF
group mobile region mobile
compute add addatoms temp
compute_modify add dynamic/dof yes extra/dof 0
fix 1 addatoms rigid/small molecule mol dimer
fix 2 mobile langevin 0.1 0.1 0.1 587283
fix 3 mobile nve
fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 &
mol dimer vz -1.0 -1.0 rigid 1
fix 5 addatoms wall/reflect zhi EDGE
thermo_style custom step atoms temp epair etotal press
thermo 100
thermo_modify temp add lost/bond ignore lost warn
#dump 1 all atom 50 dump.deposit.atom
#dump 2 all image 50 image.*.jpg type type &
# axes yes 0.8 0.02 view 80 -30
#dump_modify 2 pad 5
#dump 3 all movie 50 tmp.mpg type type &
# axes yes 0.8 0.02 view 80 -30
#dump_modify 3 pad 5
run 10000

4
examples/deposit/in.deposit.molecule.shake
View File

@ -21,11 +21,11 @@ bond_coeff 1 5.0 1.0
neigh_modify delay 0
group addatoms type 2
group addatoms empty
region mobile block 0 5 0 5 2 INF
group mobile region mobile
compute add addatoms temp
compute add addatoms temp
compute_modify add dynamic/dof yes extra/dof 0
fix 1 addatoms nve

218
examples/deposit/log.10Mar21.deposit.molecule.rigid-small.g++.1 Normal file
View File

@ -0,0 +1,218 @@
LAMMPS (10 Mar 2021)
using 1 OpenMP thread(s) per MPI task
# sample surface deposition script for molecules
units lj
atom_style bond
boundary p p f
lattice fcc 1.0
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
region box block 0 5 0 5 0 10
create_box 3 box bond/types 1 extra/bond/per/atom 1
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (7.9370053 7.9370053 15.874011)
1 by 1 by 1 MPI processor grid
region substrate block INF INF INF INF INF 3
create_atoms 1 region substrate
Created 350 atoms
create_atoms CPU = 0.001 seconds
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0
pair_coeff 1 2 1.0 1.0 5.0
mass * 1.0
bond_style harmonic
bond_coeff 1 5.0 1.0
neigh_modify delay 0
molecule dimer molecule.dimer
Read molecule template dimer:
1 molecules
2 atoms with max type 3
1 bonds with max type 1
0 angles with max type 0
0 dihedrals with max type 0
0 impropers with max type 0
region slab block 0 5 0 5 8 9
group addatoms empty
0 atoms in group addatoms
region mobile block 0 5 0 5 2 INF
group mobile region mobile
150 atoms in group mobile
compute add addatoms temp
compute_modify add dynamic/dof yes extra/dof 0
fix 1 addatoms rigid/small molecule mol dimer
create bodies CPU = 0.000 seconds
0 rigid bodies with 0 atoms
1.0000000 = max distance from body owner to body atom
fix 2 mobile langevin 0.1 0.1 0.1 587283
fix 3 mobile nve
fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 mol dimer vz -1.0 -1.0 rigid 1
fix 5 addatoms wall/reflect zhi EDGE
thermo_style custom step atoms temp epair etotal press
thermo 100
thermo_modify temp add lost/bond ignore lost warn
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:468)
#dump 1 all atom 50 dump.deposit.atom
#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 2 pad 5
#dump 3 all movie 50 tmp.mpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 3 pad 5
run 10000
WARNING: Should not allow rigid bodies to bounce off relecting walls (src/fix_wall_reflect.cpp:182)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.3
ghost atom cutoff = 5.3
binsize = 2.65, bins = 3 3 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.929 | 5.929 | 5.929 Mbytes
Step Atoms Temp E_pair TotEng Press
0 350 0 -6.9215833 -6.9215833 -1.0052629
100 352 1.0079368 -6.8875167 -6.8803581 -0.73353914
200 354 1.0081552 -6.8594643 -6.8452248 -0.70421276
300 356 1.0085803 -6.8171524 -6.7959042 -0.6917826
400 358 1.0099188 -6.7852701 -6.7570601 -0.70371699
500 360 1.0140221 -6.7493429 -6.7141338 -0.68415307
600 362 1.026148 -6.7105231 -6.6680032 -0.68314418
700 364 1.0683344 -6.6725162 -6.621154 -0.65747369
800 366 1.0958952 -6.6412275 -6.5813425 -0.68789614
900 368 1.1250033 -6.6101882 -6.541404 -0.66674346
1000 370 1.2326373 -6.5993719 -6.5160856 -0.6968868
1100 372 1.1397426 -6.5912861 -6.5070309 -0.63330356
1200 374 1.0514292 -6.5905747 -6.5062354 -0.71020362
1300 376 1.003296 -6.5747765 -6.4880555 -0.65459732
1400 378 0.82999289 -6.5681797 -6.4913285 -0.60438126
1500 380 0.90239175 -6.575298 -6.4862461 -0.66528725
1600 382 0.86399799 -6.5692206 -6.4787496 -0.65027781
1700 384 0.64747231 -6.5644237 -6.4927634 -0.6304614
1800 386 0.74288971 -6.5515735 -6.4649672 -0.67772325
1900 388 0.7257202 -6.5565091 -6.4676644 -0.66173549
2000 390 0.73381036 -6.5631515 -6.4690733 -0.64685916
2100 392 0.76476562 -6.5574124 -6.4549885 -0.68866192
2200 394 0.65932468 -6.5511557 -6.459118 -0.71728829
2300 396 0.70269509 -6.5728146 -6.4707819 -0.64362081
2400 398 0.60528919 -6.5845991 -6.4933494 -0.63956327
2500 400 0.51025744 -6.5812452 -6.5015175 -0.68706961
2600 402 0.5245131 -6.6003894 -6.5155801 -0.68972215
2700 404 0.46330251 -6.5659175 -6.4885092 -0.72870942
2800 406 0.48039778 -6.5715192 -6.488692 -0.753758
2900 408 0.53698616 -6.5813154 -6.4858951 -0.67117541
3000 410 0.50231419 -6.5886963 -6.4968096 -0.71905351
3100 412 0.49420225 -6.596733 -6.5037702 -0.65947518
3200 414 0.42703699 -6.5879338 -6.5054146 -0.80033546
3300 416 0.44306009 -6.580249 -6.4923825 -0.76503083
3400 418 0.55620672 -6.5923388 -6.4792346 -0.69367877
3500 420 0.39815033 -6.5911154 -6.5081674 -0.65569211
3600 422 0.44197847 -6.6026382 -6.5083774 -0.73299102
3700 424 0.45049389 -6.6060616 -6.5077817 -0.7552914
3800 426 0.43047295 -6.6079275 -6.51193 -0.71501328
3900 428 0.43779129 -6.6099306 -6.5102001 -0.71539515
4000 430 0.41113503 -6.6123009 -6.5166881 -0.74177096
4100 432 0.32800011 -6.5983566 -6.5205325 -0.71688103
4200 434 0.39168203 -6.6110342 -6.5162724 -0.78927697
4300 436 0.48151013 -6.6183315 -6.4996106 -0.70523035
4400 438 0.45391027 -6.6331732 -6.5191775 -0.7270855
4500 440 0.349126 -6.6091657 -6.5199006 -0.76974115
4600 442 0.43375023 -6.6219188 -6.5090653 -0.74576212
4700 444 0.40071749 -6.6184164 -6.5123707 -0.71919052
4800 446 0.414292 -6.6298132 -6.5183445 -0.76237313
4900 448 0.44210681 -6.6364174 -6.5155288 -0.78753121
5000 450 0.36101771 -6.6232703 -6.5229876 -0.73927083
5100 452 0.41481171 -6.6442404 -6.5272305 -0.76316209
5200 454 0.40283527 -6.6512252 -6.5358759 -0.79645689
5300 456 0.3642061 -6.6530346 -6.5472072 -0.77458364
5400 458 0.38449826 -6.6514864 -6.5381518 -0.73083784
5500 460 0.42559408 -6.6769326 -6.5497169 -0.78932279
5600 462 0.38905756 -6.6698705 -6.5519743 -0.77118812
5700 464 0.38354955 -6.6706904 -6.5528977 -0.75067129
5800 466 0.36760943 -6.6942519 -6.5798669 -0.685487
5900 468 0.30783118 -6.6838159 -6.5867965 -0.79233808
6000 470 0.33145368 -6.6733504 -6.5675673 -0.84390449
6100 472 0.39252324 -6.6912189 -6.5643973 -0.83342022
6200 474 0.32342144 -6.6906083 -6.5848481 -0.71262158
6300 476 0.34445238 -6.7008453 -6.5868721 -0.76650756
6400 478 0.38152782 -6.7017838 -6.5740758 -0.77113022
6500 480 0.37540166 -6.7119996 -6.5849105 -0.79907635
6600 482 0.3579419 -6.7034721 -6.5809401 -0.8141269
6700 484 0.33538235 -6.6916682 -6.575601 -0.83265486
6800 486 0.34081871 -6.6931924 -6.573976 -0.80582583
6900 488 0.3555283 -6.6939997 -6.5683263 -0.74771423
7000 490 0.3543769 -6.7093364 -6.5827732 -0.77643516
7100 492 0.31263107 -6.698361 -6.5855723 -0.73108333
7200 494 0.32107 -6.6959056 -6.5789166 -0.7575478
7300 496 0.32908165 -6.7137605 -6.592677 -0.86538023
7400 498 0.32539571 -6.7030353 -6.5821554 -0.79337428
7500 500 0.33902577 -6.7078178 -6.5806832 -0.85408988
7600 502 0.35530921 -6.707507 -6.5730274 -0.79914613
7700 504 0.32391812 -6.6978823 -6.5741635 -0.78603595
7800 506 0.36390015 -6.7151325 -6.5748943 -0.83164222
7900 508 0.3372561 -6.7086718 -6.5775535 -0.7949992
8000 510 0.36612946 -6.7225238 -6.5789437 -0.80322866
8100 512 0.34622305 -6.7229825 -6.5860486 -0.70478659
8200 514 0.3212233 -6.7202524 -6.5921381 -0.91836713
8300 516 0.3402461 -6.721488 -6.5846642 -0.88273592
8400 518 0.34070258 -6.7268378 -6.5887152 -0.76057264
8500 520 0.36267747 -6.744602 -6.5963924 -0.81051317
8600 522 0.3439948 -6.7376267 -6.595943 -0.84600203
8700 524 0.30960289 -6.7276471 -6.5991382 -0.90965986
8800 526 0.28868972 -6.7159628 -6.595218 -0.876093
8900 528 0.31020216 -6.7162903 -6.5855707 -0.83193125
9000 530 0.31836275 -6.7171479 -6.5819939 -0.82093897
9100 532 0.32543293 -6.724167 -6.5850016 -0.7690143
9200 534 0.32644265 -6.7139575 -6.5733549 -0.86903096
9300 536 0.33050759 -6.7254715 -6.5821077 -0.94504522
9400 538 0.30372582 -6.7139931 -6.5813247 -0.91128612
9500 540 0.32943659 -6.7206223 -6.5757312 -0.87818439
9600 542 0.30911968 -6.708091 -6.5712114 -0.79092372
9700 544 0.33909826 -6.7222948 -6.5711342 -0.80266151
9800 546 0.29015141 -6.7086869 -6.5784908 -0.87763769
9900 548 0.33838474 -6.7384955 -6.5856667 -0.85630604
10000 550 0.30213198 -6.7338924 -6.5965597 -0.75738882
Loop time of 17.2852 on 1 procs for 10000 steps with 550 atoms
Performance: 249924.414 tau/day, 578.529 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 9.637 | 9.637 | 9.637 | 0.0 | 55.75
Bond | 0.025444 | 0.025444 | 0.025444 | 0.0 | 0.15
Neigh | 4.6852 | 4.6852 | 4.6852 | 0.0 | 27.11
Comm | 0.65556 | 0.65556 | 0.65556 | 0.0 | 3.79
Output | 0.0099883 | 0.0099883 | 0.0099883 | 0.0 | 0.06
Modify | 2.1895 | 2.1895 | 2.1895 | 0.0 | 12.67
Other | | 0.08248 | | | 0.48
Nlocal: 550.000 ave 550 max 550 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2367.00 ave 2367 max 2367 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 36781.0 ave 36781 max 36781 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 36781
Ave neighs/atom = 66.874545
Ave special neighs/atom = 0.36363636
Neighbor list builds = 840
Dangerous builds = 0
Total wall time: 0:00:17

