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Revert "added dihedral charmfsw kokkos test"

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This reverts commit 95af3cdab2.
This commit is contained in:
alphataubio
2024-06-13 12:27:56 -04:00
parent 95af3cdab2
commit af9d97ea07
14 changed files with 8 additions and 15883 deletions
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14
unittest/force-styles/test_fix_timestep.cpp
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@ -104,13 +104,8 @@ LAMMPS *init_lammps(LAMMPS::argv & args, const TestConfig &cfg, const bool use_r
if (use_respa) command("run_style respa 2 1 bond 1 pair 2");
std::cerr << "============ test_config.input_file = " << test_config.input_file << "\n\n";
if (!utils::strmatch(test_config.input_file, "in.dpdrx-shardlow") ) {
std::cerr << "set up molecular system force field\n\n";
// set up molecular system force field
command("pair_style lj/cut 8.0");
command("pair_coeff 1 1 0.02 2.5");
command("pair_coeff 2 2 0.005 1.0");
@ -131,16 +126,11 @@ LAMMPS *init_lammps(LAMMPS::argv & args, const TestConfig &cfg, const bool use_r
command("angle_coeff 4 100.0 108.5");
command("group solute molecule 1:2");
command("group solvent molecule 3:5");
}
for (auto &post_command : cfg.post_commands)
command(post_command);
if (utils::strmatch(test_config.input_file, "in.dpdrx-shardlow") )
command("timestep 0.001");
else
command("timestep 0.25");
command("timestep 0.25");
command("run 0 post no");
command("thermo 2");
command("run 4 post no start 0 stop 8");

9603
unittest/force-styles/tests/dump.dpdrx
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File diff suppressed because it is too large Load Diff

78
unittest/force-styles/tests/fix-timestep-dt_reset.yaml
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@ -1,78 +0,0 @@
---
lammps_version: 17 Apr 2024
tags: generated
date_generated: Fri Jun 7 18:46:06 2024
epsilon: 2e-14
skip_tests:
prerequisites: ! |
atom full
fix nve
fix dt/reset
pre_commands: ! ""
post_commands: ! |
fix move all nve
fix test solute dt/reset 1 0.01 2.0 0.2 units box
input_file: in.fourmol
natoms: 29
global_scalar: 0
run_pos: ! |2
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run_vel: ! |2
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...

77
unittest/force-styles/tests/fix-timestep-freeze.yaml
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@ -1,77 +0,0 @@
---
lammps_version: 17 Feb 2022
date_generated: Fri Mar 18 22:18:00 2022
epsilon: 2e-11
skip_tests:
prerequisites: ! |
atom sphere
fix freeze
pre_commands: ! ""
post_commands: ! |
fix move all nve
fix test solute freeze
input_file: in.brownian
natoms: 29
global_vector: ! |-
3 0.031196595768690827 0.027176378299486714 -0.018248127489101762
run_pos: ! |2
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run_vel: ! |2
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...

78
unittest/force-styles/tests/fix-timestep-langevin.yaml
View File

@ -1,78 +0,0 @@
---
lammps_version: 17 Apr 2024
tags: generated
date_generated: Fri Jun 7 22:27:03 2024
epsilon: 5e-13
skip_tests:
prerequisites: ! |
atom full
fix nve
fix langevin
pre_commands: ! ""
post_commands: ! |
fix move all nve
fix test solute langevin 1.0 1.1 100.0 12345
input_file: in.fourmol
natoms: 29
global_scalar: 0
run_pos: ! |2
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27 4.5604120224184493e-04 -1.0305523011183196e-03 2.1188057828807350e-04
28 -6.2544520858559939e-03 1.4127711179204101e-03 -1.8429821887785932e-03
29 6.4110631663490928e-04 3.1273432727030488e-03 3.7253671094343694e-03
...

