Merge branch 'develop' into dhairyaiitb_develop
This commit is contained in:
Axel Kohlmeyer
2
.github/CODEOWNERS
vendored
2
.github/CODEOWNERS
vendored
@ -72,6 +72,8 @@ src/EXTRA-COMMAND/ndx_group.* @akohlmey
|
||||
src/EXTRA-COMPUTE/compute_stress_mop*.* @RomainVermorel
|
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src/EXTRA-COMPUTE/compute_born_matrix.* @Bibobu @athomps
|
||||
src/EXTRA-FIX/fix_deform_pressure.* @jtclemm
|
||||
src/EXTRA-PAIR/pair_dispersion_d3.* @soniasolomoni @arthurfl
|
||||
src/EXTRA-PAIR/d3_parameters.h @soniasolomoni @arthurfl
|
||||
src/MISC/*_tracker.* @jtclemm
|
||||
src/MC/fix_gcmc.* @athomps
|
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src/MC/fix_sgcmc.* @athomps
|
||||
|
||||
@ -87,7 +87,7 @@ values in the vector. The *sumsq* option sums the square of the
|
||||
values in the vector into a global total. The *avesq* setting does
|
||||
the same as *sumsq*, then divides the sum of squares by the number of
|
||||
values. The last two options can be useful for calculating the
|
||||
variance of some quantity (e.g., variance = sumsq :math:`-` ave\
|
||||
variance of some quantity (e.g., variance = *avesq* :math:`-` *ave*\
|
||||
:math:`^2`). The *sumabs* option sums the absolute values in the
|
||||
vector into a global total. The *aveabs* setting does the same as
|
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*sumabs*, then divides the sum of absolute values by the number of
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@ -54,7 +54,7 @@ the Langevin equation such as:
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||||
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||||
f_P = & \frac{N k_B T_{target}}{V} + \frac{1}{V d}\sum_{i=1}^{N} \vec r_i \cdot \vec f_i - P_{target} \\
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||||
Q\ddot{L} + \alpha{}\dot{L} = & f_P + \beta(t)\\
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||||
L^{n+1} = & L^{n} + bdt\dot{L}^{n} \frac{bdt^{2}}{2Q} \\
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||||
L^{n+1} = & L^{n} + bdt\dot{L}^{n} + \frac{bdt^{2}}{2Q} f^{n}_{P} + \frac{bdt}{2Q} \beta^{n+1} \\
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||||
\dot{L}^{n+1} = & \alpha\dot{L}^{n} + \frac{dt}{2Q}\left(a f^{n}_{P} + f^{n+1}_{P}\right) + \frac{b}{Q}\beta^{n+1} \\
|
||||
a = & \frac{1-\frac{\alpha{}dt}{2Q}}{1+\frac{\alpha{}dt}{2Q}} \\
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b = & \frac{1}{1+\frac{\alpha{}dt}{2Q}} \\
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|
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@ -10,7 +10,7 @@ Syntax
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pair_style dispersion/d3 damping functional cutoff cn_cutoff
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* damping = damping function: *zero*, *zerom*, *bj*, or *bjm*
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||||
* damping = damping function: *original*, *zerom*, *bj*, or *bjm*
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* functional = XC functional form: *pbe*, *pbe0*, ... (see list below)
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* cutoff = global cutoff (distance units)
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||||
* cn_cutoff = coordination number cutoff (distance units)
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@ -20,7 +20,7 @@ Examples
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|
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.. code-block:: LAMMPS
|
||||
|
||||
pair_style dispersion/d3 zero pbe 30.0 20.0
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pair_style dispersion/d3 original pbe 30.0 20.0
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pair_coeff * * C
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|
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Description
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@ -55,9 +55,16 @@ factor, and :math:`f_n^{damp}` are damping functions.
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contributions, according to, for example, the Axilrod-Teller-Muto
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||||
model.
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Available damping functions are the original "zero-damping"
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||||
:ref:`(Grimme1) <Grimme1>`, Becke-Johnson damping :ref:`(Grimme2)
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||||
<Grimme2>`, and their revised forms :ref:`(Sherrill) <Sherrill>`.
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||||
.. versionchanged:: TBD
|
||||
|
||||
renamed *zero* keyword to *original* to avoid conflicts with
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:doc:`pair style zero <pair_zero>` when used as :doc:`hybrid
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||||
sub-style <pair_hybrid>`.
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||||
|
||||
Available damping functions are the original "zero-damping" (*original*)
|
||||
:ref:`(Grimme1) <Grimme1>`, Becke-Johnson damping (*bj*) :ref:`(Grimme2)
|
||||
<Grimme2>`, and their revised forms (*zerom* and *bjm*, respectively)
|
||||
:ref:`(Sherrill) <Sherrill>`.
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||||
|
||||
Available XC functional scaling factors are listed in the table below,
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||||
and depend on the selected damping function.
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||||
@ -67,7 +74,7 @@ and depend on the selected damping function.
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||||
+==================+================================================================================+
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| | | | slater-dirac-exchange, b-lyp, b-p, b97-d, revpbe, pbe, pbesol, rpw86-pbe, |
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||||
| | | | rpbe, tpss, b3-lyp, pbe0, hse06, revpbe38, pw6b95, tpss0, b2-plyp, pwpb95, |
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||||
| | zero | | b2gp-plyp, ptpss, hf, mpwlyp, bpbe, bh-lyp, tpssh, pwb6k, b1b95, bop, o-lyp, |
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||||
| | original | | b2gp-plyp, ptpss, hf, mpwlyp, bpbe, bh-lyp, tpssh, pwb6k, b1b95, bop, o-lyp, |
|
||||
| | | | o-pbe, ssb, revssb, otpss, b3pw91, revpbe0, pbe38, mpw1b95, mpwb1k, bmk, |
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||||
| | | | cam-b3lyp, lc-wpbe, m05, m052x, m06l, m06, m062x, m06hf, hcth120 |
|
||||
+------------------+--------------------------------------------------------------------------------+
|
||||
@ -122,6 +129,8 @@ Style *dispersion/d3* is part of the EXTRA-PAIR package. It is only
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||||
enabled if LAMMPS was built with that package. See the :doc:`Build
|
||||
package <Build_package>` page for more info.
|
||||
|
||||
The compiled in parameters require the use of :doc:`metal units <units>`.
|
||||
|
||||
It is currently *not* possible to calculate three-body dispersion
|
||||
contributions according to, for example, the Axilrod-Teller-Muto model.
|
||||
|
||||
|
||||
@ -40,7 +40,7 @@ Syntax
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||||
*plane* args = px py pz nx ny nz
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px,py,pz = point on the plane (distance units)
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||||
nx,ny,nz = direction normal to plane (distance units)
|
||||
px,py,pz can be a variable (see below)
|
||||
px,py,pz,nx,ny,nz can be a variable (see below)
|
||||
*prism* args = xlo xhi ylo yhi zlo zhi xy xz yz
|
||||
xlo,xhi,ylo,yhi,zlo,zhi = bounds of untilted prism (distance units)
|
||||
xy = distance to tilt y in x direction (distance units)
|
||||
@ -211,9 +211,11 @@ equal-style :doc:`variable <variable>`. Likewise, for style *sphere*
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||||
and *ellipsoid* the x-, y-, and z- coordinates of the center of the
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||||
sphere/ellipsoid can be specified as an equal-style variable. And for
|
||||
style *cylinder* the two center positions c1 and c2 for the location of
|
||||
the cylinder axes can be specified as a equal-style variable. For style
|
||||
*cone* and *prism* all properties can be defined via equal-style variables. For
|
||||
style *plane* the point can be defined via equal-style variables.
|
||||
the cylinder axes can be specified as a equal-style variable. For styles
|
||||
*block*, *cone*, *prism*, and *plane* all properties can be defined via
|
||||
equal-style variables. For style *plane*, the components of the direction
|
||||
vector normal to plane should be either all constants or all defined by
|
||||
equal-style variables.
|
||||
|
||||
If the value is a variable, it should be specified as v_name, where
|
||||
name is the variable name. In this case, the variable will be
|
||||
@ -226,6 +228,21 @@ keywords for the simulation box parameters and timestep and elapsed
|
||||
time. Thus it is easy to specify a time-dependent radius or have
|
||||
a time dependent position of the sphere or cylinder region.
|
||||
|
||||
.. note::
|
||||
|
||||
Whenever a region property, such as a coordinate or an upper/lower
|
||||
bound, is defined via an equal-style variable, the variable should
|
||||
not cause any of the region boundaries to move
|
||||
too far within a single timestep. Otherwise, bad dynamics will occur.
|
||||
"Too far" means a small fraction of the approximate distance of
|
||||
closest approach between two particles, which for the case of Lennard-Jones
|
||||
particles is the distance of the energy minimum while for granular
|
||||
particles it is their diameter. An example is a rapidly varying direction
|
||||
vector in region plane since a small change in the normal to plane will
|
||||
shift the region surface far away from the region point by a large displacement.
|
||||
Similarly, bad dynamics can also occur for fast changing variables employed
|
||||
in the move/rotate options.
|
||||
|
||||
See the :doc:`Howto tricilinc <Howto_triclinic>` page for a
|
||||
geometric description of triclinic boxes, as defined by LAMMPS, and
|
||||
how to transform these parameters to and from other commonly used
|
||||
|
||||
@ -1,4 +1,5 @@
|
||||
LAMMPS (15 Sep 2022)
|
||||
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-106-g5d02e140d4)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# flat membrane demo
|
||||
variable r0 equal 0.97
|
||||
@ -46,7 +47,7 @@ set type 1 mass 1.0
|
||||
Setting atom values ...
|
||||
1920 settings made for mass
|
||||
|
||||
set type 1 shape 1 1 1
|
||||
set type 1 shape 1 0.99 0.99
|
||||
Setting atom values ...
|
||||
1920 settings made for shape
|
||||
|
||||
@ -99,7 +100,7 @@ CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 10 steps, check = yes
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.6
|
||||
ghost atom cutoff = 3.6
|
||||
@ -113,47 +114,47 @@ Neighbor list info ...