218
examples/deposit/log.10Mar21.deposit.molecule.rigid-small.g++.4 Normal file
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@ -0,0 +1,218 @@
LAMMPS (10 Mar 2021)
using 1 OpenMP thread(s) per MPI task
# sample surface deposition script for molecules
units lj
atom_style bond
boundary p p f
lattice fcc 1.0
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
region box block 0 5 0 5 0 10
create_box 3 box bond/types 1 extra/bond/per/atom 1
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (7.9370053 7.9370053 15.874011)
1 by 1 by 4 MPI processor grid
region substrate block INF INF INF INF INF 3
create_atoms 1 region substrate
Created 350 atoms
create_atoms CPU = 0.139 seconds
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0
pair_coeff 1 2 1.0 1.0 5.0
mass * 1.0
bond_style harmonic
bond_coeff 1 5.0 1.0
neigh_modify delay 0
molecule dimer molecule.dimer
Read molecule template dimer:
1 molecules
2 atoms with max type 3
1 bonds with max type 1
0 angles with max type 0
0 dihedrals with max type 0
0 impropers with max type 0
region slab block 0 5 0 5 8 9
group addatoms empty
0 atoms in group addatoms
region mobile block 0 5 0 5 2 INF
group mobile region mobile
150 atoms in group mobile
compute add addatoms temp
compute_modify add dynamic/dof yes extra/dof 0
fix 1 addatoms rigid/small molecule mol dimer
create bodies CPU = 0.006 seconds
0 rigid bodies with 0 atoms
1.0000000 = max distance from body owner to body atom
fix 2 mobile langevin 0.1 0.1 0.1 587283
fix 3 mobile nve
fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 mol dimer vz -1.0 -1.0 rigid 1
fix 5 addatoms wall/reflect zhi EDGE
thermo_style custom step atoms temp epair etotal press
thermo 100
thermo_modify temp add lost/bond ignore lost warn
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:468)
#dump 1 all atom 50 dump.deposit.atom
#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 2 pad 5
#dump 3 all movie 50 tmp.mpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 3 pad 5
run 10000
WARNING: Should not allow rigid bodies to bounce off relecting walls (src/fix_wall_reflect.cpp:182)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.3
ghost atom cutoff = 5.3
binsize = 2.65, bins = 3 3 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.255 | 5.852 | 6.302 Mbytes
Step Atoms Temp E_pair TotEng Press
0 350 0 -6.9215833 -6.9215833 -1.0052629
100 352 1.0079368 -6.8946578 -6.8874992 -0.73775337
200 354 1.0081552 -6.8645575 -6.850318 -0.69629729
300 356 1.0085803 -6.821677 -6.8004288 -0.69532657
400 358 1.0099188 -6.7837923 -6.7555822 -0.68879568
500 360 1.0140221 -6.7446709 -6.7094618 -0.72991641
600 362 1.026146 -6.7129201 -6.6704003 -0.67063836
700 364 1.0683193 -6.6776523 -6.6262908 -0.65572472
800 366 1.0958893 -6.6402029 -6.5803182 -0.66307281
900 368 1.1231768 -6.6050912 -6.5364187 -0.64076928
1000 370 1.1976283 -6.5942507 -6.5133299 -0.69249019
1100 372 1.0506263 -6.5772313 -6.499564 -0.63072939
1200 374 0.93724351 -6.5732957 -6.4981157 -0.64963897
1300 376 0.93899686 -6.5578406 -6.4766773 -0.65096289
1400 378 0.8704974 -6.5468498 -6.4662482 -0.67613931
1500 380 0.84490693 -6.5401094 -6.4567304 -0.64385968
1600 382 0.9243154 -6.5611604 -6.4643734 -0.62096869
1700 384 0.67202953 -6.5590557 -6.4846775 -0.67807465
1800 386 0.8712464 -6.5654953 -6.4639251 -0.65860236
1900 388 0.70011668 -6.5808612 -6.495151 -0.65146463
2000 390 0.64019295 -6.5652168 -6.4831408 -0.70291888
2100 392 0.67578277 -6.5596196 -6.469113 -0.63315981
2200 394 0.60785287 -6.558941 -6.4740885 -0.7133822
2300 396 0.8155086 -6.5756022 -6.4571887 -0.69176417
2400 398 0.69028748 -6.5875474 -6.483484 -0.63743938
2500 400 0.5013913 -6.5871851 -6.5088427 -0.65872179
2600 402 0.51268385 -6.5782356 -6.495339 -0.74289067
2700 404 0.57745388 -6.5815718 -6.4850912 -0.67922914
2800 406 0.47317895 -6.5974978 -6.5159152 -0.64657562
2900 408 0.50593124 -6.6019054 -6.5120034 -0.64211427
3000 410 0.44423233 -6.5956684 -6.5144064 -0.66526127
3100 412 0.40808865 -6.5949863 -6.5182221 -0.62722445
3200 414 0.40692632 -6.5866689 -6.5080358 -0.76440608
3300 416 0.43908529 -6.5851721 -6.4980939 -0.69345883
3400 418 0.53825907 -6.5880076 -6.478553 -0.69726204
3500 420 0.46363057 -6.6135193 -6.5169296 -0.58015901
3600 422 0.39262699 -6.621857 -6.5381213 -0.74921264
3700 424 0.42679205 -6.6146579 -6.5215488 -0.69040431
3800 426 0.38997492 -6.6139725 -6.5270063 -0.78237667
3900 428 0.5222531 -6.6403886 -6.5214174 -0.78298122
4000 430 0.47841128 -6.6502681 -6.5390097 -0.68125967
4100 432 0.44609186 -6.6610827 -6.5552392 -0.81157037
4200 434 0.4591431 -6.6858064 -6.5747234 -0.79000753
4300 436 0.40690573 -6.6800195 -6.579693 -0.6781696
4400 438 0.43023944 -6.6849804 -6.5769294 -0.7620548
4500 440 0.40889421 -6.6783124 -6.5737656 -0.8577593
4600 442 0.41452051 -6.6968565 -6.5890061 -0.70427746
4700 444 0.36740394 -6.6920933 -6.5948636 -0.69303162
4800 446 0.40112316 -6.6869413 -6.5790158 -0.84792822
4900 448 0.42437165 -6.6789835 -6.5629444 -0.82278531
5000 450 0.41822898 -6.6770254 -6.5608507 -0.72224472
5100 452 0.38445688 -6.6738997 -6.5654522 -0.7022418
5200 454 0.39998238 -6.6670536 -6.5525212 -0.73639959
5300 456 0.39471029 -6.6728592 -6.5581681 -0.70419927
5400 458 0.35817807 -6.6702423 -6.5646658 -0.81657219
5500 460 0.37151428 -6.6690855 -6.558035 -0.78076653
5600 462 0.32642513 -6.6622352 -6.5633185 -0.69118644
5700 464 0.43665879 -6.6811227 -6.5470195 -0.77500043
5800 466 0.40704721 -6.6858874 -6.5592311 -0.72683597
5900 468 0.3861903 -6.6896953 -6.5679794 -0.78001958
6000 470 0.34073346 -6.6833717 -6.574627 -0.78170837
6100 472 0.39953874 -6.7083668 -6.5792785 -0.81791744
6200 474 0.36685189 -6.7114648 -6.5915027 -0.80545451
6300 476 0.35851799 -6.7261023 -6.607475 -0.77350495
6400 478 0.41771823 -6.7427425 -6.6029205 -0.85319003
6500 480 0.36519478 -6.732662 -6.6090284 -0.78712805
6600 482 0.30669571 -6.7269784 -6.6219892 -0.76698134
6700 484 0.3384344 -6.7261448 -6.6090213 -0.79935239
6800 486 0.36420902 -6.7320259 -6.6046277 -0.84650552
6900 488 0.40181215 -6.7490619 -6.6070279 -0.75753238
7000 490 0.30536068 -6.7398924 -6.6308351 -0.73210162
7100 492 0.28813004 -6.7257287 -6.6217794 -0.92178435
7200 494 0.30956277 -6.7342688 -6.6214727 -0.77532949
7300 496 0.36625115 -6.7528159 -6.6180561 -0.76247835
7400 498 0.30935271 -6.7401433 -6.6252231 -0.82809158
7500 500 0.33222282 -6.7410421 -6.6164585 -0.81948236
7600 502 0.33318693 -6.7488106 -6.622704 -0.82395904
7700 504 0.34570598 -6.7547394 -6.6226989 -0.85644369
7800 506 0.34587242 -6.7446006 -6.6113099 -0.82476511
7900 508 0.2969166 -6.7305429 -6.6151078 -0.8210214
8000 510 0.32355758 -6.7437629 -6.6168776 -0.81719054
8100 512 0.33784479 -6.7545537 -6.6209335 -0.78082067
8200 514 0.32351289 -6.7525032 -6.6234757 -0.87093587
8300 516 0.31900134 -6.7550972 -6.6268166 -0.79928704
8400 518 0.3338521 -6.7588757 -6.6235302 -0.81699503
8500 520 0.33115184 -6.7614854 -6.6261589 -0.79958489
8600 522 0.29478929 -6.7490188 -6.6276018 -0.81954456
8700 524 0.267993 -6.7467764 -6.6355389 -0.76642994
8800 526 0.28792085 -6.7527118 -6.6322887 -0.86911619
8900 528 0.32430992 -6.75901 -6.6223453 -0.87087898
9000 530 0.33151321 -6.7534845 -6.6127478 -0.79309499
9100 532 0.32760982 -6.7599992 -6.6199028 -0.7506309
9200 534 0.32579101 -6.7671489 -6.6268269 -0.94238755
9300 536 0.35144354 -6.7782581 -6.625813 -0.77952234
9400 538 0.33689976 -6.7804455 -6.6332867 -0.75768501
9500 540 0.3052486 -6.7745436 -6.6402908 -0.89621525
9600 542 0.30617581 -6.7648172 -6.6292412 -0.90623541
9700 544 0.30097715 -6.7714379 -6.6372707 -0.85534149
9800 546 0.31297479 -6.7814978 -6.6410604 -0.88651064
9900 548 0.31832347 -6.790661 -6.6468926 -1.006
10000 550 0.29239559 -6.7823137 -6.6494066 -1.0337518
Loop time of 34.7661 on 4 procs for 10000 steps with 550 atoms
Performance: 124259.065 tau/day, 287.637 timesteps/s
73.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0076709 | 3.1286 | 9.1834 | 211.7 | 9.00
Bond | 0.0040276 | 0.010416 | 0.022169 | 7.0 | 0.03
Neigh | 0.052413 | 1.5948 | 4.885 | 155.3 | 4.59
Comm | 4.9736 | 12.242 | 20.073 | 166.2 | 35.21
Output | 0.053549 | 0.10104 | 0.21642 | 21.0 | 0.29
Modify | 13.435 | 16.191 | 23.851 | 110.0 | 46.57
Other | | 1.499 | | | 4.31
Nlocal: 137.500 ave 299 max 2 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 1898.75 ave 2679 max 524 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs: 9204.00 ave 23014 max 0 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Total # of neighbors = 36816
Ave neighs/atom = 66.938182
Ave special neighs/atom = 0.36363636
Neighbor list builds = 832
Dangerous builds = 0
Total wall time: 0:00:34