12
unittest/force-styles/tests/fix-timestep-nve_sphere.yaml
View File

@ -4,14 +4,14 @@ date_generated: Fri Mar 18 22:17:59 2022
epsilon: 5e-14
skip_tests:
prerequisites: ! |
#atom full
#atom dipole
#atom sphere
#fix nve/sphere
#pair lj/cut/dipole/cut
atom full
atom dipole
atom sphere
fix nve/sphere
pair lj/cut/dipole/cut
pre_commands: ! ""
post_commands: ! |
pair_style lj/cut/dipole/cut 2.5 5.0
pair_style lj/cut/dipole/cut 8.0
pair_coeff * * 0.0 3.0
fix test solute nve/sphere
input_file: in.dipole

91
unittest/force-styles/tests/fix-timestep-shardlow copy.yaml
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@ -1,91 +0,0 @@
---
lammps_version: 17 Feb 2022
date_generated: Fri Mar 18 22:17:59 2022
epsilon: 2e-14
skip_tests:
prerequisites: ! |
atom dpd
fix nve
pre_commands: ! ""
post_commands: ! |
fix 4 all rx kinetics.dpdrx none dense lammps_rk4 1
set atom * d_rdx 1.00
set atom * d_h2 0.0
set atom * d_no2 0.0
set atom * d_n2 0.0
set atom * d_hcn 0.0
set atom * d_no 0.0
set atom * d_h2o 0.0
set atom * d_co 0.0
set atom * d_co2 0.0
set atom * dpd/theta 2065.00
timestep 0.001
pair_style hybrid/overlay dpd/fdt/energy 16.00 234324 exp6/rx 16.00
pair_coeff * * dpd/fdt/energy 0.0 0.05 10.0 16.00
pair_coeff * * exp6/rx params.exp6 1fluid 1fluid exponent 1.0 1.0 16.00
fix 1 all shardlow
fix 2 all nve
fix 3 all eos/table/rx linear table.eos 4001 KEYWORD thermo.dpdrx
input_file: in.dpdrx-shardlow
natoms: 29
run_pos: ! |2
1 -2.7045559764772636e-01 2.4912159908661540e+00 -1.6695851750890134e-01
2 3.1004029572800829e-01 2.9612354631162883e+00 -8.5466363035055182e-01
3 -7.0398551409567367e-01 1.2305509955796761e+00 -6.2777526927691529e-01
4 -1.5818159336524433e+00 1.4837407818931854e+00 -1.2538710836034257e+00
5 -9.0719763673143938e-01 9.2652103885754256e-01 3.9954210488744507e-01
6 2.4831720509137747e-01 2.8313021474851946e-01 -1.2314233328432578e+00
7 3.4143527679197477e-01 -2.2646550369995716e-02 -2.5292291416062129e+00
8 1.1743552228749641e+00 -4.8863228576130058e-01 -6.3783432890943681e-01
9 1.3800524229486879e+00 -2.5274721030864977e-01 2.8353985887494298e-01
10 2.0510765219972789e+00 -1.4604063739897442e+00 -9.8323745066910395e-01
11 1.7878031944038735e+00 -1.9921863272595286e+00 -1.8890602447323932e+00
12 3.0063007040474412e+00 -4.9013350497870395e-01 -1.6231898104999232e+00
13 4.0515402959329752e+00 -8.9202011603544384e-01 -1.6400005529743578e+00
14 2.6066963345551839e+00 -4.1789253964855821e-01 -2.6634003608660097e+00
15 2.9695287185765005e+00 5.5422613164855661e-01 -1.2342022021736101e+00
16 2.6747029694779090e+00 -2.4124119054031508e+00 -2.3435746001955464e-02
17 2.2153577785226939e+00 -2.0897985186816044e+00 1.1963150794967707e+00
18 2.1384791188033843e+00 3.0177261773770208e+00 -3.5160827596876225e+00
19 1.5349125211132961e+00 2.6315969880333707e+00 -4.2472859440220647e+00
20 2.7641167828863153e+00 3.6833419064000221e+00 -3.9380850623312638e+00
21 4.9064454390208301e+00 -4.0751205255383196e+00 -3.6215576073601046e+00
22 4.3687453488627543e+00 -4.2054270536772504e+00 -4.4651491269372565e+00
23 5.7374928154769504e+00 -3.5763355905184966e+00 -3.8820297194230728e+00
24 2.0684115301174013e+00 3.1518221747664397e+00 3.1554242678474576e+00
25 1.2998381073113014e+00 3.2755513587518097e+00 2.5092990173114837e+00
26 2.5807438597688113e+00 4.0120175892854135e+00 3.2133398379059099e+00
27 -1.9613581876744359e+00 -4.3556300596085160e+00 2.1101467673534788e+00
28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00
29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00
run_vel: ! |2
1 8.1705745750215355e-03 1.6516406624177568e-02 4.7902269490513816e-03
2 5.4501493264497653e-03 5.1791699524041859e-03 -1.4372931188098724e-03
3 -8.2298293869533471e-03 -1.2926551603583568e-02 -4.0984178763235103e-03
4 -3.7699042632974764e-03 -6.5722892095586034e-03 -1.1184640307556133e-03
5 -1.1021961013432616e-02 -9.8906780949598733e-03 -2.8410737767347836e-03
6 -3.9676663388061570e-02 4.6817061143308802e-02 3.7148492456495326e-02
7 9.1034010711748495e-04 -1.0128523385947431e-02 -5.1568251957150528e-02
8 7.9064711492041403e-03 -3.3507255912560130e-03 3.4557098774889522e-02
9 1.5644176103896980e-03 3.7365546026078196e-03 1.5047408831488810e-02
10 2.9201446724707314e-02 -2.9249578666046938e-02 -1.5018077196173917e-02
11 -4.7835962161678980e-03 -3.7481384556453390e-03 -2.3464103658842415e-03
12 2.2696453478564947e-03 -3.4774151000032500e-04 -3.0640766808544074e-03
13 2.7531740679274967e-03 5.8171062119749019e-03 -7.9467451203004726e-04
14 3.5246182394862522e-03 -5.7939995493321130e-03 -3.9478430939281980e-03
15 -1.8547943547235332e-03 -5.8554729996935298e-03 6.2938485237843487e-03
16 1.8681499891767241e-02 -1.3262466107722061e-02 -4.5638651214503466e-02
17 -1.2896270000483427e-02 9.7527665388161214e-03 3.7296535433762990e-02
18 -6.0936815808025862e-04 -9.3774557532468582e-04 -3.3558072507805731e-04
19 -6.9919768291957119e-04 -3.6060777270430031e-03 4.2833405289822791e-03
20 4.7777805013736515e-03 5.1003745845520452e-03 1.8002873923729241e-03
21 -9.5568188553430398e-04 1.6594630943762931e-04 -1.8199788009966615e-04
22 -3.3137518957653462e-03 -2.8683968287936054e-03 3.6384389958326871e-03
23 2.4209481134686401e-04 -4.5457709985051130e-03 2.7663581642115042e-03
24 2.5447450568861086e-04 4.8412447786110117e-04 -4.8021914527341357e-04
25 4.3722771097312743e-03 -4.5184411669545515e-03 2.5200952006556795e-03
26 -1.9250110555001179e-03 -3.0342169883610837e-03 3.5062814567984532e-03
27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04
28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03
29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03
...

