SOF-7194: add lammps executable and templates

assets/deepmd/in.lammps

@@ -0,0 +1,25 @@
+# LAMMPS input, deepmd-kit version. Built from bulk water calculation.
+
+units           metal
+boundary        p p p
+atom_style      atomic
+
+neighbor        2.0 bin
+neigh_modify    every 10 delay 0 check no
+
+read_data       structure.lmp
+mass            1 16
+mass            2 2
+
+pair_style	    deepmd ./graph.pb
+pair_coeff      * *
+
+velocity        all create 330.0 23456789
+
+fix             1 all nvt temp 330.0 330.0 0.5
+timestep        0.0005
+thermo_style    custom step pe ke etotal temp press vol
+thermo          100
+dump            1 all custom 100 structure.dump id type x y z
+
+run             100

assets/deepmd/structure.lmp

@@ -0,0 +1,202 @@
+# LAMMPS data
+192 atoms
+2 atom types
+0.0 12.44470 xlo xhi
+0.0 12.44470 ylo yhi
+0.0 12.44470 zlo zhi
+0.0 0.0 0.0 xy xz yz
+
+Atoms # metal
+
+1	1	11.83 2.56 2.18
+2	1	5.36 6 1.81
+3	1	12.17 7.34 2.71
+4	1	3.38 4.28 4.84
+5	1	4.54 11.73 11.9
+6	1	7.34 0.18 2.18
+7	1	5.73 9.9 10.31
+8	1	5.32 11.19 1.83
+9	1	9.39 11.14 1.1
+10	1	12.06 0.64 8.92
+11	1	5.01 7.72 11.74
+12	1	3.64 3.19 1.08
+13	1	11.88 10.9 4.7
+14	1	3.88 8.05 2.51
+15	1	9.82 9.16 10.18
+16	1	11 5.31 5.17
+17	1	0.97 4.12 0.84
+18	1	1.24 5.99 4.76
+19	1	10.1 9.09 3.32
+20	1	8.39 5.72 10.39
+21	1	8.06 4.72 1.3
+22	1	3.23 3.34 8.26
+23	1	5.02 6.21 7.29
+24	1	3.94 10.55 3.95
+25	1	6.25 4.56 4.21
+26	1	12.18 2.35 11.11
+27	1	6.76 8.57 4.07
+28	1	5.87 5.84 9.79
+29	1	2.18 6.91 6.99
+30	1	10.89 7.69 6.78
+31	1	8.03 4.28 6.57
+32	1	5.29 1.92 11.56
+33	1	1.53 12.16 3.45
+34	1	2.04 5.49 9.71
+35	1	6.66 9.05 1.21
+36	1	11.75 6.18 11.01
+37	1	6.11 3.07 7.96
+38	1	8.22 1.38 9.43
+39	1	1.31 2.02 7.09
+40	1	9.48 2.11 5.92
+41	1	9.33 3.34 10.97
+42	1	1.31 8.49 0.81
+43	1	11.25 3.48 7.51
+44	1	11.7 0.33 0.6
+45	1	7.63 2.04 0.28
+46	1	8.86 9.52 7.4
+47	1	2.01 11.54 6.89
+48	1	8.02 11.27 4.66
+49	1	5.82 9.18 7.71
+50	1	8.11 11.19 11.22
+51	1	5.94 0.84 5.91
+52	1	1.88 11.66 0.64
+53	1	4.66 11.28 6.73
+54	1	10.32 6.26 0.89
+55	1	2.01 11.07 10.33
+56	1	5.36 2.06 3.14
+57	1	8.56 7.59 12.17
+58	1	10.51 5.81 8.66
+59	1	2.37 6.23 12.1
+60	1	0.3 8.77 10.05
+61	1	9.47 12.13 7.57
+62	1	1.41 2.32 4.17
+63	1	9.69 3.69 3.56
+64	1	0.75 9.22 7.39
+65	2	11.09 2.87 2.74
+66	2	5.51 5.51 2.6
+67	2	0.24 6.8 3.29
+68	2	4.28 4.19 4.46
+69	2	3.63 11.56 11.76
+70	2	6.53 12.07 1.99
+71	2	5.37 9.14 10.85
+72	2	5.74 10.31 1.64
+73	2	8.71 11.07 0.41
+74	2	0.27 1.04 8.27