48
examples/gcmc/in.gcmc.co2
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@ -1,4 +1,4 @@
# GCMC for CO2 molecular fluid, rigid/small/nvt dynamics
# GCMC for CO2 molecular fluid, rigid/small dynamics
# Rigid CO2 TraPPE model
# [Potoff and J.I. Siepmann, Vapor-liquid equilibria of
# mixtures containing alkanes, carbon dioxide and
@ -7,7 +7,7 @@
# variables available on command line
variable mu index -8.1
variable disp index 0.5
variable disp index 0.5
variable temp index 338.0
variable lbox index 10.0
variable spacing index 5.0
@ -17,7 +17,7 @@ variable spacing index 5.0
units real
atom_style full
boundary p p p
pair_style lj/cut/coul/long 14
pair_style lj/cut/coul/long 14
pair_modify mix arithmetic tail yes
kspace_style ewald 0.0001
bond_style harmonic
@ -25,7 +25,7 @@ angle_style harmonic
# box, start molecules on simple cubic lattice
lattice sc ${spacing}
lattice sc ${spacing}
region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box
create_box 2 box &
bond/types 1 &
@ -34,56 +34,56 @@ create_box 2 box &
extra/angle/per/atom 1 &
extra/special/per/atom 2
molecule co2mol CO2.txt
create_atoms 0 box mol co2mol 464563 units box
# rigid CO2 TraPPE model
create_atoms 0 box mol co2mol 464563 units box
# rigid CO2 TraPPE model
pair_coeff 1 1 0.053649 2.8
pair_coeff 2 2 0.156973 3.05
bond_coeff 1 0 1.16
angle_coeff 1 0 180
pair_coeff 2 2 0.156973 3.05
bond_coeff 1 0 1.16
angle_coeff 1 0 180
# masses
mass 1 12.0107
mass 2 15.9994
mass 1 12.0107
mass 2 15.9994
# MD settings
group co2 type 1 2
neighbor 2.0 bin
neigh_modify every 1 delay 10 check yes
velocity all create ${temp} 54654
velocity all create ${temp} 54654
timestep 1.0
# rigid constraints with thermostat
# rigid constraints with thermostat
fix myrigidnvt co2 rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol
fix myrigid co2 rigid/small molecule mol co2mol
# dynamically update fix rigid/nvt/small temperature ndof
fix_modify myrigidnvt dynamic/dof yes
fix_modify myrigid dynamic/dof yes
# gcmc
variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
fix mygcmc co2 gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol &
co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
co2mol tfac_insert ${tfac} group co2 rigid myrigid
# atom counts
variable carbon atom "type==1"
variable carbon atom "type==1"
variable oxygen atom "type==2"
group carbon dynamic co2 var carbon
group oxygen dynamic co2 var oxygen
group carbon dynamic co2 var carbon
group oxygen dynamic co2 var oxygen
variable nC equal count(carbon)
variable nO equal count(oxygen)
# output
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
# dynamically update default temperature ndof
compute_modify thermo_temp dynamic/dof yes

196
examples/gcmc/log.27Nov18.gcmc.co2.g++.1
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@ -1,196 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# GCMC for CO2 molecular fluid, rigid/small/nvt dynamics
# Rigid CO2 TraPPE model
# [Potoff and J.I. Siepmann, Vapor-liquid equilibria of
# mixtures containing alkanes, carbon dioxide and
# nitrogen AIChE J., 47,1676-1682 (2001)].
# variables available on command line
variable mu index -8.1
variable disp index 0.5
variable temp index 338.0
variable lbox index 10.0
variable spacing index 5.0
# global model settings
units real
atom_style full
boundary p p p
pair_style lj/cut/coul/long 14
pair_modify mix arithmetic tail yes
kspace_style ewald 0.0001
bond_style harmonic
angle_style harmonic
# box, start molecules on simple cubic lattice
lattice sc ${spacing}
lattice sc 5.0
Lattice spacing in x,y,z = 5 5 5
region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box
region box block 0 10.0 0 ${lbox} 0 ${lbox} units box
region box block 0 10.0 0 10.0 0 ${lbox} units box
region box block 0 10.0 0 10.0 0 10.0 units box
create_box 2 box bond/types 1 angle/types 1 extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2
Created orthogonal box = (0 0 0) to (10 10 10)
1 by 1 by 1 MPI processor grid
molecule co2mol CO2.txt
Read molecule co2mol:
3 atoms with max type 2
2 bonds with max type 1
1 angles with max type 1
0 dihedrals with max type 0
0 impropers with max type 0
create_atoms 0 box mol co2mol 464563 units box
Created 24 atoms
Time spent = 0.00134993 secs
# rigid CO2 TraPPE model
pair_coeff 1 1 0.053649 2.8
pair_coeff 2 2 0.156973 3.05
bond_coeff 1 0 1.16
angle_coeff 1 0 180
# masses
mass 1 12.0107
mass 2 15.9994
# MD settings
group co2 type 1 2
24 atoms in group co2
neighbor 2.0 bin
neigh_modify every 1 delay 10 check yes
velocity all create ${temp} 54654
velocity all create 338.0 54654
timestep 1.0
# rigid constraints with thermostat
fix myrigidnvt co2 rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol
fix myrigidnvt co2 rigid/nvt/small molecule temp 338.0 ${temp} 100 mol co2mol
fix myrigidnvt co2 rigid/nvt/small molecule temp 338.0 338.0 100 mol co2mol
8 rigid bodies with 24 atoms
1.16 = max distance from body owner to body atom
# dynamically update fix rigid/nvt/small temperature ndof
fix_modify myrigidnvt dynamic/dof yes
# gcmc
variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
fix mygcmc co2 gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert 1.66666666666667 group co2 rigid myrigidnvt
# atom counts
variable carbon atom "type==1"
variable oxygen atom "type==2"
group carbon dynamic co2 var carbon
dynamic group carbon defined
group oxygen dynamic co2 var oxygen
dynamic group oxygen defined
variable nC equal count(carbon)
variable nO equal count(oxygen)
# output
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
# dynamically update default temperature ndof
compute_modify thermo_temp dynamic/dof yes
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
thermo 1000
# run
run 20000
Ewald initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.164636
estimated absolute RMS force accuracy = 0.0332064
estimated relative force accuracy = 0.0001
KSpace vectors: actual max1d max3d = 16 2 62
kxmax kymax kzmax = 2 2 2
WARNING: Fix gcmc using full_energy option (src/MC/fix_gcmc.cpp:487)
0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc
0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:471)
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 16
ghost atom cutoff = 16
binsize = 8, bins = 2 2 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 15.62 | 15.62 | 15.62 Mbytes
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
0 364.27579 4238.8631 -9.6809388 13.391989 0.5846359 24 0 0 0 0 8 16
1000 267.9799 -73.919548 -3.6735999 5.8578459 0.36539744 15 0.23663972 0.2494423 0 0 5 10
2000 409.06596 -98.033864 -6.7570039 10.974131 0.43847693 18 0.29379544 0.29816284 0 0 6 12
3000 279.3225 -836.47758 -26.434976 15.819539 0.87695385 36 0.23798567 0.24203908 0 0 12 24
4000 333.6181 606.63478 -30.35312 18.894592 0.87695385 36 0.19121778 0.19481508 0 0 12 24
5000 405.98741 -103.97582 -14.180277 16.942399 0.65771539 27 0.15272841 0.15982952 0 0 9 18
6000 283.5835 -240.01076 -6.7198093 7.607777 0.43847693 18 0.1606796 0.16536735 0 0 6 12
7000 142.00717 154.95914 -0.74192319 0.98769159 0.14615898 6 0.19501993 0.20103405 0 0 2 4
8000 376.67702 -118.12474 -10.774631 13.847899 0.5846359 24 0.20133396 0.20468352 0 0 8 16
9000 305.43166 -1095.8633 -10.388279 9.7112935 0.51155641 21 0.19445239 0.19869334 0 0 7 14
10000 244.08225 -179.31274 -12.974988 8.9732748 0.5846359 24 0.19098971 0.19586397 0 0 8 16
11000 305.03389 -568.94714 -21.745425 14.244887 0.73079488 30 0.18517522 0.18978828 0 0 10 20
12000 318.29735 767.76579 -37.184231 21.189508 1.0231128 42 0.17256426 0.17580267 0 0 14 28
13000 411.21707 433.01125 -4.5149215 8.9889065 0.36539744 15 0.16329385 0.16767604 0 0 5 10
14000 304.29535 148.28607 -2.3505844 6.6516754 0.36539744 15 0.17435868 0.17897674 0 0 5 10
15000 338.00555 2384.1424 -21.438264 17.463859 0.80387436 33 0.17237066 0.17634112 0 0 11 22
16000 613.56062 610.93867 -0.057364228 1.2192718 0.073079488 3 0.17128158 0.1758886 0 0 1 2
17000 432.63323 -980.52384 -15.79844 18.054365 0.65771539 27 0.17145651 0.17504846 0 0 9 18
18000 181.74572 -352.81765 -1.8617959 2.1669979 0.21923846 9 0.17292463 0.17654774 0 0 3 6
19000 208.55292 -248.38735 -4.2287767 4.5588154 0.36539744 15 0.18168324 0.18454331 0 0 5 10
20000 304.73317 -649.9896 -16.532405 12.716924 0.65771539 27 0.18085983 0.18345574 0 0 9 18
Loop time of 21.0434 on 1 procs for 20000 steps with 27 atoms
Performance: 82.116 ns/day, 0.292 hours/ns, 950.415 timesteps/s
98.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.2373 | 2.2373 | 2.2373 | 0.0 | 10.63
Bond | 0.022895 | 0.022895 | 0.022895 | 0.0 | 0.11
Kspace | 0.16756 | 0.16756 | 0.16756 | 0.0 | 0.80
Neigh | 0.11436 | 0.11436 | 0.11436 | 0.0 | 0.54
Comm | 0.26988 | 0.26988 | 0.26988 | 0.0 | 1.28
Output | 0.0014684 | 0.0014684 | 0.0014684 | 0.0 | 0.01
Modify | 18.193 | 18.193 | 18.193 | 0.0 | 86.45
Other | | 0.03692 | | | 0.18
Nlocal: 27 ave 27 max 27 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2081 ave 2081 max 2081 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 6264 ave 6264 max 6264 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 6264
Ave neighs/atom = 232
Ave special neighs/atom = 2
Neighbor list builds = 20177
Dangerous builds = 0
Total wall time: 0:00:21