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.024 | 5.024 | 5.024 Mbytes
|
||||
Step Temp Press Pxx Pyy
|
||||
0 0.23 -0.0073508785 -0.012283389 -0.012234574
|
||||
200 0.20903886 -0.0010605951 -0.0011885957 -0.00198842
|
||||
400 0.21898026 -0.00069250685 -0.0013217981 -0.00073225707
|
||||
600 0.22689361 -0.00057919328 -0.00076880503 -0.0010242283
|
||||
800 0.22983221 -0.00032145682 -0.00051928834 -0.00059337525
|
||||
1000 0.23819392 -0.00027969126 -0.00088082301 -5.2666567e-05
|
||||
1200 0.22053795 -0.00029571329 -0.0004446455 -0.00035529929
|
||||
1400 0.22285021 -0.0002690371 -0.00068896571 -3.6258442e-05
|
||||
1600 0.22687044 2.8599875e-05 -0.00032651798 0.0004056081
|
||||
1800 0.23356905 -2.28742e-05 -0.00027073251 0.00025081131
|
||||
2000 0.22499821 8.8230586e-06 -7.5750159e-05 0.0001988705
|
||||
2200 0.23162995 -9.026855e-05 -0.00025832535 5.4904927e-05
|
||||
2400 0.22920223 0.00016700455 3.5283125e-05 0.00034955857
|
||||
2600 0.2260299 5.3095557e-05 0.00025691786 0.00013353467
|
||||
2800 0.2296401 0.00043234854 0.00058344966 0.00063645193
|
||||
3000 0.22564577 2.6423111e-05 8.9918406e-05 0.00022146229
|
||||
Loop time of 6.76659 on 1 procs for 3000 steps with 1920 atoms
|
||||
200 0.20906916 -0.0010610794 -0.0011895359 -0.00198968
|
||||
400 0.21907691 -0.00068750897 -0.0013175111 -0.00072355516
|
||||
600 0.22648739 -0.00057306694 -0.000831971 -0.00096776143
|
||||
800 0.2368957 -0.00028517767 -0.00050638195 -0.00052670236
|
||||
1000 0.22735705 -0.00032638104 -0.00037959812 -0.00071879257
|
||||
1200 0.22910882 -0.00019457758 -0.00024451315 -0.00027807764
|
||||
1400 0.22754022 -0.00033048317 -0.00010053263 -0.00075173132
|
||||
1600 0.22503496 -7.593954e-05 5.2989168e-05 -0.00022521685
|
||||
1800 0.22673577 -0.00017917699 1.0176667e-05 -0.00047893102
|
||||
2000 0.22480858 9.318318e-05 0.00031024343 1.2738253e-05
|
||||
2200 0.22387294 -6.9083174e-05 -4.6170865e-05 4.6682009e-05
|
||||
2400 0.22686231 0.00022776785 0.00028204391 0.00030116273
|
||||
2600 0.23055637 8.2778175e-05 0.00027137529 4.2254076e-05
|
||||
2800 0.23126717 0.00044863024 0.00071654709 0.00057652233
|
||||
3000 0.22234736 0.00031577792 0.00051797227 0.00039087282
|
||||
Loop time of 7.17991 on 1 procs for 3000 steps with 1920 atoms
|
||||
|
||||
Performance: 383058.431 tau/day, 443.355 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 361007.348 tau/day, 417.833 timesteps/s, 802.239 katom-step/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 5.7968 | 5.7968 | 5.7968 | 0.0 | 85.67
|
||||
Neigh | 0.086077 | 0.086077 | 0.086077 | 0.0 | 1.27
|
||||
Comm | 0.034761 | 0.034761 | 0.034761 | 0.0 | 0.51
|
||||
Output | 0.00038014 | 0.00038014 | 0.00038014 | 0.0 | 0.01
|
||||
Modify | 0.8268 | 0.8268 | 0.8268 | 0.0 | 12.22
|
||||
Other | | 0.02181 | | | 0.32
|
||||
Pair | 6.2257 | 6.2257 | 6.2257 | 0.0 | 86.71
|
||||
Neigh | 0.11392 | 0.11392 | 0.11392 | 0.0 | 1.59
|
||||
Comm | 0.036614 | 0.036614 | 0.036614 | 0.0 | 0.51
|
||||
Output | 0.00052672 | 0.00052672 | 0.00052672 | 0.0 | 0.01
|
||||
Modify | 0.78577 | 0.78577 | 0.78577 | 0.0 | 10.94
|
||||
Other | | 0.01743 | | | 0.24
|
||||
|
||||
Nlocal: 1920 ave 1920 max 1920 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 772 ave 772 max 772 min
|
||||
Nghost: 771 ave 771 max 771 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 46804 ave 46804 max 46804 min
|
||||
Neighs: 46750 ave 46750 max 46750 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 46804
|
||||
Ave neighs/atom = 24.377083
|
||||
Neighbor list builds = 99
|
||||
Total # of neighbors = 46750
|
||||
Ave neighs/atom = 24.348958
|
||||
Neighbor list builds = 98
|
||||
Dangerous builds = 0
|
||||
|
||||
|
||||
Total wall time: 0:00:06
|
||||
Total wall time: 0:00:07
|
||||
@ -1,4 +1,5 @@
|
||||
LAMMPS (15 Sep 2022)
|
||||
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-106-g5d02e140d4)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# flat membrane demo
|
||||
variable r0 equal 0.97
|
||||
@ -46,7 +47,7 @@ set type 1 mass 1.0
|
||||
Setting atom values ...
|
||||
1920 settings made for mass
|
||||
|
||||
set type 1 shape 1 1 1
|
||||
set type 1 shape 1 0.99 0.99
|
||||
Setting atom values ...
|
||||
1920 settings made for shape
|
||||
|
||||
@ -99,7 +100,7 @@ CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 10 steps, check = yes
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.6
|
||||
ghost atom cutoff = 3.6
|
||||
@ -113,47 +114,47 @@ Neighbor list info ...
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.182 | 4.794 | 5.472 Mbytes
|
||||
Step Temp Press Pxx Pyy
|
||||
0 0.23 -0.0073508785 -0.012283389 -0.012234574
|
||||
200 0.20647718 -0.0012368074 -0.0021167303 -0.0015343502
|
||||
400 0.21648371 -0.00085695085 -0.0015627331 -0.0011177093
|
||||
600 0.22929515 -0.00050218657 -0.0008332 -0.00062622609
|
||||
800 0.22062664 -0.00049172378 -0.000611884 -0.00075089294
|
||||
1000 0.22422425 -0.00039405068 -0.00037600355 -0.00070786572
|
||||
1200 0.2298767 -0.00025939082 -0.00021616578 -0.00053125505
|
||||
1400 0.2335927 5.8028332e-05 0.00017530192 -3.1675138e-05
|
||||
1600 0.22884878 -0.0001733902 -0.0008056431 0.00014276754
|
||||
1800 0.22813498 0.00019873459 0.00051040124 5.8860949e-05
|
||||
2000 0.2273166 -3.3595127e-05 0.0001705632 -0.00026498213
|
||||
2200 0.2251643 -2.4517311e-05 -4.0618888e-05 1.066658e-05
|
||||
2400 0.22460629 -4.5661259e-05 -0.00019144039 -1.6649099e-05
|
||||
2600 0.23085675 0.00014029405 0.00017983536 0.00017895001
|
||||
2800 0.22364591 4.2999164e-05 -0.00011000466 0.00024363243
|
||||
3000 0.23421357 0.00023505702 0.00020752013 0.00053567111
|
||||
Loop time of 4.68577 on 4 procs for 3000 steps with 1920 atoms
|
||||
200 0.21866566 -0.0011213114 -0.0017540296 -0.0017008786
|
||||
400 0.22409469 -0.00055137604 -0.00050366017 -0.0012846672
|
||||
600 0.21623646 -0.0004808564 -0.00063496522 -0.00071617302
|
||||
800 0.22248339 -0.00066333806 -0.00093812145 -0.00099410261
|
||||
1000 0.22367907 -0.0003439459 -0.00076259578 -0.00013354375
|
||||
1200 0.23276206 8.5764334e-06 -0.00036165178 0.00038543803
|
||||
1400 0.23129049 -5.1997966e-06 -0.00040514787 0.00017093646
|
||||
1600 0.22074564 -0.0001604642 -0.00053959031 9.0463391e-05
|
||||
1800 0.2276062 -0.00015655254 -0.00042925633 5.4938379e-05
|
||||
2000 0.22469391 -3.6198836e-05 -1.8538296e-06 -0.00010464749
|
||||
2200 0.22737515 -1.8967356e-05 0.0001341006 -0.00022739894
|
||||
2400 0.22607533 0.00014650382 -2.4871789e-05 0.00058296255
|
||||
2600 0.24044743 0.00045066449 0.00049153595 0.00078042437
|
||||
2800 0.23346628 0.00017994019 -5.0897724e-05 0.00046011801
|
||||
3000 0.22427206 0.00040437022 0.00049580531 0.00046259202
|
||||
Loop time of 5.04539 on 4 procs for 3000 steps with 1920 atoms
|
||||
|
||||
Performance: 553164.568 tau/day, 640.237 timesteps/s
|
||||
95.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 513736.789 tau/day, 594.603 timesteps/s, 1.142 Matom-step/s
|
||||
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00015072 | 1.6029 | 3.8573 | 131.7 | 34.21
|
||||
Neigh | 0.00055747 | 0.025423 | 0.065858 | 17.0 | 0.54
|
||||
Comm | 0.0052259 | 0.48173 | 1.624 | 96.5 | 10.28
|
||||
Output | 0.0003894 | 0.023428 | 0.047223 | 15.0 | 0.50
|
||||
Modify | 0.00037337 | 0.2141 | 0.44595 | 46.3 | 4.57
|
||||
Other | | 2.338 | | | 49.90
|
||||
Pair | 4.1163 | 4.2634 | 4.4004 | 6.5 | 84.50
|
||||
Neigh | 0.00088605 | 0.032793 | 0.083516 | 19.1 | 0.65
|
||||
Comm | 0.006704 | 0.20003 | 0.40672 | 42.5 | 3.96
|
||||
Output | 0.00033812 | 0.0012192 | 0.0020905 | 2.3 | 0.02
|
||||
Modify | 0.00035967 | 0.20167 | 0.42535 | 45.0 | 4.00
|
||||
Other | | 0.3462 | | | 6.86
|
||||
|
||||
Nlocal: 480 ave 1011 max 0 min
|
||||
Nlocal: 480 ave 1052 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Nghost: 860 ave 1771 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 11697.8 ave 30095 max 0 min
|
||||
Nghost: 854.5 ave 1801 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Neighs: 11684.2 ave 31145 max 0 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 46791
|
||||
Ave neighs/atom = 24.370313
|
||||
Neighbor list builds = 99
|
||||
Total # of neighbors = 46737
|
||||
Ave neighs/atom = 24.342188
|
||||
Neighbor list builds = 98
|
||||
Dangerous builds = 0
|
||||
|
||||
|
||||
Total wall time: 0:00:04
|
||||
Total wall time: 0:00:05
|
||||
@ -32,7 +32,7 @@
|
||||
#include <cmath>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using MathConst::MY_4PI;
|
||||
using MathConst::MY_PI;
|
||||
using MathConst::MY_PI2;
|
||||
using MathConst::MY_TWOBYSIXTH;
|
||||
|
||||
@ -487,7 +487,7 @@ double PairYLZ::ylz_analytic(const int i, const int j, double a1[3][3], double a
|
||||
|
||||
uA = -energy_well * t1 * cos_t;
|
||||