1753
unittest/force-styles/tests/fix-timestep-shardlow.yaml
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76
unittest/force-styles/tests/fix-timestep-viscous.yaml
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@ -1,76 +0,0 @@
---
lammps_version: 17 Apr 2024
tags: generated
date_generated: Fri Jun 7 18:38:01 2024
epsilon: 5e-13
skip_tests:
prerequisites: ! |
atom full
fix nve
fix viscous
pre_commands: ! ""
post_commands: ! |
fix test solute viscous 0.5
input_file: in.fourmol
natoms: 29
run_pos: ! |2
1 -2.7993683669226832e-01 2.4726588069312840e+00 -1.7200860244148433e-01
2 3.0197083955402204e-01 2.9515239068888608e+00 -8.5689735572907566e-01
3 -6.9435377880558602e-01 1.2440473127136711e+00 -6.2233801468892025e-01
4 -1.5771614164685133e+00 1.4915333140468066e+00 -1.2487126845040522e+00
5 -8.9501761359359255e-01 9.3568128743071344e-01 4.0227731871484346e-01
6 2.9412607937706009e-01 2.2719282656652909e-01 -1.2843094067857870e+00
7 3.4019871062879609e-01 -9.1277350075786561e-03 -2.4633113224304561e+00
8 1.1641187171852805e+00 -4.8375305955385234e-01 -6.7659823767368688e-01
9 1.3777459838125838e+00 -2.5366338669522998e-01 2.6877644730326306e-01
10 2.0185283555536988e+00 -1.4283966846517357e+00 -9.6733527271133024e-01
11 1.7929780509347666e+00 -1.9871047540768743e+00 -1.8840626643185674e+00
12 3.0030247876861225e+00 -4.8923319967572748e-01 -1.6188658531537248e+00
13 4.0447273787895934e+00 -9.0131998547446246e-01 -1.6384447268320836e+00
14 2.6033152817257075e+00 -4.0789761505963579e-01 -2.6554413538823063e+00
15 2.9756315249791303e+00 5.6334269722969288e-01 -1.2437650754599008e+00
16 2.6517554244980306e+00 -2.3957110424978438e+00 3.2908335999178327e-02
17 2.2309964792710639e+00 -2.1022918943319384e+00 1.1491948328949437e+00
18 2.1384791188033843e+00 3.0177261773770208e+00 -3.5160827596876225e+00
19 1.5349125211132961e+00 2.6315969880333707e+00 -4.2472859440220647e+00
20 2.7641167828863153e+00 3.6833419064000221e+00 -3.9380850623312638e+00
21 4.9064454390208301e+00 -4.0751205255383196e+00 -3.6215576073601046e+00
22 4.3687453488627543e+00 -4.2054270536772504e+00 -4.4651491269372565e+00
23 5.7374928154769504e+00 -3.5763355905184966e+00 -3.8820297194230728e+00
24 2.0684115301174013e+00 3.1518221747664397e+00 3.1554242678474576e+00
25 1.2998381073113014e+00 3.2755513587518097e+00 2.5092990173114837e+00
26 2.5807438597688113e+00 4.0120175892854135e+00 3.2133398379059099e+00
27 -1.9613581876744359e+00 -4.3556300596085160e+00 2.1101467673534788e+00
28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00
29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00
run_vel: ! |2
1 7.7867804888392077e-04 5.8970331623292821e-04 -2.2179517633030531e-04
2 2.7129529964126462e-03 4.6286427111164284e-03 3.5805549693846352e-03
3 -1.2736791029204805e-03 1.6108674226414498e-03 -3.3618185901550799e-04
4 -9.2828595122009308e-04 -1.2537885319521818e-03 -4.1204974953432108e-03
5 -1.1800848061603740e-03 7.5424401975844038e-04 6.9023177964912290e-05
6 -3.0914004879905335e-04 1.2755385764678133e-03 7.9574303350202582e-04
7 -1.1037894966874103e-04 -7.6764845099077425e-04 -7.7217630460203659e-04
8 3.9060281273221989e-04 -8.1444231918053418e-04 1.5134641148324972e-04
9 1.2475530960659720e-03 -2.6608454451432528e-03 1.1117602907112732e-03
10 4.5008983776042893e-04 4.9530197647538077e-04 -2.3336234361093645e-04
11 -3.6977669078869707e-04 -1.5289071951960539e-03 -2.9176389881837113e-03
12 1.0850834530183159e-03 -6.4965897903201833e-04 -1.2971152622619948e-03
13 4.0754559196230639e-03 3.5043502394946119e-03 -7.8324487687854666e-04
14 -1.3837220448746613e-04 -4.0656048637594394e-03 -3.9333461173944500e-03
15 -4.3301707382721859e-03 -3.1802661664634938e-03 3.2037919043360571e-03
16 -9.6715751018414326e-05 -5.0016572678960377e-04 1.4945658875149626e-03
17 6.5692180538157174e-04 3.6635779995305095e-04 8.3495414466050911e-04
18 -6.0936815808025862e-04 -9.3774557532468582e-04 -3.3558072507805731e-04
19 -6.9919768291957119e-04 -3.6060777270430031e-03 4.2833405289822791e-03
20 4.7777805013736515e-03 5.1003745845520452e-03 1.8002873923729241e-03
21 -9.5568188553430398e-04 1.6594630943762931e-04 -1.8199788009966615e-04
22 -3.3137518957653462e-03 -2.8683968287936054e-03 3.6384389958326871e-03
23 2.4209481134686401e-04 -4.5457709985051130e-03 2.7663581642115042e-03
24 2.5447450568861086e-04 4.8412447786110117e-04 -4.8021914527341357e-04
25 4.3722771097312743e-03 -4.5184411669545515e-03 2.5200952006556795e-03
26 -1.9250110555001179e-03 -3.0342169883610837e-03 3.5062814567984532e-03
27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04
28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03
29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03
...