196
examples/gcmc/log.31Mar21.gcmc.co2.g++.1 Normal file
View File

@ -0,0 +1,196 @@
LAMMPS (10 Mar 2021)
using 1 OpenMP thread(s) per MPI task
# GCMC for CO2 molecular fluid, rigid/small dynamics
# Rigid CO2 TraPPE model
# [Potoff and J.I. Siepmann, Vapor-liquid equilibria of
# mixtures containing alkanes, carbon dioxide and
# nitrogen AIChE J., 47,1676-1682 (2001)].
# variables available on command line
variable mu index -8.1
variable disp index 0.5
variable temp index 338.0
variable lbox index 10.0
variable spacing index 5.0
# global model settings
units real
atom_style full
boundary p p p
pair_style lj/cut/coul/long 14
pair_modify mix arithmetic tail yes
kspace_style ewald 0.0001
bond_style harmonic
angle_style harmonic
# box, start molecules on simple cubic lattice
lattice sc ${spacing}
lattice sc 5.0
Lattice spacing in x,y,z = 5.0000000 5.0000000 5.0000000
region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box
region box block 0 10.0 0 ${lbox} 0 ${lbox} units box
region box block 0 10.0 0 10.0 0 ${lbox} units box
region box block 0 10.0 0 10.0 0 10.0 units box
create_box 2 box bond/types 1 angle/types 1 extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (10.000000 10.000000 10.000000)
1 by 1 by 1 MPI processor grid
molecule co2mol CO2.txt
Read molecule template co2mol:
1 molecules
3 atoms with max type 2
2 bonds with max type 1
1 angles with max type 1
0 dihedrals with max type 0
0 impropers with max type 0
create_atoms 0 box mol co2mol 464563 units box
Created 24 atoms
create_atoms CPU = 0.002 seconds
# rigid CO2 TraPPE model
pair_coeff 1 1 0.053649 2.8
pair_coeff 2 2 0.156973 3.05
bond_coeff 1 0 1.16
angle_coeff 1 0 180
# masses
mass 1 12.0107
mass 2 15.9994
# MD settings
group co2 type 1 2
24 atoms in group co2
neighbor 2.0 bin
neigh_modify every 1 delay 10 check yes
velocity all create ${temp} 54654
velocity all create 338.0 54654
timestep 1.0
# rigid constraints with thermostat
fix myrigid co2 rigid/small molecule mol co2mol
create bodies CPU = 0.000 seconds
8 rigid bodies with 24 atoms
1.1600000 = max distance from body owner to body atom
# dynamically update fix rigid/nvt/small temperature ndof
fix_modify myrigid dynamic/dof yes
# gcmc
variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
fix mygcmc co2 gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigid
fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigid
fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigid
fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert ${tfac} group co2 rigid myrigid
fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert 1.66666666666667 group co2 rigid myrigid
# atom counts
variable carbon atom "type==1"
variable oxygen atom "type==2"
group carbon dynamic co2 var carbon
dynamic group carbon defined
group oxygen dynamic co2 var oxygen
dynamic group oxygen defined
variable nC equal count(carbon)
variable nO equal count(oxygen)
# output
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
# dynamically update default temperature ndof
compute_modify thermo_temp dynamic/dof yes
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
thermo 1000
# run
run 20000
Ewald initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
G vector (1/distance) = 0.16463644
estimated absolute RMS force accuracy = 0.033206372
estimated relative force accuracy = 0.0001
KSpace vectors: actual max1d max3d = 16 2 62
kxmax kymax kzmax = 2 2 2
WARNING: Fix gcmc using full_energy option (src/MC/fix_gcmc.cpp:482)
0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc
0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:486)
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 16
ghost atom cutoff = 16
binsize = 8, bins = 2 2 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 15.62 | 15.62 | 15.62 Mbytes
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
0 364.27579 4238.8631 -9.6809388 13.391989 0.5846359 24 0 0 0 0 8 16
1000 261.50949 -204.60974 -9.6459249 8.3147747 0.51155641 21 0.096366192 0.097590121 0 0 7 14
2000 479.39697 231.28436 -7.0089345 10.47927 0.36539744 15 0.085531005 0.085453295 0 0 5 10
3000 318.31766 -433.17133 -7.3680951 8.5396005 0.43847693 18 0.078556687 0.080101462 0 0 6 12
4000 357.40776 -186.78 -16.453111 14.915105 0.65771539 27 0.082003877 0.08249082 0 0 9 18
5000 399.94731 1524.2909 -16.624678 18.677282 0.73079488 30 0.071285101 0.072731705 0 0 10 20
6000 354.71736 60.134827 -18.988979 16.565073 0.73079488 30 0.071615663 0.071713414 0 0 10 20
7000 483.32057 966.32174 -5.7393251 10.565037 0.36539744 15 0.087027775 0.089855826 0 0 5 10
8000 547.68562 494.96891 -4.125626 11.97201 0.36539744 15 0.11738082 0.11937373 0 0 5 10
9000 433.76488 390.91467 -0.85312985 5.1718828 0.21923846 9 0.13265238 0.13513212 0 0 3 6
10000 330.01685 -862.07457 -26.494645 18.690633 0.87695385 36 0.13775034 0.13905403 0 0 12 24
11000 334.26318 -578.48274 -13.236965 12.288625 0.5846359 24 0.13713936 0.13960485 0 0 8 16
12000 243.68657 -1244.7156 -25.757644 12.590645 0.80387436 33 0.1339588 0.13588739 0 0 11 22
13000 307.66758 -429.66928 -17.864639 14.367878 0.73079488 30 0.12604721 0.1278094 0 0 10 20
14000 330.91434 495.97112 -15.374248 13.809499 0.65771539 27 0.12011756 0.12145865 0 0 9 18
15000 564.87966 982.72332 -14.810525 26.379517 0.73079488 30 0.12164324 0.12343521 0 0 10 20
16000 342.63867 -54.776299 -2.2580523 5.7875978 0.29231795 12 0.13535812 0.13790758 0 0 4 8
17000 461.07005 -2.4317694 -1.145154 3.2068452 0.14615898 6 0.1444739 0.14730804 0 0 2 4
18000 197.21207 -40.124433 -7.0857418 5.2906654 0.43847693 18 0.14403997 0.14574329 0 0 6 12
19000 393.36395 -420.49802 -11.172739 14.461366 0.5846359 24 0.15005606 0.15142063 0 0 8 16
20000 356.48539 56.071962 -1.7861789 4.2504609 0.21923846 9 0.15422732 0.15627984 0 0 3 6
Loop time of 19.5982 on 1 procs for 20000 steps with 9 atoms
Performance: 88.171 ns/day, 0.272 hours/ns, 1020.502 timesteps/s
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.3404 | 2.3404 | 2.3404 | 0.0 | 11.94
Bond | 0.033919 | 0.033919 | 0.033919 | 0.0 | 0.17
Kspace | 0.19974 | 0.19974 | 0.19974 | 0.0 | 1.02
Neigh | 0.11478 | 0.11478 | 0.11478 | 0.0 | 0.59
Comm | 0.22538 | 0.22538 | 0.22538 | 0.0 | 1.15
Output | 0.00096536 | 0.00096536 | 0.00096536 | 0.0 | 0.00
Modify | 16.627 | 16.627 | 16.627 | 0.0 | 84.84
Other | | 0.05594 | | | 0.29
Nlocal: 9.00000 ave 9 max 9 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 703.000 ave 703 max 703 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 719.000 ave 719 max 719 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 719
Ave neighs/atom = 79.888889
Ave special neighs/atom = 2.0000000
Neighbor list builds = 20196
Dangerous builds = 0
Total wall time: 0:00:19

2
src/BODY/fix_wall_body_polygon.cpp
View File

@ -195,7 +195,7 @@ void FixWallBodyPolygon::init()
void FixWallBodyPolygon::setup(int vflag)
{
if (strstr(update->integrate_style,"verlet"))
if (utils::strmatch(update->integrate_style,"^verlet"))
post_force(vflag);
}

2
src/BODY/fix_wall_body_polyhedron.cpp
View File

@ -202,7 +202,7 @@ void FixWallBodyPolyhedron::init()
void FixWallBodyPolyhedron::setup(int vflag)
{
if (strstr(update->integrate_style,"verlet"))
if (utils::strmatch(update->integrate_style,"^verlet"))
post_force(vflag);
}

4
src/CLASS2/pair_lj_class2.cpp
View File

@ -491,7 +491,7 @@ void PairLJClass2::init_style()
int irequest;
int respa = 0;
if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) {
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
}
@ -506,7 +506,7 @@ void PairLJClass2::init_style()
// set rRESPA cutoffs
if (strstr(update->integrate_style,"respa") &&
if (utils::strmatch(update->integrate_style,"^respa") &&
((Respa *) update->integrate)->level_inner >= 0)
cut_respa = ((Respa *) update->integrate)->cutoff;
else cut_respa = nullptr;