U = uA * phi;
|
||||
dUdr = MY_4PI / (rcut - rmin) * (t1) *sin(t) * phi * energy_well;
|
||||
dUdr = MY_PI * zt / (rcut - rmin) * (t1) *sin(t) * phi * energy_well;
|
||||
dUdphi = uA;
|
||||
}
|
||||
|
||||
|
||||
@ -74,6 +74,10 @@ void PairDPD::compute(int eflag, int vflag)
|
||||
evdwl = 0.0;
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
// precompute random force scaling factors
|
||||
|
||||
for (int i = 0; i < 4; ++i) special_sqrt[i] = sqrt(force->special_lj[i]);
|
||||
|
||||
double **x = atom->x;
|
||||
double **v = atom->v;
|
||||
double **f = atom->f;
|
||||
@ -266,10 +270,6 @@ void PairDPD::init_style()
|
||||
error->warning(FLERR, "Pair dpd needs newton pair on for momentum conservation");
|
||||
|
||||
neighbor->add_request(this);
|
||||
|
||||
// precompute random force scaling factors
|
||||
|
||||
for (int i = 0; i < 4; ++i) special_sqrt[i] = sqrt(force->special_lj[i]);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
|
||||
@ -90,6 +90,10 @@ void PairDPDCoulSlaterLong::compute(int eflag, int vflag)
|
||||
evdwl = ecoul = 0.0;
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
// precompute random force scaling factors
|
||||
|
||||
for (int i = 0; i < 4; ++i) special_sqrt[i] = sqrt(force->special_lj[i]);
|
||||
|
||||
double **x = atom->x;
|
||||
double **v = atom->v;
|
||||
double **f = atom->f;
|
||||
@ -334,11 +338,6 @@ void PairDPDCoulSlaterLong::init_style()
|
||||
|
||||
neighbor->add_request(this);
|
||||
|
||||
// precompute random force scaling factors
|
||||
|
||||
for (int i = 0; i < 4; ++i) special_sqrt[i] = sqrt(force->special_lj[i]);
|
||||
|
||||
|
||||
// ensure use of KSpace long-range solver, set g_ewald
|
||||
|
||||
if (force->kspace == nullptr)
|
||||
|
||||
@ -81,6 +81,10 @@ void PairDPDExt::compute(int eflag, int vflag)
|
||||
evdwl = 0.0;
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
// precompute random force scaling factors
|
||||
|
||||
for (int i = 0; i < 4; ++i) special_sqrt[i] = sqrt(force->special_lj[i]);
|
||||
|
||||
double **x = atom->x;
|
||||
double **v = atom->v;
|
||||
double **f = atom->f;
|
||||
@ -325,10 +329,6 @@ void PairDPDExt::init_style()
|
||||
error->warning(FLERR, "Pair dpd needs newton pair on for momentum conservation");
|
||||
|
||||
neighbor->add_request(this);
|
||||
|
||||
// precompute random force scaling factors
|
||||
|
||||
for (int i = 0; i < 4; ++i) special_sqrt[i] = sqrt(force->special_lj[i]);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
|
||||
@ -54,6 +54,10 @@ void PairDPDExtTstat::compute(int eflag, int vflag)
|
||||
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
// precompute random force scaling factors
|
||||
|
||||
for (int i = 0; i < 4; ++i) special_sqrt[i] = sqrt(force->special_lj[i]);
|
||||
|
||||
// adjust sigma if target T is changing
|
||||
|
||||
if (t_start != t_stop) {
|
||||
|
||||
@ -48,6 +48,10 @@ void PairDPDTstat::compute(int eflag, int vflag)
|
||||
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
// precompute random force scaling factors
|
||||
|
||||
for (int i = 0; i < 4; ++i) special_sqrt[i] = sqrt(force->special_lj[i]);
|
||||
|
||||
// adjust sigma if target T is changing
|
||||
|
||||
if (t_start != t_stop) {
|
||||
|
||||
@ -89,8 +89,6 @@ void AngleCosineDelta::compute(int eflag, int vflag)
|
||||
|
||||
s = sqrt(1.0 - c*c);
|
||||
if (s < SMALL) s = SMALL;
|
||||
s = 1.0/s;
|
||||
|
||||
cot = c/s;
|
||||
|
||||
// force & energy
|
||||
|
||||
@ -29,6 +29,7 @@
|
||||
#include "memory.h"
|
||||
#include "neigh_list.h"
|
||||
#include "neighbor.h"
|
||||
#include "update.h"
|
||||
|
||||
#include <algorithm>
|
||||
#include <cmath>
|
||||
@ -58,6 +59,7 @@ static constexpr double autoang = 0.52917725; // atomic units (Bohr) to Angst
|
||||
static constexpr double autoev = 27.21140795; // atomic units (Hartree) to eV
|
||||
|
||||
#include "d3_parameters.h"
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Constructor (Required)
|
||||
------------------------------------------------------------------------- */
|
||||
@ -75,6 +77,7 @@ PairDispersionD3::PairDispersionD3(LAMMPS *lmp) :
|
||||
one_coeff = 1;
|
||||
single_enable = 0;
|
||||
|
||||
dampingCode = 0;
|
||||
s6 = s8 = s18 = rs6 = rs8 = rs18 = a1 = a2 = alpha = alpha6 = alpha8 = 0.0;
|
||||
}
|
||||
|
||||
@ -130,12 +133,20 @@ void PairDispersionD3::allocate()
|
||||
|
||||
void PairDispersionD3::settings(int narg, char **arg)
|
||||
{
|
||||
if (narg != 4) error->all(FLERR, "Pair_style dispersion/d3 needs 4 arguments");
|
||||
if (narg != 4) error->all(FLERR, "Pair style dispersion/d3 needs 4 arguments");
|
||||
if (strcmp("metal", update->unit_style) != 0)
|
||||
error->all(FLERR, Error::NOLASTLINE, "Pair style dispersion/d3 requires metal units");
|
||||
|
||||
damping_type = arg[0];
|
||||
std::string damping_type = arg[0];
|
||||
std::string functional_name = arg[1];
|
||||
|
||||
std::transform(damping_type.begin(), damping_type.end(), damping_type.begin(), ::tolower);
|
||||
std::unordered_map<std::string, int> dampingMap = {
|
||||
{"original", 1}, {"zero", 1}, {"zerom", 2}, {"bj", 3}, {"bjm", 4}};
|
||||
if (!dampingMap.count(damping_type))
|
||||
error->all(FLERR, Error::NOPOINTER, "Unknown damping type {} for pair style dispersion/d3",
|
||||
damping_type);
|
||||
dampingCode = dampingMap[damping_type];
|
||||
|
||||
rthr = utils::numeric(FLERR, arg[2], false, lmp);
|
||||
cn_thr = utils::numeric(FLERR, arg[3], false, lmp);
|
||||
@ -154,7 +165,7 @@ int PairDispersionD3::find_atomic_number(std::string &key)
|
||||
{
|
||||
std::transform(key.begin(), key.end(), key.begin(), ::tolower);
|
||||
if (key.length() == 1) key += " ";
|
||||
key.resize(2);
|
||||
if (key.length() > 2) return -1;
|
||||
|
||||
std::vector<std::string> element_table = {
|
||||
"h ", "he", "li", "be", "b ", "c ", "n ", "o ", "f ", "ne", "na", "mg", "al", "si",
|
||||
@ -283,6 +294,8 @@ void PairDispersionD3::coeff(int narg, char **arg)
|
||||
for (int i = 0; i < ntypes; i++) {
|
||||
element = arg[i + 2];
|
||||
atomic_numbers[i] = find_atomic_number(element);
|
||||
if (atomic_numbers[i] < 0)
|
||||
error->all(FLERR, Error::NOLASTLINE, "Element {} not supported", element);
|
||||
}
|
||||
|
||||
int count = 0;
|
||||
@ -450,11 +463,6 @@ double *PairDispersionD3::get_dC6(int iat, int jat, double cni, double cnj)
|
||||
|
||||
void PairDispersionD3::compute(int eflag, int vflag)
|
||||
{
|
||||
|
||||
std::unordered_map<std::string, int> dampingMap = {
|
||||
{"zero", 1}, {"zerom", 2}, {"bj", 3}, {"bjm", 4}};
|
||||
int dampingCode = dampingMap[damping_type];
|
||||
|
||||
double evdwl = 0.0;
|
||||
ev_init(eflag, vflag);
|
||||
|
||||
@ -518,7 +526,8 @@ void PairDispersionD3::compute(int eflag, int vflag)
|
||||
t6 = t8 = e6 = e8 = evdwl = fpair = fpair1 = fpair2 = 0.0;
|
||||
|
||||
switch (dampingCode) {
|
||||
case 1: { // zero
|
||||
|
||||
case 1: { // original
|
||||
|
||||
double r0 = r / r0ab[type[i]][type[j]];
|
||||
|
||||
@ -539,6 +548,7 @@ void PairDispersionD3::compute(int eflag, int vflag)
|
||||
fpair = fpair1 + fpair2;
|
||||
fpair *= factor_lj;
|
||||
} break;
|
||||
|
||||
case 2: { // zerom
|
||||
|
||||
double r0 = r0ab[type[i]][type[j]];
|
||||
@ -564,6 +574,7 @@ void PairDispersionD3::compute(int eflag, int vflag)
|
||||
fpair = fpair1 + fpair2;
|
||||
fpair *= factor_lj;
|
||||
} break;
|
||||
|
||||
case 3: { // bj
|
||||
|
||||
double r0 = sqrt(C8 / C6);
|
||||
@ -584,6 +595,7 @@ void PairDispersionD3::compute(int eflag, int vflag)
|
||||
fpair = -(tmp6 + tmp8);
|
||||
fpair *= factor_lj;
|
||||
} break;
|
||||
|
||||
case 4: { // bjm
|
||||
|
||||
double r0 = sqrt(C8 / C6);
|
||||
@ -603,10 +615,15 @@ void PairDispersionD3::compute(int eflag, int vflag)
|
||||
|
||||
fpair = -(tmp6 + tmp8);
|
||||
fpair *= factor_lj;
|
||||
}
|
||||
} break;
|
||||
|
||||
default: {
|
||||
// this should not happen with the error check in the init_style function
|
||||
error->all(FLERR, Error::NOLASTLINE, "Damping code {} unknown", dampingCode);
|
||||
} break;
|
||||
}
|
||||
|
||||
if (eflag) { evdwl = -(s6 * e6 + s8 * e8) * factor_lj; }
|
||||
if (eflag) evdwl = -(s6 * e6 + s8 * e8) * factor_lj;
|
||||
|
||||
double rest = (s6 * e6 + s8 * e8) / C6;
|
||||
|
||||
@ -693,12 +710,6 @@ void PairDispersionD3::compute(int eflag, int vflag)
|
||||
|
||||
void PairDispersionD3::set_funcpar(std::string &functional_name)
|
||||
{
|
||||
|
||||
std::unordered_map<std::string, int> dampingMap = {
|
||||
{"zero", 1}, {"zerom", 2}, {"bj", 3}, {"bjm", 4}};
|
||||
|
||||
int dampingCode = dampingMap[damping_type];
|
||||
|
||||
switch (dampingCode) {
|
||||
|
||||
case 1: { // zero
|
||||
@ -962,14 +973,10 @@ void PairDispersionD3::set_funcpar(std::string &functional_name)
|
||||
s8 = 1.206;
|
||||