58
unittest/force-styles/tests/in.dpdrx-shardlow
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@ -1,58 +0,0 @@
# Example for running DPD-RX
boundary p p p
units metal # ev, ps
atom_style dpd
atom_modify map array
#fix 4 all rx kinetics.dpdrx none dense lammps_rk4 1
lattice hcp 6.6520898 origin 0.0833333333333 0.25 0.25 orient z 1 0 0 orient x 0 1 0 orient y 0 0 1
region box block 0 6.0 0 6.0 0.0 6.0 units lattice
create_box 2 box
region atoms block 0 6.0 0 6.0 0.0 6.0 units lattice
create_atoms 1 region atoms
comm_modify mode single vel yes
mass * 222.12
#Set concentrations
#set atom * d_rdx 1.00
#set atom * d_h2 0.0
#set atom * d_no2 0.0
#set atom * d_n2 0.0
#set atom * d_hcn 0.0
#set atom * d_no 0.0
#set atom * d_h2o 0.0
#set atom * d_co 0.0
#set atom * d_co2 0.0
#Set the kinetic temperature of the particles
#velocity all create 2065.0 875661 dist gaussian
#Set the internal temperature of the particles
#set atom * dpd/theta 2065.00
#timestep 0.001
#pair_style hybrid/overlay dpd/fdt/energy 16.00 234324 exp6/rx 16.00
#pair_coeff * * dpd/fdt/energy 0.0 0.05 10.0 16.00
#pair_coeff * * exp6/rx params.exp6 1fluid 1fluid exponent 1.0 1.0 16.00
#fix 1 all shardlow
#fix 2 all nve
#fix 3 all eos/table/rx linear table.eos 4001 KEYWORD thermo.dpdrx
#compute dpdU all dpd
#compute dpdUatom all dpd/atom
#compute crdx all property/atom d_rdx
#variable totEnergy equal pe+c_dpdU[1]+c_dpdU[2]+c_dpdU[3]
#thermo 1
#thermo_style custom step temp press vol pe ke c_dpdU[1] c_dpdU[2] c_dpdU[3] v_totEnergy c_dpdU[4]
#thermo_modify format float %15.8f flush yes
#dump 2 all custom 1 dump.dpdrx id x y z vx vy vz c_dpdUatom[1] c_dpdUatom[2] c_dpdUatom[3] c_dpdUatom[4] c_crdx
#dump_modify 2 sort id
#run 10