4
src/CLASS2/pair_lj_class2_coul_long.cpp
View File

@ -671,7 +671,7 @@ void PairLJClass2CoulLong::init_style()
int irequest;
int respa = 0;
if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) {
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
}
@ -688,7 +688,7 @@ void PairLJClass2CoulLong::init_style()
// set rRESPA cutoffs
if (strstr(update->integrate_style,"respa") &&
if (utils::strmatch(update->integrate_style,"^respa") &&
((Respa *) update->integrate)->level_inner >= 0)
cut_respa = ((Respa *) update->integrate)->cutoff;
else cut_respa = nullptr;

2
src/GPU/fix_gpu.cpp
View File

@ -297,7 +297,7 @@ void FixGPU::setup(int vflag)
error->all(FLERR,
"Cannot use neigh_modify exclude with GPU neighbor builds");
if (strstr(update->integrate_style,"verlet")) post_force(vflag);
if (utils::strmatch(update->integrate_style,"^verlet")) post_force(vflag);
else {
// In setup only, all forces calculated on GPU are put in the outer level
((Respa *) update->integrate)->copy_flevel_f(_nlevels_respa-1);

2
src/GPU/fix_nh_gpu.cpp
View File

@ -63,7 +63,7 @@ FixNHGPU::~FixNHGPU()
void FixNHGPU::setup(int vflag)
{
FixNH::setup(vflag);
if (strstr(update->integrate_style,"respa"))
if (utils::strmatch(update->integrate_style,"^respa"))
_respa_on = 1;
else
_respa_on = 0;

2
src/GPU/fix_nve_gpu.cpp
View File

@ -52,7 +52,7 @@ FixNVEGPU::~FixNVEGPU()
void FixNVEGPU::setup(int vflag)
{
FixNVE::setup(vflag);
if (strstr(update->integrate_style,"respa"))
if (utils::strmatch(update->integrate_style,"^respa"))
_respa_on = 1;
else
_respa_on = 0;

2
src/GPU/pppm_gpu.cpp
View File

@ -149,7 +149,7 @@ void PPPMGPU::init()
// GPU precision specific init
bool respa_value=false;
if (strstr(update->integrate_style,"respa"))
if (utils::strmatch(update->integrate_style,"^respa"))
respa_value=true;
if (order>8)

2
src/GRANULAR/fix_freeze.cpp
View File

@ -69,7 +69,7 @@ void FixFreeze::init()
void FixFreeze::setup(int vflag)
{
if (strstr(update->integrate_style,"verlet"))
if (utils::strmatch(update->integrate_style,"^verlet"))
post_force(vflag);
else {
int nlevels_respa = ((Respa *) update->integrate)->nlevels;

49
src/GRANULAR/fix_wall_gran.cpp
View File

@ -17,29 +17,25 @@
------------------------------------------------------------------------- */
#include "fix_wall_gran.h"
#include <cmath>
#include <cstring>
#include "atom.h"
#include "domain.h"
#include "update.h"
#include "error.h"
#include "force.h"
#include "modify.h"
#include "respa.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "modify.h"
#include "neighbor.h"
#include "respa.h"
#include "update.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace FixConst;
using namespace MathConst;
// XYZ PLANE need to be 0,1,2
enum{XPLANE=0,YPLANE=1,ZPLANE=2,ZCYLINDER,REGION};
enum{HOOKE,HOOKE_HISTORY,HERTZ_HISTORY,GRANULAR};
enum{NONE,CONSTANT,EQUAL};
#define PI27SQ 266.47931882941264802866 // 27*PI**2
#define THREEROOT3 5.19615242270663202362 // 3*sqrt(3)
#define SIXROOT6 14.69693845669906728801 // 6*sqrt(6)
@ -48,18 +44,20 @@ enum{NONE,CONSTANT,EQUAL};
#define THREEQUARTERS 0.75 // 3/4
#define TWOPI 6.28318530717959 // 2*PI
#define EPSILON 1e-10
enum {NORMAL_HOOKE, NORMAL_HERTZ, HERTZ_MATERIAL, DMT, JKR};
enum {VELOCITY, MASS_VELOCITY, VISCOELASTIC, TSUJI};
enum {TANGENTIAL_NOHISTORY, TANGENTIAL_HISTORY,
TANGENTIAL_MINDLIN, TANGENTIAL_MINDLIN_RESCALE};
enum {TWIST_NONE, TWIST_SDS, TWIST_MARSHALL};
enum {ROLL_NONE, ROLL_SDS};
#define BIG 1.0e20
#define EPSILON 1e-10
// XYZ PLANE need to be 0,1,2
enum {XPLANE=0,YPLANE=1,ZPLANE=2,ZCYLINDER,REGION};
enum {NONE,CONSTANT,EQUAL};
enum {DAMPING_NONE, VELOCITY, MASS_VELOCITY, VISCOELASTIC, TSUJI};
enum {TANGENTIAL_NONE, TANGENTIAL_NOHISTORY, TANGENTIAL_HISTORY,
TANGENTIAL_MINDLIN, TANGENTIAL_MINDLIN_RESCALE};
enum {TWIST_NONE, TWIST_SDS, TWIST_MARSHALL};
enum {ROLL_NONE, ROLL_SDS};
/* ---------------------------------------------------------------------- */
FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) :
@ -84,6 +82,10 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) :
use_history = restart_peratom = 1;
if (pairstyle == HOOKE) use_history = restart_peratom = 0;
tangential_history = roll_history = twist_history = 0;
normal_model = NORMAL_NONE;
tangential_model = TANGENTIAL_NONE;
damping_model = DAMPING_NONE;
// wall/particle coefficients
@ -120,7 +122,6 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) :
iarg = 4;
damping_model = VISCOELASTIC;
roll_model = twist_model = NONE;
tangential_history = roll_history = twist_history = 0;
while (iarg < narg) {
if (strcmp(arg[iarg], "hooke") == 0) {
if (iarg + 2 >= narg)
@ -464,7 +465,7 @@ void FixWallGran::init()
dt = update->dt;
if (strstr(update->integrate_style,"respa"))
if (utils::strmatch(update->integrate_style,"^respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
// check for FixRigid so can extract rigid body masses
@ -511,7 +512,7 @@ void FixWallGran::init()
void FixWallGran::setup(int vflag)
{
if (strstr(update->integrate_style,"verlet"))
if (utils::strmatch(update->integrate_style,"^verlet"))
post_force(vflag);
else {
((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);

4
src/GRANULAR/fix_wall_gran.h
View File

@ -26,6 +26,10 @@ namespace LAMMPS_NS {
class FixWallGran : public Fix {
public:
enum {HOOKE,HOOKE_HISTORY,HERTZ_HISTORY,GRANULAR};
enum {NORMAL_NONE, NORMAL_HOOKE, NORMAL_HERTZ, HERTZ_MATERIAL, DMT, JKR};
FixWallGran(class LAMMPS *, int, char **);
virtual ~FixWallGran();
int setmask();

33
src/GRANULAR/fix_wall_gran_region.cpp
View File

@ -16,26 +16,21 @@
------------------------------------------------------------------------- */
#include "fix_wall_gran_region.h"
#include <cstring>
#include "region.h"
#include "atom.h"
#include "domain.h"
#include "update.h"
#include "memory.h"
#include "error.h"
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "memory.h"
#include "neighbor.h"
#include "region.h"
#include "update.h"
#include <cstring>
using namespace LAMMPS_NS;
using namespace FixConst;
// same as FixWallGran
enum{HOOKE,HOOKE_HISTORY,HERTZ_HISTORY,GRANULAR};
enum {NORMAL_HOOKE, NORMAL_HERTZ, HERTZ_MATERIAL, DMT, JKR};
#define BIG 1.0e20
/* ---------------------------------------------------------------------- */
FixWallGranRegion::FixWallGranRegion(LAMMPS *lmp, int narg, char **arg) :
@ -186,7 +181,7 @@ void FixWallGranRegion::post_force(int /*vflag*/)
if (mask[i] & groupbit) {
if (!region->match(x[i][0],x[i][1],x[i][2])) continue;
if (pairstyle == GRANULAR && normal_model == JKR) {
if (pairstyle == FixWallGran::GRANULAR && normal_model == FixWallGran::JKR) {
nc = region->surface(x[i][0],x[i][1],x[i][2],
radius[i]+pulloff_distance(radius[i]));
}
@ -228,7 +223,7 @@ void FixWallGranRegion::post_force(int /*vflag*/)
rsq = region->contact[ic].r*region->contact[ic].r;
if (pairstyle == GRANULAR && normal_model == JKR) {
if (pairstyle == FixWallGran::GRANULAR && normal_model == FixWallGran::JKR) {
if (history_many[i][c2r[ic]][0] == 0.0 && rsq > radius[i]*radius[i]) {
for (m = 0; m < size_history; m++)
history_many[i][0][m] = 0.0;
@ -264,18 +259,18 @@ void FixWallGranRegion::post_force(int /*vflag*/)
else
contact = nullptr;
if (pairstyle == HOOKE)
if (pairstyle == FixWallGran::HOOKE)
hooke(rsq,dx,dy,dz,vwall,v[i],f[i],
omega[i],torque[i],radius[i],meff, contact);
else if (pairstyle == HOOKE_HISTORY)
else if (pairstyle == FixWallGran::HOOKE_HISTORY)
hooke_history(rsq,dx,dy,dz,vwall,v[i],f[i],
omega[i],torque[i],radius[i],meff,
history_many[i][c2r[ic]], contact);
else if (pairstyle == HERTZ_HISTORY)
else if (pairstyle == FixWallGran::HERTZ_HISTORY)
hertz_history(rsq,dx,dy,dz,vwall,region->contact[ic].radius,
v[i],f[i],omega[i],torque[i],
radius[i],meff,history_many[i][c2r[ic]], contact);
else if (pairstyle == GRANULAR)
else if (pairstyle == FixWallGran::GRANULAR)
granular(rsq,dx,dy,dz,vwall,region->contact[ic].radius,
v[i],f[i],omega[i],torque[i],
radius[i],meff,history_many[i][c2r[ic]],contact);

6
src/GRANULAR/pair_granular.cpp
View File

@ -446,9 +446,9 @@ void PairGranular::compute(int eflag, int vflag)
if (tangential_model[itype][jtype] == TANGENTIAL_MINDLIN_FORCE ||
tangential_model[itype][jtype] ==
TANGENTIAL_MINDLIN_RESCALE_FORCE)
frameupdate = fabs(rsht) < EPSILON*Fscrit;
frameupdate = fabs(rsht) > EPSILON*Fscrit;
else
frameupdate = fabs(rsht)*k_tangential < EPSILON*Fscrit;
frameupdate = fabs(rsht)*k_tangential > EPSILON*Fscrit;
if (frameupdate) {
shrmag = sqrt(history[0]*history[0] + history[1]*history[1] +
history[2]*history[2]);
@ -568,7 +568,7 @@ void PairGranular::compute(int eflag, int vflag)
if (historyupdate) {
rolldotn = history[rhist0]*nx + history[rhist1]*ny + history[rhist2]*nz;
frameupdate = fabs(rolldotn)*k_roll < EPSILON*Frcrit;
frameupdate = fabs(rolldotn)*k_roll > EPSILON*Frcrit;
if (frameupdate) { // rotate into tangential plane
rollmag = sqrt(history[rhist0]*history[rhist0] +
history[rhist1]*history[rhist1] +