break;
|
||||
default:
|
||||
error->all(FLERR, "Functional name unknown");
|
||||
error->all(FLERR, Error::NOLASTLINE,
|
||||
"Functional {} not supported with original damping function", functional_name);
|
||||
break;
|
||||
}
|
||||
//fprintf(stderr,"s6 : %f\n", s6);
|
||||
//fprintf(stderr,"s8 : %f\n", s8);
|
||||
//fprintf(stderr,"rs6 : %f\n", rs6);
|
||||
//fprintf(stderr,"rs8 : %f\n", rs8);
|
||||
//fprintf(stderr,"alpha : %f\n", alpha);
|
||||
} break;
|
||||
|
||||
case 2: { // zerom
|
||||
@ -1024,14 +1031,10 @@ void PairDispersionD3::set_funcpar(std::string &functional_name)
|
||||
rs8 = 0.003160;
|
||||
break;
|
||||
default:
|
||||
error->all(FLERR, "Functional name unknown");
|
||||
error->all(FLERR, Error::NOLASTLINE,
|
||||
"Functional {} not supported with zerom damping function", functional_name);
|
||||
break;
|
||||
}
|
||||
//fprintf(stderr,"s6 : %f\n", s6);
|
||||
//fprintf(stderr,"s8 : %f\n", s8);
|
||||
//fprintf(stderr,"rs6 : %f\n", rs6);
|
||||
//fprintf(stderr,"rs8 : %f\n", rs8);
|
||||
//fprintf(stderr,"alpha : %f\n", alpha);
|
||||
|
||||
rs8 = rs8 / autoang;
|
||||
} break;
|
||||
@ -1334,16 +1337,11 @@ void PairDispersionD3::set_funcpar(std::string &functional_name)
|
||||
a2 = 4.5000;
|
||||
break;
|
||||
default:
|
||||
error->all(FLERR, "Functional name unknown");
|
||||
error->all(FLERR, Error::NOLASTLINE,
|
||||
"Functional {} not supported with bj damping function", functional_name);
|
||||
break;
|
||||
}
|
||||
|
||||
//fprintf(stderr,"s6 : %f\n", s6);
|
||||
//fprintf(stderr,"s8 : %f\n", s8);
|
||||
//fprintf(stderr,"a1 : %f\n", a1);
|
||||
//fprintf(stderr,"a2 : %f\n", a2);
|
||||
//fprintf(stderr,"alpha : %f\n", alpha);
|
||||
|
||||
a2 = a2 * autoang;
|
||||
} break;
|
||||
|
||||
@ -1400,21 +1398,17 @@ void PairDispersionD3::set_funcpar(std::string &functional_name)
|
||||
a2 = 3.593680;
|
||||
break;
|
||||
default:
|
||||
error->all(FLERR, "Functional name unknown");
|
||||
error->all(FLERR, Error::NOLASTLINE,
|
||||
"Functional {} not supported with bjm damping function", functional_name);
|
||||
break;
|
||||
}
|
||||
|
||||
//fprintf(stderr,"s6 : %f\n", s6);
|
||||
//fprintf(stderr,"s8 : %f\n", s8);
|
||||
//fprintf(stderr,"a1 : %f\n", a1);
|
||||
//fprintf(stderr,"a2 : %f\n", a2);
|
||||
//fprintf(stderr,"alpha : %f\n", alpha);
|
||||
|
||||
a2 = a2 * autoang;
|
||||
|
||||
} break;
|
||||
default:
|
||||
error->all(FLERR, "Damping type unknown");
|
||||
// this should not happen with the error check in the init_style function
|
||||
error->all(FLERR, Error::NOLASTLINE, "Damping code {} unknown", dampingCode);
|
||||
break;
|
||||
}
|
||||
}
|
||||
@ -1436,8 +1430,6 @@ double PairDispersionD3::init_one(int i, int j)
|
||||
void PairDispersionD3::init_style()
|
||||
{
|
||||
if (atom->tag_enable == 0) error->all(FLERR, "Pair style D3 requires atom IDs");
|
||||
//if (force->newton_pair == 0)
|
||||
// error->all(FLERR,"Pair style D3 requires newton pair on");
|
||||
|
||||
// need an half neighbor list
|
||||
neighbor->add_request(this);
|
||||
|
||||
@ -48,7 +48,7 @@ class PairDispersionD3 : public Pair {
|
||||
double rthr; // R^2 distance to cutoff for D3_calculation
|
||||
double cn_thr; // R^2 distance to cutoff for CN_calculation
|
||||
|
||||
std::string damping_type; // damping function type
|
||||
int dampingCode;
|
||||
double s6, s8, s18, rs6, rs8, rs18; // XC parameters
|
||||
double a1, a2, alpha, alpha6, alpha8;
|
||||
|
||||
|
||||
@ -16,15 +16,16 @@
|
||||
Contributing author: Axel Kohlmeyer (Temple U)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "omp_compat.h"
|
||||
#include "angle_cosine_delta_omp.h"
|
||||
#include <cmath>
|
||||
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "neighbor.h"
|
||||
|
||||
#include <cmath>
|
||||
|
||||
#include "omp_compat.h"
|
||||
#include "suffix.h"
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
@ -128,8 +129,6 @@ void AngleCosineDeltaOMP::eval(int nfrom, int nto, ThrData * const thr)
|
||||
|
||||
s = sqrt(1.0 - c*c);
|
||||
if (s < SMALL) s = SMALL;
|
||||
s = 1.0/s;
|
||||
|
||||
cot = c/s;
|
||||
|
||||
// force & energy
|
||||
|
||||
@ -229,7 +229,7 @@ void FixRigidSmallOMP::compute_forces_and_torques()
|
||||
#if defined(_OPENMP)
|
||||
#pragma omp parallel for LMP_DEFAULT_NONE schedule(static)
|
||||
#endif
|
||||
for (int ibody = 0; ibody < nbody; ibody++) {
|
||||
for (int ibody = 0; ibody < nlocal_body; ibody++) {
|
||||
double * _noalias const fcm = body[ibody].fcm;
|
||||
const double mass = body[ibody].mass;
|
||||
fcm[0] += gvec[0]*mass;
|
||||
|
||||
@ -60,6 +60,10 @@ void PairDPDExtOMP::compute(int eflag, int vflag)
|
||||
{
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
// precompute random force scaling factors
|
||||
|
||||
for (int i = 0; i < 4; ++i) special_sqrt[i] = sqrt(force->special_lj[i]);
|
||||
|
||||
const int nall = atom->nlocal + atom->nghost;
|
||||
const int inum = list->inum;
|
||||
|
||||
|
||||
@ -60,6 +60,10 @@ void PairDPDExtTstatOMP::compute(int eflag, int vflag)
|
||||
{
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
// precompute random force scaling factors
|
||||
|
||||
for (int i = 0; i < 4; ++i) special_sqrt[i] = sqrt(force->special_lj[i]);
|
||||
|
||||
const int nall = atom->nlocal + atom->nghost;
|
||||
const int inum = list->inum;
|
||||
|
||||
|
||||
@ -59,6 +59,10 @@ void PairDPDOMP::compute(int eflag, int vflag)
|
||||
{
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
// precompute random force scaling factors
|
||||
|
||||
for (int i = 0; i < 4; ++i) special_sqrt[i] = sqrt(force->special_lj[i]);
|
||||
|
||||
const int nall = atom->nlocal + atom->nghost;
|
||||
const int inum = list->inum;
|
||||
|
||||
|
||||
@ -60,6 +60,10 @@ void PairDPDTstatOMP::compute(int eflag, int vflag)
|
||||
{
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
// precompute random force scaling factors
|
||||
|
||||
for (int i = 0; i < 4; ++i) special_sqrt[i] = sqrt(force->special_lj[i]);
|
||||
|
||||
const int nall = atom->nlocal + atom->nghost;
|
||||
const int inum = list->inum;
|
||||
|
||||
|
||||
@ -57,8 +57,8 @@ namespace ReaxFF {
|
||||
class control_parser_error : public std::exception {
|
||||
std::string message;
|
||||
public:
|
||||
explicit control_parser_error(const std::string &msg) {
|
||||
message = msg;
|
||||
explicit control_parser_error(const std::string &format, const std::string &keyword) {
|
||||
message = fmt::format(fmt::runtime(format), keyword);
|
||||
}
|
||||
const char *what() const noexcept override { return message.c_str(); }
|
||||
};
|
||||
@ -92,11 +92,11 @@ namespace ReaxFF {
|
||||
auto keyword = values.next_string();
|
||||
|
||||
if (!values.has_next())
|
||||
throw control_parser_error(
|
||||
fmt::format("No value(s) for control parameter: {}\n", keyword));
|
||||
throw control_parser_error("No value(s) for control parameter: {}\n", keyword);
|
||||
|
||||
if (inactive_keywords.find(keyword) != inactive_keywords.end()) {
|
||||
error->warning(FLERR,fmt::format("Ignoring inactive control parameter: {}", keyword));
|
||||
error->warning(FLERR, fmt::format(fmt::runtime("Ignoring inactive control parameter: {}"),
|
||||
keyword));
|
||||
} else if (keyword == "nbrhood_cutoff") {
|
||||
control->bond_cut = values.next_double();
|
||||
} else if (keyword == "bond_graph_cutoff") {
|
||||
@ -114,7 +114,7 @@ namespace ReaxFF {
|
||||
error->warning(FLERR,"Support for writing native trajectories has "
|
||||
"been removed after LAMMPS version 8 April 2021");
|
||||
} else {
|
||||
throw control_parser_error(fmt::format("Unknown parameter {} in control file", keyword));
|
||||
throw control_parser_error("Unknown parameter {} in control file", keyword);
|
||||
}
|
||||
}
|
||||
} catch (LAMMPS_NS::EOFException &) {
|
||||
|
||||
@ -42,8 +42,8 @@ using namespace MathExtra;
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
ComputeRHEOVShift::ComputeRHEOVShift(LAMMPS *lmp, int narg, char **arg) :
|
||||
Compute(lmp, narg, arg), vshift(nullptr), ct(nullptr), wsame(nullptr), cgradt(nullptr),
|
||||
fix_rheo(nullptr), rho0(nullptr), list(nullptr), compute_interface(nullptr),
|
||||
Compute(lmp, narg, arg), vshift(nullptr), fix_rheo(nullptr), rho0(nullptr), wsame(nullptr),
|
||||
ct(nullptr), cgradt(nullptr), shift_type(nullptr), list(nullptr), compute_interface(nullptr),
|
||||
compute_kernel(nullptr), compute_surface(nullptr)
|
||||
{
|
||||
if (narg != 3) error->all(FLERR, "Illegal compute RHEO/VShift command");
|
||||
@ -316,8 +316,7 @@ void ComputeRHEOVShift::correct_type_interface()
|
||||
{
|
||||
int i, j, a, ii, jj, jnum, itype, jtype;
|
||||
int fluidi, fluidj;
|
||||
double xtmp, ytmp, ztmp, rsq, r, rinv;
|
||||
double w, wp, dr, w0, prefactor;
|
||||