12
unittest/force-styles/tests/kinetics.dpdrx
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@ -1,12 +0,0 @@
# reaction equations and parameters
# multiple entries can be added to this file
# these entries are in LAMMPS "metal" units:
# Arr = 1/picosec or Angstroms^3/mol/picosec; Ern = eV
# format of a single entry (one or more lines):
# rxn equation, Arn, Ern
1.0 rdx = 3.0 hcn + 1.5 no2 + 1.5 no + 1.5 h2o 2.51000000000000E+04 0.0 1.912325921964536
1.0 hcn + 1.0 no2 = 1.0 no + 0.5 n2 + 0.5 h2 + 1.0 co 2.49081028001241E+01 0.0 1.344265387322009
1.0 hcn + 1.0 no = 1.0 co + 1.0 n2 + 0.5 h2 4.98162056E+00 0.0 1.517718985686140
1.0 no + 1.0 co = 0.5 n2 + 1.0 co2 1.66054018667494E+06 0.0 6.938245245

16
unittest/force-styles/tests/params.exp6
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@ -1,16 +0,0 @@
# rx parameters for various molecules
# multiple entries can be added to this file, LAMMPS reads the ones it needs
# these entries are in LAMMPS "metal" units:
# alpha = unitless; epsilon = eV; rho = Angstroms;
# format of a single entry (one or more lines):
# species, exp6, alpha, epsilon, rm
hcn exp6 13.57 0.030862657941745 5.3725
no2 exp6 13.57 0.029126283357001 4.2744
no exp6 13.10 0.013090454747817 3.7142
h2o exp6 11.01 0.022473771300313 3.5348
co exp6 13.24 0.0086353397713660428 4.1759
co2 exp6 14.09 0.019672305322873507 4.1757
h2 exp6 11.23 0.002618780329051 3.4925
n2 exp6 12.97 0.008635339808299 4.1778

4006
unittest/force-styles/tests/table.eos
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17
unittest/force-styles/tests/thermo.dpdrx
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@ -1,17 +0,0 @@
# rx heats of formation for various molecules
# multiple entries can be added to this file, LAMMPS reads the ones it needs
# the entries are in LAMMPS "metal" units (eV)
# Be sure the units are consistent with your input file
# format of a single entry (one or more lines):
# species DeltaHformation
rdx 1.989907438211819
h2 0.000000000000000
no2 0.343004076201018
n2 0.000000000000000
hcn 1.400635733970104
no 0.935781955892458
h2o -2.506184777415379
co -1.145533746031845
co2 -4.078501848437456