1
src/KOKKOS/atom_vec_hybrid_kokkos.cpp
View File

@ -1171,7 +1171,6 @@ void AtomVecHybridKokkos::build_styles()
allstyles = new char*[nallstyles];
int n;
nallstyles = 0;
#define ATOM_CLASS
#define AtomStyle(key,Class) \

2
src/KOKKOS/fix_setforce_kokkos.cpp
View File

@ -67,7 +67,7 @@ void FixSetForceKokkos<DeviceType>::init()
{
FixSetForce::init();
if (strstr(update->integrate_style,"respa"))
if (utils::strmatch(update->integrate_style,"^respa"))
error->all(FLERR,"Cannot (yet) use respa with Kokkos");
}

2
src/KOKKOS/fix_shake_kokkos.cpp
View File

@ -156,7 +156,7 @@ void FixShakeKokkos<DeviceType>::init()
{
FixShake::init();
if (strstr(update->integrate_style,"respa"))
if (utils::strmatch(update->integrate_style,"^respa"))
error->all(FLERR,"Cannot yet use respa with Kokkos");
if (rattle)

2
src/KOKKOS/pair_buck_coul_cut_kokkos.cpp
View File

@ -285,7 +285,7 @@ void PairBuckCoulCutKokkos<DeviceType>::init_style()
// error if rRESPA with inner levels
if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) {
int respa = 0;
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;

2
src/KOKKOS/pair_buck_coul_long_kokkos.cpp
View File

@ -447,7 +447,7 @@ void PairBuckCoulLongKokkos<DeviceType>::init_style()
// error if rRESPA with inner levels
if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) {
int respa = 0;
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;

2
src/KOKKOS/pair_buck_kokkos.cpp
View File

@ -205,7 +205,7 @@ void PairBuckKokkos<DeviceType>::init_style()
// error if rRESPA with inner levels
if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) {
int respa = 0;
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;

2
src/KOKKOS/pair_coul_long_kokkos.cpp
View File

@ -405,7 +405,7 @@ void PairCoulLongKokkos<DeviceType>::init_style()
// error if rRESPA with inner levels
if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) {
int respa = 0;
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;

2
src/KOKKOS/pair_hybrid_kokkos.cpp
View File

@ -90,7 +90,7 @@ void PairHybridKokkos::compute(int eflag, int vflag)
Respa *respa = nullptr;
respaflag = 0;
if (strstr(update->integrate_style,"respa")) {
if (utils::strmatch(update->integrate_style,"^respa")) {
respa = (Respa *) update->integrate;
if (respa->nhybrid_styles > 0) respaflag = 1;
}

2
src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp
View File

@ -450,7 +450,7 @@ void PairLJCharmmCoulCharmmImplicitKokkos<DeviceType>::init_style()
// error if rRESPA with inner levels
if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) {
int respa = 0;
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;

2
src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp
View File

@ -451,7 +451,7 @@ void PairLJCharmmCoulCharmmKokkos<DeviceType>::init_style()
// error if rRESPA with inner levels
if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) {
int respa = 0;
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;

2
src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp
View File

@ -459,7 +459,7 @@ void PairLJCharmmCoulLongKokkos<DeviceType>::init_style()
// error if rRESPA with inner levels
if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) {
int respa = 0;
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;

2
src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp
View File

@ -287,7 +287,7 @@ void PairLJClass2CoulCutKokkos<DeviceType>::init_style()
// error if rRESPA with inner levels
if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) {
int respa = 0;
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;

2
src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp
View File

@ -442,7 +442,7 @@ void PairLJClass2CoulLongKokkos<DeviceType>::init_style()
// error if rRESPA with inner levels
if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) {
int respa = 0;
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;

2
src/KOKKOS/pair_lj_class2_kokkos.cpp
View File

@ -223,7 +223,7 @@ void PairLJClass2Kokkos<DeviceType>::init_style()
// error if rRESPA with inner levels
if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) {
int respa = 0;
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;

2
src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp
View File

@ -278,7 +278,7 @@ void PairLJCutCoulCutKokkos<DeviceType>::init_style()
// error if rRESPA with inner levels
if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) {
int respa = 0;
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;

2
src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp
View File

@ -307,7 +307,7 @@ void PairLJCutCoulDebyeKokkos<DeviceType>::init_style()
// error if rRESPA with inner levels
if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) {
int respa = 0;
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;

2
src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp
View File

@ -300,7 +300,7 @@ void PairLJCutCoulDSFKokkos<DeviceType>::init_style()
// error if rRESPA with inner levels
if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) {
int respa = 0;
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;

2
src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp
View File

@ -440,7 +440,7 @@ void PairLJCutCoulLongKokkos<DeviceType>::init_style()
// error if rRESPA with inner levels
if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) {
int respa = 0;
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;

2
src/KOKKOS/pair_lj_cut_kokkos.cpp
View File

@ -217,7 +217,7 @@ void PairLJCutKokkos<DeviceType>::init_style()
// error if rRESPA with inner levels
if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) {
int respa = 0;
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;

2
src/KOKKOS/pair_lj_expand_kokkos.cpp
View File

@ -227,7 +227,7 @@ void PairLJExpandKokkos<DeviceType>::init_style()
// error if rRESPA with inner levels
if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) {
int respa = 0;
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;

2
src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp
View File

@ -436,7 +436,7 @@ void PairLJGromacsCoulGromacsKokkos<DeviceType>::init_style()
// error if rRESPA with inner levels
if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) {
int respa = 0;
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;

2
src/KOKKOS/pair_lj_gromacs_kokkos.cpp
View File

@ -272,7 +272,7 @@ void PairLJGromacsKokkos<DeviceType>::init_style()
// error if rRESPA with inner levels
if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) {
int respa = 0;
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;

2
src/KOKKOS/pair_lj_sdk_kokkos.cpp
View File

@ -255,7 +255,7 @@ void PairLJSDKKokkos<DeviceType>::init_style()
// error if rRESPA with inner levels
if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) {
int respa = 0;
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;

2
src/KOKKOS/pair_morse_kokkos.cpp
View File

@ -234,7 +234,7 @@ void PairMorseKokkos<DeviceType>::init_style()
// error if rRESPA with inner levels
if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) {
int respa = 0;
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;

2
src/KOKKOS/pair_yukawa_kokkos.cpp
View File

@ -107,7 +107,7 @@ void PairYukawaKokkos<DeviceType>::init_style()
// error if rRESPA with inner levels
if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) {
int respa = 0;
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;

2
src/KOKKOS/pair_zbl_kokkos.cpp
View File

@ -81,7 +81,7 @@ void PairZBLKokkos<DeviceType>::init_style()
// error if rRESPA with inner levels
if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) {
int respa = 0;
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;

4
src/KSPACE/pair_buck_long_coul_long.cpp
View File

@ -248,7 +248,7 @@ void PairBuckLongCoulLong::init_style()
// set rRESPA cutoffs
if (strstr(update->integrate_style,"respa") &&
if (utils::strmatch(update->integrate_style,"^respa") &&
((Respa *) update->integrate)->level_inner >= 0)
cut_respa = ((Respa *) update->integrate)->cutoff;
else cut_respa = nullptr;
@ -264,7 +264,7 @@ void PairBuckLongCoulLong::init_style()
int irequest;
int respa = 0;
if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) {
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
}

4
src/KSPACE/pair_lj_charmmfsw_coul_long.cpp
View File

@ -740,7 +740,7 @@ void PairLJCharmmfswCoulLong::init_style()
int irequest;
int respa = 0;
if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) {
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
}
@ -779,7 +779,7 @@ void PairLJCharmmfswCoulLong::init_style()
// set & error check interior rRESPA cutoffs
if (strstr(update->integrate_style,"respa") &&
if (utils::strmatch(update->integrate_style,"^respa") &&
((Respa *) update->integrate)->level_inner >= 0) {
cut_respa = ((Respa *) update->integrate)->cutoff;
if (MIN(cut_lj,cut_coul) < cut_respa[3])

4
src/KSPACE/pair_lj_long_coul_long.cpp
View File

@ -242,7 +242,7 @@ void PairLJLongCoulLong::init_style()
// set rRESPA cutoffs
if (strstr(update->integrate_style,"respa") &&
if (utils::strmatch(update->integrate_style,"^respa") &&
((Respa *) update->integrate)->level_inner >= 0)
cut_respa = ((Respa *) update->integrate)->cutoff;
else cut_respa = nullptr;
@ -258,7 +258,7 @@ void PairLJLongCoulLong::init_style()
int irequest;
int respa = 0;
if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) {
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
}

2
src/MANYBODY/fix_qeq_comb.cpp
View File

@ -138,7 +138,7 @@ void FixQEQComb::init()
void FixQEQComb::setup(int vflag)
{
firstflag = 1;
if (strstr(update->integrate_style,"verlet"))
if (utils::strmatch(update->integrate_style,"^verlet"))
post_force(vflag);
else {
((Respa *) update->integrate)->copy_flevel_f(ilevel_respa);

2
src/MC/fix_bond_break.cpp
View File

@ -143,7 +143,7 @@ int FixBondBreak::setmask()
void FixBondBreak::init()
{
if (strstr(update->integrate_style,"respa"))
if (utils::strmatch(update->integrate_style,"^respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
// enable angle/dihedral/improper breaking if any defined

2
src/MC/fix_bond_create.cpp
View File

@ -232,7 +232,7 @@ int FixBondCreate::setmask()
void FixBondCreate::init()
{
if (strstr(update->integrate_style,"respa"))
if (utils::strmatch(update->integrate_style,"^respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
// check cutoff for iatomtype,jatomtype

4
src/MISC/fix_efield.cpp
View File

@ -209,7 +209,7 @@ void FixEfield::init()
update->whichflag == 2 && estyle == NONE)
error->all(FLERR,"Must use variable energy with fix efield");
if (strstr(update->integrate_style,"respa")) {
if (utils::strmatch(update->integrate_style,"^respa")) {
ilevel_respa = ((Respa *) update->integrate)->nlevels-1;
if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa);
}
@ -219,7 +219,7 @@ void FixEfield::init()
void FixEfield::setup(int vflag)
{
if (strstr(update->integrate_style,"verlet"))
if (utils::strmatch(update->integrate_style,"^verlet"))
post_force(vflag);
else {
((Respa *) update->integrate)->copy_flevel_f(ilevel_respa);

2
src/MISC/fix_gld.cpp
View File

@ -206,7 +206,7 @@ void FixGLD::init()
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
if (strstr(update->integrate_style,"respa"))
if (utils::strmatch(update->integrate_style,"^respa"))
step_respa = ((Respa *) update->integrate)->step;
}