double xtmp, ytmp, ztmp, rsq, r, w;
|
||||
double imass, jmass, voli, volj, rhoi, rhoj;
|
||||
double dx[3];
|
||||
int dim = domain->dimension;
|
||||
@ -327,14 +326,12 @@ void ComputeRHEOVShift::correct_type_interface()
|
||||
|
||||
int *type = atom->type;
|
||||
int *status = atom->rheo_status;
|
||||
int *mask = atom->mask;
|
||||
double **x = atom->x;
|
||||
double *rho = atom->rho;
|
||||
double *mass = atom->mass;
|
||||
double *rmass = atom->rmass;
|
||||
|
||||
int nlocal = atom->nlocal;
|
||||
int nall = nlocal + atom->nghost;
|
||||
int newton_pair = force->newton_pair;
|
||||
|
||||
inum = list->inum;
|
||||
|
||||
@ -1,3 +1,4 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
@ -51,8 +52,6 @@ enum { XYZ, SHIFT, BISECTION };
|
||||
enum { NONE, UNIFORM, USER };
|
||||
enum { X, Y, Z };
|
||||
|
||||
// clang-format off
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
Balance::Balance(LAMMPS *lmp) : Command(lmp)
|
||||
@ -114,13 +113,13 @@ Balance::~Balance()
|
||||
void Balance::command(int narg, char **arg)
|
||||
{
|
||||
if (domain->box_exist == 0)
|
||||
error->all(FLERR,"Balance command before simulation box is defined");
|
||||
error->all(FLERR, -1, "Balance command before simulation box is defined");
|
||||
|
||||
if (comm->me == 0) utils::logmesg(lmp,"Balancing ...\n");
|
||||
|
||||
// parse required arguments
|
||||
|
||||
if (narg < 2) error->all(FLERR,"Illegal balance command");
|
||||
if (narg < 2) utils::missing_cmd_args(FLERR,"balance", error);
|
||||
|
||||
thresh = utils::numeric(FLERR,arg[0],false,lmp);
|
||||
|
||||
@ -132,16 +131,15 @@ void Balance::command(int narg, char **arg)
|
||||
int iarg = 1;
|
||||
while (iarg < narg) {
|
||||
if (strcmp(arg[iarg],"x") == 0) {
|
||||
if (style != -1 && style != XYZ)
|
||||
error->all(FLERR,"Illegal balance command");
|
||||
if ((style != -1) && (style != XYZ))
|
||||
error->all(FLERR, iarg, "Must not combine multiple balancing styles");
|
||||
style = XYZ;
|
||||
if (iarg+2 > narg) utils::missing_cmd_args(FLERR,"balance x", error);
|
||||
if (strcmp(arg[iarg+1],"uniform") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal balance command");
|
||||
xflag = UNIFORM;
|
||||
iarg += 2;
|
||||
} else {
|
||||
if (1 + procgrid[0]-1 > narg)
|
||||
error->all(FLERR,"Illegal balance command");
|
||||
if (iarg + procgrid[0]-1 > narg) utils::missing_cmd_args(FLERR,"balance x", error);
|
||||
xflag = USER;
|
||||
delete[] user_xsplit;
|
||||
user_xsplit = new double[procgrid[0]+1];
|
||||
@ -152,16 +150,15 @@ void Balance::command(int narg, char **arg)
|
||||
user_xsplit[procgrid[0]] = 1.0;
|
||||
}
|
||||
} else if (strcmp(arg[iarg],"y") == 0) {
|
||||
if (style != -1 && style != XYZ)
|
||||
error->all(FLERR,"Illegal balance command");
|
||||
if ((style != -1) && (style != XYZ))
|
||||
error->all(FLERR, iarg, "Must not combine multiple balancing styles");
|
||||
style = XYZ;
|
||||
if (iarg+2 > narg) utils::missing_cmd_args(FLERR,"balance y", error);
|
||||
if (strcmp(arg[iarg+1],"uniform") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal balance command");
|
||||
yflag = UNIFORM;
|
||||
iarg += 2;
|
||||
} else {
|
||||
if (1 + procgrid[1]-1 > narg)
|
||||
error->all(FLERR,"Illegal balance command");
|
||||
if (iarg + procgrid[1]-1 > narg) utils::missing_cmd_args(FLERR,"balance y", error);
|
||||
yflag = USER;
|
||||
delete[] user_ysplit;
|
||||
user_ysplit = new double[procgrid[1]+1];
|
||||
@ -172,16 +169,15 @@ void Balance::command(int narg, char **arg)
|
||||
user_ysplit[procgrid[1]] = 1.0;
|
||||
}
|
||||
} else if (strcmp(arg[iarg],"z") == 0) {
|
||||
if (style != -1 && style != XYZ)
|
||||
error->all(FLERR,"Illegal balance command");
|
||||
if ((style != -1) && (style != XYZ))
|
||||
error->all(FLERR, iarg, "Must not combine multiple balancing styles");
|
||||
style = XYZ;
|
||||
if (iarg+2 > narg) utils::missing_cmd_args(FLERR,"balance z", error);
|
||||
if (strcmp(arg[iarg+1],"uniform") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal balance command");
|
||||
zflag = UNIFORM;
|
||||
iarg += 2;
|
||||
} else {
|
||||
if (1 + procgrid[2]-1 > narg)
|
||||
error->all(FLERR,"Illegal balance command");
|
||||
if (iarg + procgrid[2]-1 > narg) utils::missing_cmd_args(FLERR,"balance z", error);
|
||||
zflag = USER;
|
||||
delete[] user_zsplit;
|
||||
user_zsplit = new double[procgrid[2]+1];
|
||||
@ -193,19 +189,21 @@ void Balance::command(int narg, char **arg)
|
||||
}
|
||||
|
||||
} else if (strcmp(arg[iarg],"shift") == 0) {
|
||||
if (style != -1) error->all(FLERR,"Illegal balance command");
|
||||
if (style != -1) error->all(FLERR, iarg, "Must not combine multiple balancing styles");
|
||||
if (iarg+4 > narg) utils::missing_cmd_args(FLERR, "balance shift", error);
|
||||
style = SHIFT;
|
||||
bstr = arg[iarg+1];
|
||||
if (bstr.size() > BSTR_SIZE) error->all(FLERR,"Illegal balance shift command");
|
||||
if (bstr.size() > BSTR_SIZE) error->all(FLERR, iarg + 1, "Illegal balance shift command");
|
||||
nitermax = utils::inumeric(FLERR,arg[iarg+2],false,lmp);
|
||||
if (nitermax <= 0) error->all(FLERR,"Illegal balance command");
|
||||
if (nitermax <= 0)
|
||||
error->all(FLERR,iarg+2,"Illegal balance shift value {}", arg[iarg+2]);
|
||||
stopthresh = utils::numeric(FLERR,arg[iarg+3],false,lmp);
|
||||
if (stopthresh < 1.0) error->all(FLERR,"Illegal balance command");
|
||||
if (stopthresh < 1.0)
|
||||
error->all(FLERR,iarg+3,"Illegal balance stop threshold value {}", arg[iarg+3]);
|
||||
iarg += 4;
|
||||
|
||||
} else if (strcmp(arg[iarg],"rcb") == 0) {
|
||||
if (style != -1) error->all(FLERR,"Illegal balance command");
|
||||
if (style != -1) error->all(FLERR,"Must not combine multiple balancing styles");
|
||||
style = BISECTION;
|
||||
iarg++;
|
||||
|
||||
@ -221,32 +219,32 @@ void Balance::command(int narg, char **arg)
|
||||
if (xflag == USER)
|
||||
for (int i = 1; i <= procgrid[0]; i++)
|
||||
if (user_xsplit[i-1] >= user_xsplit[i])
|
||||
error->all(FLERR,"Illegal balance command");
|
||||
error->all(FLERR,"Slices for balance x command must be in ascending order");
|
||||
if (yflag == USER)
|
||||
for (int i = 1; i <= procgrid[1]; i++)
|
||||
if (user_ysplit[i-1] >= user_ysplit[i])
|
||||
error->all(FLERR,"Illegal balance command");
|
||||
error->all(FLERR,"Slices for balance y command must be in ascending order");
|
||||
if (zflag == USER)
|
||||
for (int i = 1; i <= procgrid[2]; i++)
|
||||
if (user_zsplit[i-1] >= user_zsplit[i])
|
||||
error->all(FLERR,"Illegal balance command");
|
||||
error->all(FLERR,"Slices for balance z command must be in ascending order");
|
||||
}
|
||||
|
||||
if (style == SHIFT) {
|
||||
const int blen = bstr.size();
|
||||
for (int i = 0; i < blen; i++) {
|
||||
if (bstr[i] != 'x' && bstr[i] != 'y' && bstr[i] != 'z')
|
||||
error->all(FLERR,"Balance shift string is invalid");
|
||||
error->all(FLERR,"Balance shift string {} is invalid", bstr);
|
||||
if (bstr[i] == 'z' && dimension == 2)
|
||||
error->all(FLERR,"Balance shift string is invalid");
|
||||
error->all(FLERR,"Balance shift string {} is invalid", bstr);
|
||||
for (int j = i+1; j < blen; j++)
|
||||
if (bstr[i] == bstr[j])
|
||||
error->all(FLERR,"Balance shift string is invalid");
|
||||
error->all(FLERR,"Balance shift string {} is invalid", bstr);
|
||||
}
|
||||
}
|
||||
|
||||
if (style == BISECTION && comm->style == Comm::BRICK)
|
||||
error->all(FLERR,"Balance rcb cannot be used with comm_style brick");
|
||||
error->all(FLERR, Error::ARGZERO, "Balance rcb cannot be used with comm_style brick");
|
||||
|
||||
// process remaining optional args
|
||||
|
||||
@ -467,16 +465,16 @@ void Balance::options(int iarg, int narg, char **arg, int sortflag_default)
|
||||
nopt = imb->options(narg-iarg,arg+iarg+2);
|
||||
imbalances[nimbalance++] = imb;
|
||||
} else {
|
||||
error->all(FLERR,"Unknown (fix) balance weight method: {}", arg[iarg+1]);
|
||||
error->all(FLERR, iarg + 1, "Unknown (fix) balance weight method: {}", arg[iarg+1]);
|
||||
}
|
||||
iarg += 2+nopt;
|
||||
|
||||
} else if (strcmp(arg[iarg],"sort") == 0) {
|
||||
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "balance sort", error);
|
||||
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "(fix) balance sort", error);
|
||||
sortflag = utils::logical(FLERR,arg[iarg+1],false,lmp);
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"out") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal (fix) balance command");
|
||||
if (iarg+2 > narg) utils::missing_cmd_args(FLERR,"(fix) balance out", error);
|
||||
outflag = 1;
|
||||
outarg = iarg+1;
|
||||
iarg += 2;
|
||||
@ -485,7 +483,7 @@ void Balance::options(int iarg, int narg, char **arg, int sortflag_default)
|
||||
oldrcb = 1;
|
||||
iarg++;
|
||||
|
||||
} else error->all(FLERR,"Illegal (fix) balance command");
|
||||
} else error->all(FLERR, iarg, "Unknown (fix) balance keyword {}", arg[iarg]);
|
||||
}
|
||||
|
||||
// output file
|
||||
@ -493,8 +491,8 @@ void Balance::options(int iarg, int narg, char **arg, int sortflag_default)
|
||||
if (outflag && comm->me == 0) {
|
||||
fp = fopen(arg[outarg],"w");
|
||||
if (fp == nullptr)
|
||||
error->one(FLERR,"Cannot open (fix) balance output file {}: {}",
|
||||
arg[outarg], utils::getsyserror());
|
||||
error->one(FLERR, outarg, "Cannot open (fix) balance output file {}: {}",
|
||||
arg[outarg], utils::getsyserror());
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
@ -42,7 +42,7 @@ enum { SHIFT, BISECTION };
|
||||
FixBalance::FixBalance(LAMMPS *lmp, int narg, char **arg) :
|
||||
Fix(lmp, narg, arg), balance(nullptr), irregular(nullptr)
|
||||
{
|
||||
if (narg < 6) error->all(FLERR,"Illegal fix balance command");
|
||||
if (narg < 6) utils::missing_cmd_args(FLERR, "fix balance", error);
|
||||
|
||||
box_change = BOX_CHANGE_DOMAIN;
|
||||
pre_exchange_migrate = 1;
|
||||
@ -58,7 +58,7 @@ FixBalance::FixBalance(LAMMPS *lmp, int narg, char **arg) :
|
||||
int dimension = domain->dimension;
|
||||
|
||||
nevery = utils::inumeric(FLERR,arg[3],false,lmp);
|
||||
if (nevery < 0) error->all(FLERR,"Illegal fix balance command");
|
||||
if (nevery < 0) error->all(FLERR, 3, "Illegal fix balance nevery value {}", arg[3]);
|
||||
thresh = utils::numeric(FLERR,arg[4],false,lmp);
|
||||
|
||||
reportonly = 0;
|
||||
@ -69,7 +69,7 @@ FixBalance::FixBalance(LAMMPS *lmp, int narg, char **arg) :
|
||||
} else if (strcmp(arg[5],"report") == 0) {
|
||||
lbstyle = SHIFT;
|
||||
reportonly = 1;
|
||||
} else error->all(FLERR,"Unknown fix balance style {}", arg[5]);
|
||||
} else error->all(FLERR, 5, "Unknown fix balance style {}", arg[5]);
|
||||
|
||||
int iarg = 5;
|
||||
if (lbstyle == SHIFT) {
|
||||
@ -84,11 +84,14 @@ FixBalance::FixBalance(LAMMPS *lmp, int narg, char **arg) :
|
||||
} else {
|
||||
if (iarg+4 > narg) utils::missing_cmd_args(FLERR, "fix balance shift", error);
|
||||
bstr = arg[iarg+1];
|
||||
if (bstr.size() > Balance::BSTR_SIZE) error->all(FLERR,"Illegal fix balance shift command");
|
||||
if (bstr.size() > Balance::BSTR_SIZE)
|
||||
error->all(FLERR, iarg + 1, "Illegal fix balance shift argument {}", bstr);
|
||||
nitermax = utils::inumeric(FLERR,arg[iarg+2],false,lmp);
|
||||
if (nitermax <= 0) error->all(FLERR,"Illegal fix balance command");
|
||||
if (nitermax <= 0)
|
||||
error->all(FLERR, iarg + 2, "Illegal fix balance shift niter argument {}", nitermax);
|
||||
stopthresh = utils::numeric(FLERR,arg[iarg+3],false,lmp);
|
||||
if (stopthresh < 1.0) error->all(FLERR,"Illegal fix balance command");
|
||||
if (stopthresh < 1.0)
|
||||
error->all(FLERR, iarg + 3, "Illegal fix balance stop threshold argument {}", stopthresh);
|
||||
iarg += 4;
|
||||
}
|
||||
|
||||
@ -102,12 +105,12 @@ FixBalance::FixBalance(LAMMPS *lmp, int narg, char **arg) :
|
||||
const int blen = bstr.size();
|
||||
for (int i = 0; i < blen; i++) {
|
||||
if (bstr[i] != 'x' && bstr[i] != 'y' && bstr[i] != 'z')
|
||||
error->all(FLERR,"Fix balance shift string is invalid");
|
||||
error->all(FLERR,"Fix balance shift string {} is invalid", bstr);
|
||||
if (bstr[i] == 'z' && dimension == 2)
|
||||
error->all(FLERR,"Fix balance shift string is invalid");
|
||||
error->all(FLERR,"Fix balance shift string {} is invalid", bstr);
|
||||
for (int j = i+1; j < blen; j++)
|
||||
if (bstr[i] == bstr[j])
|
||||
error->all(FLERR,"Fix balance shift string is invalid");
|
||||
error->all(FLERR,"Fix balance shift string {} is invalid", bstr);
|
||||
}
|
||||
}
|
||||
|
||||
@ -125,7 +128,7 @@ FixBalance::FixBalance(LAMMPS *lmp, int narg, char **arg) :
|
||||
sortflag = balance->sortflag;
|
||||
|
||||
if (balance->varflag && nevery == 0)
|
||||
error->all(FLERR,"Fix balance nevery = 0 cannot be used with weight var");
|
||||
error->all(FLERR, 3, "Fix balance nevery = 0 cannot be used with weight var");
|
||||
|
||||
// create instance of Irregular class
|
||||
|
||||
|
||||
@ -25,9 +25,11 @@ using namespace LAMMPS_NS;
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
RegPlane::RegPlane(LAMMPS *lmp, int narg, char **arg) :
|
||||
Region(lmp, narg, arg), xstr(nullptr), ystr(nullptr), zstr(nullptr)
|
||||
Region(lmp, narg, arg), xstr(nullptr), ystr(nullptr), zstr(nullptr),
|
||||
nxstr(nullptr), nystr(nullptr), nzstr(nullptr)
|
||||
{
|
||||
xvar = yvar = zvar = 0.0;
|
||||
nxvar = nyvar = nzvar = 0.0;
|
||||
|
||||
options(narg - 8, &arg[8]);
|
||||
|
||||
@ -61,15 +63,34 @@ RegPlane::RegPlane(LAMMPS *lmp, int narg, char **arg) :
|
||||
zstyle = CONSTANT;
|
||||
}
|
||||
|
||||
int nxstyle = (utils::strmatch(arg[5], "^v_")) ? 1 : 0;
|
||||
int nystyle = (utils::strmatch(arg[6], "^v_")) ? 1 : 0;
|
||||
int nzstyle = (utils::strmatch(arg[7], "^v_")) ? 1 : 0;
|
||||
|
||||
if (!nxstyle && !nystyle && !nzstyle) nstyle = CONSTANT;
|
||||
if (nxstyle && nystyle && nzstyle) nstyle = VARIABLE;
|
||||
|
||||
if (nstyle == CONSTANT) {
|
||||
normal[0] = xscale * utils::numeric(FLERR, arg[5], false, lmp);
|
||||
normal[1] = yscale * utils::numeric(FLERR, arg[6], false, lmp);
|
||||
normal[2] = zscale * utils::numeric(FLERR, arg[7], false, lmp);
|
||||
} else if (nstyle == VARIABLE) {
|
||||
normal[0] = 0.0;
|
||||
normal[1] = 0.0;
|
||||
normal[2] = 0.0;
|
||||
nxstr = utils::strdup(arg[5] + 2);
|
||||
nystr = utils::strdup(arg[6] + 2);
|
||||
nzstr = utils::strdup(arg[7] + 2);
|
||||
varshape = 1;
|
||||
} else {
|
||||
error->all(FLERR, "The components of the normal vector should be either all variables or all constants");
|
||||
}
|
||||
|
||||
if (varshape) {
|
||||
variable_check();
|
||||
RegPlane::shape_update();
|
||||
}
|
||||
|
||||
normal[0] = xscale * utils::numeric(FLERR, arg[5], false, lmp);
|
||||
normal[1] = yscale * utils::numeric(FLERR, arg[6], false, lmp);
|
||||
normal[2] = zscale * utils::numeric(FLERR, arg[7], false, lmp);
|
||||
|
||||
// enforce unit normal
|
||||
|
||||
double rsq = normal[0] * normal[0] + normal[1] * normal[1] + normal[2] * normal[2];
|
||||
@ -95,6 +116,9 @@ RegPlane::~RegPlane()
|
||||
delete[] xstr;
|
||||
delete[] ystr;
|
||||
delete[] zstr;
|
||||
delete[] nxstr;
|
||||
delete[] nystr;
|
||||
delete[] nzstr;
|
||||
delete[] contact;
|
||||
}
|
||||
|
||||
@ -174,6 +198,20 @@ void RegPlane::shape_update()
|
||||
if (ystyle == VARIABLE) yp = yscale * input->variable->compute_equal(yvar);
|
||||
|
||||
if (zstyle == VARIABLE) zp = zscale * input->variable->compute_equal(zvar);
|
||||
|
||||
if (nstyle == VARIABLE) {
|
||||
normal[0] = xscale * input->variable->compute_equal(nxvar);
|
||||
normal[1] = yscale * input->variable->compute_equal(nyvar);
|
||||
normal[2] = zscale * input->variable->compute_equal(nzvar);
|
||||
|
||||
// enforce unit normal
|
||||
double rsq = normal[0] * normal[0] + normal[1] * normal[1] + normal[2] * normal[2];
|
||||
|
||||
if (rsq == 0.0) error->all(FLERR, "Illegal region plane normal vector: {} {} {}", normal[0], normal[1], normal[2]);
|
||||
normal[0] /= sqrt(rsq);
|
||||
normal[1] /= sqrt(rsq);
|
||||
normal[2] /= sqrt(rsq);
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -202,4 +240,21 @@ void RegPlane::variable_check()
|
||||
if (!input->variable->equalstyle(zvar))
|
||||
error->all(FLERR, "Variable {} for region plane is invalid style", zstr);
|
||||
}
|
||||
|
||||
if (nstyle == VARIABLE) {
|
||||
nxvar = input->variable->find(nxstr);
|
||||
if (nxvar < 0) error->all(FLERR, "Variable {} for region plane does not exist", nxstr);
|
||||
if (!input->variable->equalstyle(nxvar))
|
||||
error->all(FLERR, "Variable {} for region plane is invalid style", nxstr);
|
||||
|
||||
nyvar = input->variable->find(nystr);
|
||||
if (nyvar < 0) error->all(FLERR, "Variable {} for region plane does not exist", nystr);
|
||||
if (!input->variable->equalstyle(nyvar))
|
||||
error->all(FLERR, "Variable {} for region plane is invalid style", nystr);
|
||||
|
||||
nzvar = input->variable->find(nzstr);
|
||||
if (nzvar < 0) error->all(FLERR, "Variable {} for region plane does not exist", nzstr);
|
||||
if (!input->variable->equalstyle(nzvar))
|
||||
error->all(FLERR, "Variable {} for region plane is invalid style", nzstr);
|
||||
}
|
||||
}
|
||||
|
||||
@ -45,6 +45,10 @@ class RegPlane : public Region {
|
||||
int zstyle, zvar;
|
||||
char *xstr, *ystr, *zstr;
|
||||
|
||||
int nstyle;
|
||||
int nxvar, nyvar, nzvar;
|
||||
char *nxstr, *nystr, *nzstr;
|
||||
|
||||
void variable_check();
|
||||
};
|
||||
|
||||
|
||||
@ -156,7 +156,7 @@ std::string utils::strcompress(const std::string &text)
|
||||
}
|
||||
|
||||
// remove trailing blank
|
||||
if (output.back() == ' ') output.erase(output.size() - 1, 1);