4
src/MISC/fix_orient_bcc.cpp
View File

@ -202,7 +202,7 @@ int FixOrientBCC::setmask()
void FixOrientBCC::init()
{
if (strstr(update->integrate_style,"respa")) {
if (utils::strmatch(update->integrate_style,"^respa")) {
ilevel_respa = ((Respa *) update->integrate)->nlevels-1;
if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa);
}
@ -228,7 +228,7 @@ void FixOrientBCC::init_list(int /*id*/, NeighList *ptr)
void FixOrientBCC::setup(int vflag)
{
if (strstr(update->integrate_style,"verlet"))
if (utils::strmatch(update->integrate_style,"^verlet"))
post_force(vflag);
else {
((Respa *) update->integrate)->copy_flevel_f(ilevel_respa);

4
src/MISC/fix_orient_fcc.cpp
View File

@ -200,7 +200,7 @@ int FixOrientFCC::setmask()
void FixOrientFCC::init()
{
if (strstr(update->integrate_style,"respa")) {
if (utils::strmatch(update->integrate_style,"^respa")) {
ilevel_respa = ((Respa *) update->integrate)->nlevels-1;
if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa);
}
@ -226,7 +226,7 @@ void FixOrientFCC::init_list(int /*id*/, NeighList *ptr)
void FixOrientFCC::setup(int vflag)
{
if (strstr(update->integrate_style,"verlet"))
if (utils::strmatch(update->integrate_style,"^verlet"))
post_force(vflag);
else {
((Respa *) update->integrate)->copy_flevel_f(ilevel_respa);

2
src/MISC/fix_ttm.cpp
View File

@ -207,7 +207,7 @@ void FixTTM::init()
for (int iznode = 0; iznode < nznodes; iznode++)
net_energy_transfer_all[ixnode][iynode][iznode] = 0;
if (strstr(update->integrate_style,"respa"))
if (utils::strmatch(update->integrate_style,"^respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}

2
src/MOLECULE/dihedral_charmm.cpp
View File

@ -368,7 +368,7 @@ void DihedralCharmm::coeff(int narg, char **arg)
void DihedralCharmm::init_style()
{
if (strstr(update->integrate_style,"respa")) {
if (utils::strmatch(update->integrate_style,"^respa")) {
Respa *r = (Respa *) update->integrate;
if (r->level_pair >= 0 && (r->level_pair != r->level_dihedral))
error->all(FLERR,"Dihedral style charmm must be set to same"

2
src/MOLECULE/dihedral_charmmfsw.cpp
View File

@ -386,7 +386,7 @@ void DihedralCharmmfsw::coeff(int narg, char **arg)
void DihedralCharmmfsw::init_style()
{
if (strstr(update->integrate_style,"respa")) {
if (utils::strmatch(update->integrate_style,"^respa")) {
Respa *r = (Respa *) update->integrate;
if (r->level_pair >= 0 && (r->level_pair != r->level_dihedral))
error->all(FLERR,"Dihedral style charmmfsw must be set to same"

17
src/MOLECULE/fix_cmap.cpp
View File

@ -81,6 +81,8 @@ FixCMAP::FixCMAP(LAMMPS *lmp, int narg, char **arg) :
extvector = 1;
wd_header = 1;
wd_section = 1;
respa_level_support = 1;
ilevel_respa = 0;
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
@ -182,6 +184,11 @@ void FixCMAP::init()
// define newton_bond here in case restart file was read (not data file)
newton_bond = force->newton_bond;
if (utils::strmatch(update->integrate_style,"^respa")) {
ilevel_respa = ((Respa *) update->integrate)->nlevels-1;
if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa);
}
}
/* --------------------------------------------------------------------- */
@ -190,12 +197,12 @@ void FixCMAP::setup(int vflag)
{
pre_neighbor();
if (strstr(update->integrate_style,"verlet"))
if (utils::strmatch(update->integrate_style,"^verlet"))
post_force(vflag);
else {
((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
post_force_respa(vflag,nlevels_respa-1,0);
((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
((Respa *) update->integrate)->copy_flevel_f(ilevel_respa);
post_force_respa(vflag,ilevel_respa,0);
((Respa *) update->integrate)->copy_f_flevel(ilevel_respa);
}
}
@ -596,7 +603,7 @@ void FixCMAP::post_force(int vflag)
void FixCMAP::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
if (ilevel == ilevel_respa) post_force(vflag);
}
/* ---------------------------------------------------------------------- */

2
src/MOLECULE/fix_cmap.h
View File

@ -67,7 +67,7 @@ class FixCMAP : public Fix {
private:
int nprocs,me;
int newton_bond,eflag_caller;
int ctype,nlevels_respa;
int ctype,ilevel_respa;
int ncrosstermtypes,crossterm_per_atom,maxcrossterm;
int ncrosstermlist;
bigint ncmap;

2
src/POEMS/fix_poems.cpp
View File

@ -389,7 +389,7 @@ void FixPOEMS::init()
// rRESPA info
if (strstr(update->integrate_style,"respa")) {
if (utils::strmatch(update->integrate_style,"^respa")) {
step_respa = ((Respa *) update->integrate)->step;
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}

4
src/PYTHON/python_impl.cpp
View File

@ -56,6 +56,8 @@ PythonImpl::PythonImpl(LAMMPS *lmp) : Pointers(lmp)
nfunc = 0;
pfuncs = nullptr;
#if PY_MAJOR_VERSION >= 3
#ifndef Py_LIMITED_API
// check for PYTHONUNBUFFERED environment variable
const char * PYTHONUNBUFFERED = getenv("PYTHONUNBUFFERED");
@ -64,6 +66,8 @@ PythonImpl::PythonImpl(LAMMPS *lmp) : Pointers(lmp)
// Force the stdout and stderr streams to be unbuffered.
Py_UnbufferedStdioFlag = 1;
}
#endif
#endif
// one-time initialization of Python interpreter
// pyMain stores pointer to main module

2
src/QEQ/fix_qeq_dynamic.cpp
View File

@ -78,7 +78,7 @@ void FixQEqDynamic::init()
error->warning(FLERR,"Fix qeq/dynamic tolerance may be too small"
" for damped dynamics");
if (strstr(update->integrate_style,"respa"))
if (utils::strmatch(update->integrate_style,"^respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}

2
src/QEQ/fix_qeq_fire.cpp
View File

@ -91,7 +91,7 @@ void FixQEqFire::init()
error->warning(FLERR,"Fix qeq/fire tolerance may be too small"
" for damped fires");
if (strstr(update->integrate_style,"respa"))
if (utils::strmatch(update->integrate_style,"^respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
comb = (PairComb *) force->pair_match("comb",1);

2
src/QEQ/fix_qeq_point.cpp
View File

@ -57,7 +57,7 @@ void FixQEqPoint::init()
int ntypes = atom->ntypes;
memory->create(shld,ntypes+1,ntypes+1,"qeq:shielding");
if (strstr(update->integrate_style,"respa"))
if (utils::strmatch(update->integrate_style,"^respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}

2
src/QEQ/fix_qeq_shielded.cpp
View File

@ -68,7 +68,7 @@ void FixQEqShielded::init()
error->all(FLERR,"Invalid param file for fix qeq/shielded");
}
if (strstr(update->integrate_style,"respa"))
if (utils::strmatch(update->integrate_style,"^respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}

2
src/QEQ/fix_qeq_slater.cpp
View File

@ -79,7 +79,7 @@ void FixQEqSlater::init()
error->all(FLERR,"Invalid param file for fix qeq/slater");
}
if (strstr(update->integrate_style,"respa"))
if (utils::strmatch(update->integrate_style,"^respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}

21
src/RIGID/fix_rigid.cpp
View File

@ -720,17 +720,14 @@ void FixRigid::init()
}
}
// error if npt,nph fix comes before rigid fix
for (i = 0; i < modify->nfix; i++) {
if (strcmp(modify->fix[i]->style,"npt") == 0) break;
if (strcmp(modify->fix[i]->style,"nph") == 0) break;
}
// error if a fix changing the box comes before rigid fix
for (i = 0; i < modify->nfix; i++)
if (modify->fix[i]->box_change) break;
if (i < modify->nfix) {
for (int j = i; j < modify->nfix; j++)
if (strcmp(modify->fix[j]->style,"rigid") == 0)
error->all(FLERR,"Rigid fix must come before NPT/NPH fix");
for (int j = i+1; j < modify->nfix; j++)
if (utils::strmatch(modify->fix[j]->style,"^rigid"))
error->all(FLERR,"Rigid fixes must come before any box changing fix");
}
// add gravity forces based on gravity vector from fix
@ -738,8 +735,8 @@ void FixRigid::init()
if (id_gravity) {
int ifix = modify->find_fix(id_gravity);
if (ifix < 0) error->all(FLERR,"Fix rigid cannot find fix gravity ID");
if (strcmp(modify->fix[ifix]->style,"gravity") != 0)
error->all(FLERR,"Fix rigid gravity fix is invalid");
if (!utils::strmatch(modify->fix[ifix]->style,"^gravity"))
error->all(FLERR,"Fix rigid gravity fix ID is not a gravity fix style");
int tmp;
gvec = (double *) modify->fix[ifix]->extract("gvec",tmp);
}
@ -750,7 +747,7 @@ void FixRigid::init()
dtf = 0.5 * update->dt * force->ftm2v;
dtq = 0.5 * update->dt;
if (strstr(update->integrate_style,"respa"))
if (utils::strmatch(update->integrate_style,"^respa"))
step_respa = ((Respa *) update->integrate)->step;
// setup rigid bodies, using current atom info. if reinitflag is not set,

37
src/RIGID/fix_rigid_nh_small.cpp
View File

@ -19,22 +19,24 @@
#include "fix_rigid_nh_small.h"
#include <cmath>
#include <cstring>
#include "math_extra.h"
#include "atom.h"
#include "comm.h"
#include "compute.h"
#include "domain.h"
#include "update.h"
#include "modify.h"
#include "fix_deform.h"
#include "group.h"
#include "comm.h"
#include "force.h"
#include "kspace.h"
#include "memory.h"
#include "error.h"
#include "fix_deform.h"
#include "force.h"
#include "group.h"
#include "kspace.h"
#include "math_extra.h"
#include "memory.h"
#include "modify.h"
#include "molecule.h"
#include "rigid_const.h"
#include "update.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace FixConst;
@ -1365,6 +1367,19 @@ int FixRigidNHSmall::modify_param(int narg, char **arg)
return FixRigidSmall::modify_param(narg,arg);
}
/* ----------------------------------------------------------------------
disallow using fix rigid/n??/small fixes with fix deposit
we would need custom functionality to update data structures
used by all fixes derived from this class but not fix rigid/small
------------------------------------------------------------------------- */
void FixRigidNHSmall::set_molecule(int, tagint, int,
double *, double *, double *)
{
error->all(FLERR,fmt::format("Molecule update not (yet) implemented for "
"fix {}", style));
}
/* ---------------------------------------------------------------------- */
void FixRigidNHSmall::allocate_chain()