|
||||
if (!output.empty() && output.back() == ' ') output.erase(output.size() - 1, 1);
|
||||
return output;
|
||||
}
|
||||
|
||||
|
||||
@ -415,19 +415,19 @@ TEST_F(SimpleCommandsTest, Plugin)
|
||||
if (!bindir) GTEST_SKIP() << "LAMMPS_PLUGIN_DIR not set";
|
||||
std::string loadfmt = "plugin load {}/{}plugin.so";
|
||||
::testing::internal::CaptureStdout();
|
||||
lmp->input->one(fmt::format(loadfmt, bindir, "hello"));
|
||||
lmp->input->one(fmt::format(fmt::runtime(loadfmt), bindir, "hello"));
|
||||
auto text = ::testing::internal::GetCapturedStdout();
|
||||
if (verbose) std::cout << text;
|
||||
ASSERT_THAT(text, ContainsRegex(".*\n.*Loading plugin: Hello world command.*"));
|
||||
|
||||
::testing::internal::CaptureStdout();
|
||||
lmp->input->one(fmt::format(loadfmt, bindir, "xxx"));
|
||||
lmp->input->one(fmt::format(fmt::runtime(loadfmt), bindir, "xxx"));
|
||||
text = ::testing::internal::GetCapturedStdout();
|
||||
if (verbose) std::cout << text;
|
||||
ASSERT_THAT(text, ContainsRegex(".*Open of file .*xxx.* failed.*"));
|
||||
|
||||
::testing::internal::CaptureStdout();
|
||||
lmp->input->one(fmt::format(loadfmt, bindir, "nve2"));
|
||||
lmp->input->one(fmt::format(fmt::runtime(loadfmt), bindir, "nve2"));
|
||||
text = ::testing::internal::GetCapturedStdout();
|
||||
if (verbose) std::cout << text;
|
||||
ASSERT_THAT(text, ContainsRegex(".*Loading plugin: NVE2 variant fix style.*"));
|
||||
@ -438,7 +438,7 @@ TEST_F(SimpleCommandsTest, Plugin)
|
||||
ASSERT_THAT(text, ContainsRegex(".*1: command style plugin hello\n.*2: fix style plugin nve2.*"));
|
||||
|
||||
::testing::internal::CaptureStdout();
|
||||
lmp->input->one(fmt::format(loadfmt, bindir, "hello"));
|
||||
lmp->input->one(fmt::format(fmt::runtime(loadfmt), bindir, "hello"));
|
||||
text = ::testing::internal::GetCapturedStdout();
|
||||
if (verbose) std::cout << text;
|
||||
ASSERT_THAT(text, ContainsRegex(".*Ignoring load of command style hello: "
|
||||
|
||||
@ -1,6 +1,7 @@
|
||||
---
|
||||
lammps_version: 17 Feb 2022
|
||||
date_generated: Fri Mar 18 22:17:51 2022
|
||||
lammps_version: 4 Feb 2025
|
||||
tags: generated
|
||||
date_generated: Fri Feb 21 16:17:55 2025
|
||||
epsilon: 5e-13
|
||||
skip_tests: numdiff
|
||||
prerequisites: ! |
|
||||
@ -20,68 +21,68 @@ extract: ! ""
|
||||
natoms: 29
|
||||
init_energy: 20.65098133017812
|
||||
init_stress: ! |2-
|
||||
4.0957903125808471e+01 -2.2499632589286236e+01 -1.8458270536522217e+01 3.4849378298981264e+01 -4.9327943096381759e+00 -2.6124108916945294e+00
|
||||
4.4473180621356008e+01 -4.3463840015691233e+01 -1.0093406056647736e+00 4.5637584879601796e+01 -1.3907393586961433e+01 -4.2824939510892590e-01
|
||||
init_forces: ! |2
|
||||
1 1.6023996455832325e+01 2.4226311046592137e+00 -1.8589204266697958e+01
|
||||
2 -9.3711866901463381e-02 -7.5876216223294790e-01 -6.1013759002633705e-01
|
||||
3 -6.0380408211033587e-01 2.6993032298913775e+01 2.7951913775716850e+01
|
||||
4 -4.3564633502451269e+00 -1.0062417183984081e+01 2.1642186242701338e+00
|
||||
5 -1.5386439746171822e+01 -2.3440313238754023e+01 -1.0067874149174445e+01
|
||||
6 9.6873286040901903e+00 6.5740743013867231e-02 -2.6313308270088624e+00
|
||||
7 -4.1923658452230708e+00 3.7873664481235689e+00 -9.2297211491112741e-01
|
||||
8 -4.1328674241018124e+00 -1.3752082356191019e+01 9.4169257319147519e+00
|
||||
9 -5.2849046978682424e+00 5.1551127779597277e+00 -6.0440022931290430e-02
|
||||
10 8.5785584536205555e+00 1.9092658049053345e+01 -1.3500832217122007e+01
|
||||
11 -8.2548956740792931e+00 -3.8384442674446007e+00 4.3703985032254611e+00
|
||||
12 -2.2390516462227508e+00 -2.4339015686808576e+00 -5.7125783103934751e+00
|
||||
13 7.0748633959583906e-01 1.7495942830019229e+00 8.1749690284178111e-01
|
||||
14 5.0293855034635815e+00 -4.3347315249911471e+00 -2.2794877131015205e+00
|
||||
15 4.2836129602031709e+00 -2.6803643297135835e+00 7.8342386854077670e+00
|
||||
16 -1.6475295059196460e+00 4.5975354658004379e+00 4.3681254253354895e-01
|
||||
17 1.8816655220378973e+00 -2.5626545385335930e+00 1.3828524454567255e+00
|
||||
18 1.6064693296025290e-01 1.6787555240920624e+00 -6.8129331975320220e+00
|
||||
19 -1.9670041679005905e+00 -2.4504879220906162e+00 2.9176882347102016e+00
|
||||
20 1.8063572349403376e+00 7.7173239799855375e-01 3.8952449628218204e+00
|
||||
21 2.3714039975200247e+00 2.9686059791249759e+00 -8.8717809550958702e+00
|
||||
22 -4.2227815913112092e+00 -2.8790902397071427e+00 3.1362978814995639e+00
|
||||
23 1.8513775937911845e+00 -8.9515739417833418e-02 5.7354830735963063e+00
|
||||
24 -1.4568411370574479e+00 5.6628278324597936e+00 -3.3714304805753512e+00
|
||||
25 -1.1685952378028448e+00 -3.9152363566022288e+00 6.4031275969729240e-01
|
||||
26 2.6254363748602927e+00 -1.7475914758575648e+00 2.7311177208780588e+00
|
||||
27 -6.3244441950917718e-01 5.1918732409438757e+00 -1.7685243510997146e+00
|
||||
28 -1.3828773692511866e+00 -3.1042973063575481e+00 7.2112563744890223e-02
|
||||
29 2.0153217887603638e+00 -2.0875759345863276e+00 1.6964117873548243e+00
|
||||
run_energy: 20.572797398210106
|
||||
1 2.3703974495881418e+01 3.8584484587903516e+00 -1.5929138796293980e+01
|
||||
2 -5.5592010971213179e-01 -4.5011497307751007e+00 -3.6194749630118039e+00
|
||||
3 -2.8457465117799385e+00 2.6325352833001663e+01 2.5623331548006441e+01
|
||||
4 -7.9894054979056088e+00 -1.2258360452072225e+01 6.4168233111021600e+00
|
||||
5 -2.2204738294831444e+01 -2.3698109015673438e+01 -1.1480776479805904e+01
|
||||
6 2.3347569650102201e+01 -4.7137825565345990e+00 -1.6078168111448818e+01
|
||||
7 -8.0686673030183851e+00 7.1975893900877121e+00 -1.7579980765823877e+00
|
||||
8 -3.1824458002558198e+00 -1.2503128164663320e+01 4.0602708742130751e+01
|
||||
9 -7.7323033517797342e+00 8.0399091320421157e+00 -2.0951400051039776e-01
|
||||
10 4.9524658729988271e+00 2.0621211528107622e+01 -3.2638235652308239e+01
|
||||
11 -1.0127717019112277e+01 -3.1783095109070576e+00 4.4288595135259623e+00
|
||||
12 -5.4777124732518541e+00 -5.3066394246038655e+00 -4.8409352484994574e+00
|
||||
13 1.4412505843466221e+00 3.6458164082141984e+00 -5.3031504624386550e-02
|
||||
14 7.6148261062259106e+00 -4.7428356370992075e+00 -3.3084707170534466e+00
|
||||
15 6.1963584357832016e+00 -3.1286786554578465e+00 9.2319462456089330e+00
|
||||
16 1.9503516089515505e-01 5.3411834252929946e+00 3.0732566957386886e+00
|
||||
17 7.3317605541385511e-01 -9.9851802775000564e-01 5.3881749402587964e-01
|
||||
18 7.8915981928254553e-02 8.2466959163160869e-01 -3.3467760833494964e+00
|
||||
19 -9.6626846530114285e-01 -1.2037743703637904e+00 1.4332812196273430e+00
|
||||
20 8.8735248337288830e-01 3.7910477873218174e-01 1.9134948637221534e+00
|
||||
21 1.7083446765076102e+00 2.1385652661420855e+00 -6.3911757682915322e+00
|
||||
22 -3.0420655692218990e+00 -2.0740786847506296e+00 2.2593694686375940e+00
|
||||
23 1.3337208927142887e+00 -6.4486581391455855e-02 4.1318062996539382e+00
|
||||
24 -6.5262931439741845e-01 2.5368088200155672e+00 -1.5103186662621493e+00
|
||||
25 -5.2350217841582225e-01 -1.7539304417736190e+00 2.8684450674231776e-01
|
||||
26 1.1761314928132407e+00 -7.8287837824194817e-01 1.2234741595198315e+00
|
||||
27 -1.4360109768190377e-01 1.1788525179864244e+00 -4.0155629532187376e-01
|
||||
28 -3.1399234787785879e-01 -7.0485324397341742e-01 1.6373681213693980e-02
|
||||
29 4.5759344555976256e-01 -4.7399927401300701e-01 3.8518261410817978e-01
|
||||
run_energy: 20.563089678525095
|
||||
run_stress: ! |2-
|
||||
4.0414601145881797e+01 -2.2259720000355955e+01 -1.8154881145525852e+01 3.4356097430708779e+01 -5.1760682620031364e+00 -3.0219001073831251e+00
|
||||
4.3757504913648717e+01 -4.3136475705003690e+01 -6.2102920864502398e-01 4.4978336549538170e+01 -1.4195605982625462e+01 -9.5958875069195426e-01
|
||||
run_forces: ! |2
|
||||
1 1.5854493147994468e+01 2.5625041903632799e+00 -1.8403707584219106e+01
|
||||
2 -1.0778147157154638e-01 -8.7954374413252623e-01 -7.1033263283976922e-01
|
||||
3 -3.5903740231368531e-01 2.6747382244473858e+01 2.7776094765308645e+01
|
||||
4 -4.3667455132582980e+00 -9.9043336720965058e+00 2.2554137013679947e+00
|
||||
5 -1.5435306686274892e+01 -2.3368620551346410e+01 -1.0071205010683158e+01
|
||||
6 9.7004722937707939e+00 2.8185574443369887e-02 -2.6469111215932326e+00
|
||||
7 -4.2051376166149819e+00 3.8059875922956321e+00 -9.2948254913796591e-01
|
||||
8 -4.0811558306056437e+00 -1.3725195219352738e+01 9.4305267102762365e+00
|
||||
9 -5.3018040121457650e+00 5.1712375236873847e+00 -5.5170438746634645e-02
|
||||
10 8.5884631851414728e+00 1.8977169595422669e+01 -1.3503733846157115e+01
|
||||
11 -8.2489793835708181e+00 -3.8307795657532537e+00 4.3670355271621792e+00
|
||||
12 -2.2854196014066837e+00 -2.5730964210485521e+00 -5.5327026624884477e+00
|
||||
13 6.8857552776933151e-01 1.7099649678302227e+00 8.4476951940005041e-01
|
||||
14 5.0388676050555423e+00 -4.1380632752237698e+00 -2.2619786920581912e+00
|
||||
15 4.2713089863647395e+00 -2.6164691252678471e+00 7.6327855841331855e+00
|
||||
16 -1.6264161996020632e+00 4.5902884407035716e+00 4.2906258286847709e-01
|
||||
17 1.8756029712680284e+00 -2.5566185549983906e+00 1.3795361474068475e+00
|
||||
18 1.5949074618033343e-01 1.6020315457790089e+00 -6.4757984092122420e+00
|
||||
19 -1.8652368265982364e+00 -2.3286173150011749e+00 2.7801057275919980e+00
|
||||
20 1.7057460804179030e+00 7.2658576922216600e-01 3.6956926816202440e+00
|
||||
21 2.3015994659382928e+00 2.8609989652412211e+00 -8.6002184142674114e+00
|
||||
22 -4.0843967543541595e+00 -2.7748751066344699e+00 3.0465239349836377e+00
|
||||
23 1.7827972884158667e+00 -8.6123858606751036e-02 5.5536944792837737e+00
|
||||
24 -1.4105671680157181e+00 5.4757757163248080e+00 -3.2567653472769562e+00
|
||||
25 -1.1213719131694626e+00 -3.7848791001392499e+00 6.1939772997237075e-01
|
||||
26 2.5319390811851807e+00 -1.6908966161855581e+00 2.6373676173045855e+00
|
||||
27 -6.3028932344593613e-01 5.1333019072249222e+00 -1.7384473964198608e+00
|
||||
28 -1.3620336377103808e+00 -3.0692701554272155e+00 6.6735136389115879e-02
|
||||
29 1.9923229611563169e+00 -2.0640317517977067e+00 1.6717122600307448e+00
|
||||
1 2.3451032879726370e+01 4.0617257197173897e+00 -1.5621894955519736e+01
|
||||
2 -5.7421401726330101e-01 -4.6835780748393674e+00 -3.7823299076024632e+00
|
||||
3 -2.4306027199459486e+00 2.6072519970009257e+01 2.5364241217921947e+01
|
||||
4 -8.0249953558852880e+00 -1.2074108242088608e+01 6.5482299702187063e+00
|
||||
5 -2.2289140460440823e+01 -2.3631032649621293e+01 -1.1494387406884398e+01
|
||||
6 2.3354057831390289e+01 -4.7586966738793901e+00 -1.6119827865958250e+01
|
||||
7 -8.0844064733133774e+00 7.2149529473510370e+00 -1.7660273021312418e+00
|
||||
8 -3.1478296151921232e+00 -1.2498537099228518e+01 4.0622223121616166e+01
|
||||
9 -7.7511017876278920e+00 8.0605427659852786e+00 -2.0241485109620189e-01
|
||||
10 4.9915744598623162e+00 2.0482598351331305e+01 -3.2624972375682837e+01
|
||||
11 -1.0123311005215982e+01 -3.1688924167926276e+00 4.4252676678697700e+00
|
||||
12 -5.5513668937759473e+00 -5.4355045396603447e+00 -4.6167965020560917e+00
|
||||
13 1.4059367926919679e+00 3.5728783709008667e+00 2.5935291038754471e-03
|
||||
14 7.6143970879681024e+00 -4.5037794326053131e+00 -3.2831360392059907e+00
|
||||
15 6.2058701073495151e+00 -3.0406636127154227e+00 8.9669093364259496e+00
|
||||
16 2.2902239968198557e-01 5.3178918884056445e+00 3.0490139755759853e+00
|
||||
17 7.2507676999013526e-01 -9.8831727226989585e-01 5.3330838740480679e-01
|
||||
18 7.1127024594080268e-02 7.1445956198119154e-01 -2.8880230496978854e+00
|
||||
19 -8.3188306575710236e-01 -1.0385320257838888e+00 1.2398389619370178e+00
|
||||
20 7.6075604116302209e-01 3.2407246380269727e-01 1.6481840877608676e+00
|
||||
21 1.6140194966539338e+00 2.0063050011497334e+00 -6.0309928490009383e+00
|
||||
22 -2.8643056040092603e+00 -1.9459468475255317e+00 2.1363729514270524e+00
|
||||
23 1.2502861073553264e+00 -6.0358153624201771e-02 3.8946198975738859e+00
|
||||
24 -5.8408404963238691e-01 2.2673919964618818e+00 -1.3485518584960339e+00
|
||||
25 -4.6437462735412272e-01 -1.5672547533259689e+00 2.5645620543256875e-01
|
||||
26 1.0484586769865096e+00 -7.0013724313591297e-01 1.0920956530634651e+00
|
||||
27 -1.3425430939812166e-01 1.0934202317724093e+00 -3.7029815332428351e-01
|
||||
28 -2.9014265041938359e-01 -6.5377692091134065e-01 1.4204173363709049e-02
|
||||
29 4.2439695981750525e-01 -4.3964331086106867e-01 3.5609397996057446e-01
|
||||
...
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
---
|
||||
lammps_version: 17 Feb 2022
|
||||
date_generated: Fri Mar 18 22:17:50 2022
|
||||
epsilon: 4e-13
|
||||
epsilon: 5e-13
|
||||
skip_tests:
|
||||
prerequisites: ! |
|
||||
atom full
|
||||
|
||||
@ -24,30 +24,30 @@ using ::testing::Eq;
|
||||
|
||||
TEST(FmtLib, insert_string)
|
||||
{
|
||||
const char val[] = "word";
|
||||
auto text = fmt::format("word {}", val);
|
||||
constexpr char val[] = "word";
|
||||
auto text = fmt::format("word {}", val);
|
||||
ASSERT_THAT(text, Eq("word word"));
|
||||
}
|
||||
|
||||
TEST(FmtLib, insert_int)
|
||||
{
|
||||
const int val = 333;
|
||||
auto text = fmt::format("word {}", val);
|
||||
constexpr int val = 333;
|
||||
auto text = fmt::format("word {}", val);
|
||||
ASSERT_THAT(text, Eq("word 333"));
|
||||
}
|
||||
|
||||
TEST(FmtLib, insert_neg_int)
|
||||
{
|
||||
const int val = -333;
|
||||
auto text = fmt::format("word {}", val);
|
||||
constexpr int val = -333;
|
||||
auto text = fmt::format("word {}", val);
|
||||
ASSERT_THAT(text, Eq("word -333"));
|
||||
}
|
||||
|
||||
TEST(FmtLib, insert_bigint)
|
||||
{
|
||||
#if defined(LAMMPS_BIGBIG) || defined(LAMMPS_SMALLBIG)
|
||||
const bigint val = 9945234592L;
|
||||
auto text = fmt::format("word {}", val);
|
||||
constexpr bigint val = 9945234592L;
|
||||
auto text = fmt::format("word {}", val);
|
||||
ASSERT_THAT(text, Eq("word 9945234592"));
|
||||
#else
|
||||
GTEST_SKIP();
|
||||
@ -57,8 +57,8 @@ TEST(FmtLib, insert_bigint)
|
||||
TEST(FmtLib, insert_neg_bigint)
|
||||
{
|
||||
#if defined(LAMMPS_BIGBIG) || defined(LAMMPS_SMALLBIG)
|
||||
const bigint val = -9945234592L;
|
||||
auto text = fmt::format("word {}", val);
|
||||
constexpr bigint val = -9945234592L;
|
||||
auto text = fmt::format("word {}", val);
|
||||
ASSERT_THAT(text, Eq("word -9945234592"));
|
||||
#else
|
||||
GTEST_SKIP();
|
||||
@ -68,8 +68,8 @@ TEST(FmtLib, insert_neg_bigint)
|
||||
TEST(FmtLib, insert_tagint)
|
||||
{
|
||||
#if defined(LAMMPS_BIGBIG)
|
||||
const tagint val = 9945234592L;
|
||||
auto text = fmt::format("word {}", val);
|
||||
constexpr tagint val = 9945234592L;
|
||||
auto text = fmt::format("word {}", val);
|
||||
ASSERT_THAT(text, Eq("word 9945234592"));
|
||||
#else
|
||||
GTEST_SKIP();
|
||||
@ -79,8 +79,8 @@ TEST(FmtLib, insert_tagint)
|
||||
TEST(FmtLib, insert_neg_tagint)
|
||||
{
|
||||
#if defined(LAMMPS_BIGBIG)
|
||||
const tagint val = -9945234592L;
|
||||
auto text = fmt::format("word {}", val);
|
||||
constexpr tagint val = -9945234592L;
|
||||
auto text = fmt::format("word {}", val);
|
||||
ASSERT_THAT(text, Eq("word -9945234592"));
|
||||
#else
|
||||
GTEST_SKIP();
|
||||
@ -90,8 +90,8 @@ TEST(FmtLib, insert_neg_tagint)
|
||||
TEST(FmtLib, insert_imageint)
|
||||
{
|
||||
#if defined(LAMMPS_BIGBIG)
|
||||
const imageint val = 9945234592L;
|
||||
auto text = fmt::format("word {}", val);
|
||||
constexpr imageint val = 9945234592L;
|
||||
auto text = fmt::format("word {}", val);
|
||||
ASSERT_THAT(text, Eq("word 9945234592"));
|
||||
#else
|
||||
GTEST_SKIP();
|
||||
@ -101,8 +101,8 @@ TEST(FmtLib, insert_imageint)
|
||||
TEST(FmtLib, insert_neg_imageint)
|
||||
{
|
||||
#if defined(LAMMPS_BIGBIG)
|
||||
const imageint val = -9945234592L;
|
||||
auto text = fmt::format("word {}", val);
|
||||
constexpr imageint val = -9945234592L;
|
||||
auto text = fmt::format("word {}", val);
|
||||
ASSERT_THAT(text, Eq("word -9945234592"));
|
||||
#else
|
||||
GTEST_SKIP();
|
||||
@ -111,26 +111,38 @@ TEST(FmtLib, insert_neg_imageint)
|
||||
|
||||
TEST(FmtLib, insert_double)
|
||||
{
|
||||
const double val = 1.5;
|
||||
auto text = fmt::format("word {}", val);
|
||||
constexpr double val = 1.5;
|
||||
auto text = fmt::format("word {}", val);
|
||||
ASSERT_THAT(text, Eq("word 1.5"));
|
||||
}
|
||||
|
||||
TEST(FmtLib, insert_neg_double)
|
||||
{
|
||||
const double val = -1.5;
|
||||
auto text = fmt::format("word {}", val);
|
||||
constexpr double val = -1.5;
|
||||
auto text = fmt::format("word {}", val);
|
||||
ASSERT_THAT(text, Eq("word -1.5"));
|
||||
}
|
||||
|
||||
TEST(FmtLib, int_for_double)
|
||||
{
|
||||
const double val = -1.5;
|
||||
ASSERT_THROW(auto text = fmt::format("word {:d}", val), std::exception);
|
||||
ASSERT_THROW(auto text = fmt::format(fmt::runtime("word {:d}"), val), std::exception);
|
||||
}
|
||||
|
||||
TEST(FmtLib, double_for_int)
|
||||
{
|
||||
const int val = 15;
|
||||
ASSERT_THROW(auto text = fmt::format("word {:g}", val), std::exception);
|
||||
ASSERT_THROW(auto text = fmt::format(fmt::runtime("word {:g}"), val), std::exception);
|
||||
}
|
||||
|
||||
TEST(FmtLib, double_for_string)
|
||||
{
|
||||
ASSERT_THROW(auto text = fmt::format(fmt::runtime("word {:g}"), "I am not a number"),
|
||||
std::exception);
|
||||
}
|
||||
|
||||
TEST(FmtLib, int_for_string)
|
||||
{
|
||||
ASSERT_THROW(auto text = fmt::format(fmt::runtime("word {:d}"), "I am not a number"),
|
||||
std::exception);
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user