1
src/RIGID/fix_rigid_nh_small.h
View File

@ -80,6 +80,7 @@ class FixRigidNHSmall : public FixRigidSmall {
void nh_epsilon_dot();
void compute_dof();
void set_molecule(int, tagint, int, double *, double *, double *);
void allocate_chain();
void allocate_order();
void deallocate_chain();

20
src/RIGID/fix_rigid_small.cpp
View File

@ -571,16 +571,14 @@ void FixRigidSmall::init()
}
}
// error if npt,nph fix comes before rigid fix
// error if a fix changing the box comes before rigid fix
for (i = 0; i < modify->nfix; i++) {
if (strcmp(modify->fix[i]->style,"npt") == 0) break;
if (strcmp(modify->fix[i]->style,"nph") == 0) break;
}
for (i = 0; i < modify->nfix; i++)
if (modify->fix[i]->box_change) break;
if (i < modify->nfix) {
for (int j = i; j < modify->nfix; j++)
if (strcmp(modify->fix[j]->style,"rigid") == 0)
error->all(FLERR,"Rigid fix must come before NPT/NPH fix");
for (int j = i+1; j < modify->nfix; j++)
if (utils::strmatch(modify->fix[j]->style,"^rigid"))
error->all(FLERR,"Rigid fixes must come before any box changing fix");
}
// add gravity forces based on gravity vector from fix
@ -588,8 +586,8 @@ void FixRigidSmall::init()
if (id_gravity) {
int ifix = modify->find_fix(id_gravity);
if (ifix < 0) error->all(FLERR,"Fix rigid/small cannot find fix gravity ID");
if (strcmp(modify->fix[ifix]->style,"gravity") != 0)
error->all(FLERR,"Fix rigid/small gravity fix is invalid");
if (!utils::strmatch(modify->fix[ifix]->style,"^gravity"))
error->all(FLERR,"Fix rigid gravity fix ID is not a gravity fix style");
int tmp;
gvec = (double *) modify->fix[ifix]->extract("gvec",tmp);
}
@ -600,7 +598,7 @@ void FixRigidSmall::init()
dtf = 0.5 * update->dt * force->ftm2v;
dtq = 0.5 * update->dt;
if (strstr(update->integrate_style,"respa"))
if (utils::strmatch(update->integrate_style,"^respa"))
step_respa = ((Respa *) update->integrate)->step;
}

2
src/RIGID/fix_rigid_small.h
View File

@ -43,7 +43,7 @@ class FixRigidSmall : public Fix {
void grow_arrays(int);
void copy_arrays(int, int, int);
void set_arrays(int);
void set_molecule(int, tagint, int, double *, double *, double *);
virtual void set_molecule(int, tagint, int, double *, double *, double *);
int pack_exchange(int, double *);
int unpack_exchange(int, double *);

4
src/RIGID/fix_shake.cpp
View File

@ -456,7 +456,7 @@ void FixShake::setup(int vflag)
// set respa to 0 if verlet is used and to 1 otherwise
if (strstr(update->integrate_style,"verlet"))
if (utils::strmatch(update->integrate_style,"^verlet"))
respa = 0;
else
respa = 1;
@ -2956,7 +2956,7 @@ void FixShake::unpack_forward_comm(int n, int first, double *buf)
void FixShake::reset_dt()
{
if (strstr(update->integrate_style,"verlet")) {
if (utils::strmatch(update->integrate_style,"^verlet")) {
dtv = update->dt;
if (rattle) dtfsq = 0.5 * update->dt * update->dt * force->ftm2v;
else dtfsq = update->dt * update->dt * force->ftm2v;

4
src/SPIN/fix_precession_spin.cpp
View File

@ -186,7 +186,7 @@ void FixPrecessionSpin::init()
k1ch = k1c/hbar;
k2ch = k2c/hbar;
if (strstr(update->integrate_style,"respa")) {
if (utils::strmatch(update->integrate_style,"^respa")) {
ilevel_respa = ((Respa *) update->integrate)->nlevels-1;
if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa);
}
@ -225,7 +225,7 @@ void FixPrecessionSpin::init()
void FixPrecessionSpin::setup(int vflag)
{
if (strstr(update->integrate_style,"verlet"))
if (utils::strmatch(update->integrate_style,"^verlet"))
post_force(vflag);
else {
((Respa *) update->integrate)->copy_flevel_f(ilevel_respa);

4
src/USER-BOCS/fix_bocs.cpp
View File

@ -590,7 +590,7 @@ void FixBocs::init()
if (force->kspace) kspace_flag = 1;
else kspace_flag = 0;
if (strstr(update->integrate_style,"respa")) {
if (utils::strmatch(update->integrate_style,"^respa")) {
nlevels_respa = ((Respa *) update->integrate)->nlevels;
step_respa = ((Respa *) update->integrate)->step;
dto = 0.5*step_respa[0];
@ -1850,7 +1850,7 @@ void FixBocs::reset_dt()
// If using respa, then remap is performed in innermost level
if (strstr(update->integrate_style,"respa"))
if (utils::strmatch(update->integrate_style,"^respa"))
dto = 0.5*step_respa[0];
if (pstat_flag)

4
src/USER-COLVARS/fix_colvars.cpp
View File

@ -412,7 +412,7 @@ void FixColvars::init()
if ((me == 0) && (update->whichflag == 2))
error->warning(FLERR,"Using fix colvars with minimization");
if (strstr(update->integrate_style,"respa"))
if (utils::strmatch(update->integrate_style,"^respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}
@ -680,7 +680,7 @@ void FixColvars::setup(int vflag)
proxy->setup();
// initialize forces
if (strstr(update->integrate_style,"verlet") || (update->whichflag == 2))
if (utils::strmatch(update->integrate_style,"^verlet") || (update->whichflag == 2))
post_force(vflag);
else {
((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);

4
src/USER-COLVARS/ndx_group.cpp
View File

@ -78,7 +78,6 @@ void Ndx2Group::command(int narg, char **arg)
int len;
bigint num;
FILE *fp;
tagint *tagbuf;
std::string name = "", next;
if (narg < 1) error->all(FLERR,"Illegal ndx2group command");
@ -191,11 +190,10 @@ void Ndx2Group::create(const std::string &name, const std::vector<tagint> &tags)
// map from global to local
const int nlocal = atom->nlocal;
int *flags = (int *)calloc(nlocal,sizeof(int));
for (bigint i=0; i < tags.size(); ++i) {
for (bigint i=0; i < (int)tags.size(); ++i) {
const int id = atom->map(tags[i]);
if (id < nlocal && id >= 0) flags[id] = 1;
}
group->create(name,flags);
free(flags);
}

1
src/USER-DPD/pair_exp6_rx.cpp
View File

@ -587,7 +587,6 @@ void PairExp6rx::coeff(int narg, char **arg)
if (!allocated) allocate();
int ilo,ihi,jlo,jhi;
int n;
utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error);
utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error);

2
src/USER-DRUDE/fix_langevin_drude.cpp
View File

@ -156,7 +156,7 @@ void FixLangevinDrude::init()
void FixLangevinDrude::setup(int /*vflag*/)
{
if (!strstr(update->integrate_style,"verlet"))
if (!utils::strmatch(update->integrate_style,"^verlet"))
error->all(FLERR,"RESPA style not compatible with fix langevin/drude");
if (!comm->ghost_velocity)
error->all(FLERR,"fix langevin/drude requires ghost velocities. Use comm_modify vel yes");

4
src/USER-DRUDE/fix_tgnh_drude.cpp
View File

@ -671,7 +671,7 @@ void FixTGNHDrude::init()
if (force->kspace) kspace_flag = 1;
else kspace_flag = 0;
if (strstr(update->integrate_style,"respa")) {
if (utils::strmatch(update->integrate_style,"^respa")) {
nlevels_respa = ((Respa *) update->integrate)->nlevels;
step_respa = ((Respa *) update->integrate)->step;
dto = 0.5*step_respa[0];
@ -1593,7 +1593,7 @@ void FixTGNHDrude::reset_dt()
// If using respa, then remap is performed in innermost level
if (strstr(update->integrate_style,"respa"))
if (utils::strmatch(update->integrate_style,"^respa"))
dto = 0.5*step_respa[0];
}

2
src/USER-EFF/fix_nve_eff.cpp
View File

@ -58,7 +58,7 @@ void FixNVEEff::init()
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
if (strstr(update->integrate_style,"respa"))
if (utils::strmatch(update->integrate_style,"^respa"))
step_respa = ((Respa *) update->integrate)->step;
}

2
src/USER-FEP/fix_adapt_fep.cpp
View File

@ -356,7 +356,7 @@ void FixAdaptFEP::init()
fix_chg = (FixStore *) modify->fix[ifix];
}
if (strstr(update->integrate_style,"respa"))
if (utils::strmatch(update->integrate_style,"^respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}

2
src/USER-INTEL/fix_nh_intel.cpp
View File

@ -317,7 +317,7 @@ void FixNHIntel::reset_dt()
// If using respa, then remap is performed in innermost level
if (strstr(update->integrate_style,"respa"))
if (utils::strmatch(update->integrate_style,"^respa"))
dto = 0.5*step_respa[0];
if (pstat_flag)

4
src/USER-LB/fix_lb_viscous.cpp
View File

@ -79,7 +79,7 @@ int FixLbViscous::setmask()
void FixLbViscous::init()
{
if (strcmp(update->integrate_style,"respa") == 0)
if (utils::strmatch(update->integrate_style,"^respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}
@ -88,7 +88,7 @@ void FixLbViscous::init()
void FixLbViscous::setup(int vflag)
{
if (strstr(update->integrate_style,"verlet") != nullptr)
if (utils::strmatch(update->integrate_style,"^verlet"))
post_force(vflag);
else {
((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);

2
src/USER-MANIFOLD/fix_manifoldforce.cpp
View File

@ -120,7 +120,7 @@ void FixManifoldForce::init()
void FixManifoldForce::setup(int vflag)
{
if (strstr(update->integrate_style,"verlet"))
if (utils::strmatch(update->integrate_style,"^verlet"))
post_force(vflag);
else {
int nlevels_respa = ((Respa *) update->integrate)->nlevels;

5
src/USER-MISC/dihedral_table_cut.cpp
View File

@ -134,11 +134,6 @@ static double cyc_splintD(double const *xa,
} // cyc_splintD()
// --------------------------------------------
// ------- Calculate the dihedral angle -------
// --------------------------------------------
static const int g_dim=3;
/* ---------------------------------------------------------------------- */
DihedralTableCut::DihedralTableCut(LAMMPS *lmp) : DihedralTable(lmp)

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