+75	2	5.46 7.08 11.15
+76	2	3.84 4.17 1.06
+77	2	11.55 10.19 4.15
+78	2	3 8.17 2.14
+79	2	9.53 10.04 10.56
+80	2	11.18 4.84 6.05
+81	2	0.68 3.76 12.44
+82	2	0.43 5.51 4.88
+83	2	9.51 9.48 3.94
+84	2	9.08 5.89 9.68
+85	2	7.92 3.83 0.8
+86	2	4.23 3.22 8.21
+87	2	5.27 5.9 8.19
+88	2	4.44 10.9 3.14
+89	2	6.93 4.56 4.89
+90	2	11.88 1.61 11.75
+91	2	6.79 8.54 3.09
+92	2	5.62 4.99 10.13
+93	2	3.09 6.66 6.98
+94	2	11.73 8.22 6.86
+95	2	8.4 3.45 6.18
+96	2	4.64 2.37 12.16
+97	2	0.74 11.69 3.86
+98	2	1.1 5.3 9.72
+99	2	7.54 9.11 0.83
+100	2	11.36 6.2 11.9
+101	2	5.85 2.21 7.53
+102	2	8.81 2.01 9.89
+103	2	2.17 2.43 7.46
+104	2	10.1 2.53 6.55
+105	2	9.07 4.29 10.91
+106	2	0.64 8.13 1.45
+107	2	11.12 4.2 8.14
+108	2	11.03 12.03 0.58
+109	2	6.83 1.84 12.19
+110	2	9.13 10.45 7.25
+111	2	1.76 12.44 6.8
+112	2	7.37 11.88 5.08
+113	2	5.59 8.29 7.44
+114	2	8.14 12.12 10.86
+115	2	5.48 0.06 6.32
+116	2	0.99 11.99 0.41
+117	2	4.54 10.95 5.79
+118	2	10.94 6.29 1.65
+119	2	2.52 10.55 9.76
+120	2	4.74 2.41 2.42
+121	2	8.84 8.27 11.56
+122	2	10.89 6.06 9.58
+123	2	2.15 5.99 11.18
+124	2	0.49 9.06 9.13
+125	2	8.69 12.34 8.15
+126	2	1.76 1.44 4.07
+127	2	10.05 4.44 4.1
+128	2	1.44 8.49 7.32
+129	2	12.25 3.32 1.68
+130	2	6.27 6.22 1.56
+131	2	11.5 7.85 3.14
+132	2	2.96 3.44 4.61
+133	2	5.04 11.17 11.3
+134	2	7.6 12.39 3.03
+135	2	5.94 9.68 9.37
+136	2	4.93 11.46 0.96
+137	2	8.92 11.68 1.69
+138	2	12.07 1.36 9.54
+139	2	4.17 7.28 11.8
+140	2	2.67 3.09 1.05
+141	2	11.89 10.59 5.56
+142	2	4.27 7.23 2.16
+143	2	10.8 9.22 10.18
+144	2	10.68 6.2 5.44
+145	2	1.51 4.9 0.53
+146	2	1.94 5.36 4.61
+147	2	10.02 9.64 2.47
+148	2	8.41 6.43 11.04
+149	2	8.58 4.29 2.01
+150	2	3.12 4.28 8.41
+151	2	5.12 5.54 6.6
+152	2	3.97 9.58 3.89
+153	2	6.17 3.63 3.9
+154	2	11.4 2.92 10.99
+155	2	5.96 8.02 4.26
+156	2	6.81 5.9 9.83
+157	2	1.83 6.59 6.16
+158	2	10.19 8.36 6.88
+159	2	8.74 4.67 7.12
+160	2	4.84 1.08 11.38
+161	2	2.38 11.71 3.7
+162	2	2.02 6.1 8.92
+163	2	6.05 8.48 0.61
+164	2	12.12 7.05 10.81
+165	2	6.81 3.46 7.31
+166	2	7.52 1.99 9.1
+167	2	1.25 2.26 6.18
+168	2	9.31 1.19 6.35
+169	2	8.84 2.9 11.69
+170	2	1.39 9.44 0.85
+171	2	12.13 3.22 7.5
+172	2	11.38 0.95 1.34
+173	2	7.43 1.82 1.24
+174	2	9.15 9.43 8.28
+175	2	2.97 11.66 6.88
+176	2	7.5 10.43 4.47
+177	2	6.69 9.4 7.47
+178	2	7.29 10.77 10.93
+179	2	5.45 1.07 5.12
+180	2	1.92 11.57 1.62
+181	2	5.05 10.55 7.26
+182	2	9.73 5.52 1.11
+183	2	1.73 11.85 9.82
+184	2	6.02 1.57 2.67
+185	2	9.34 7.2 0.21
+186	2	10.71 6.56 7.97
+187	2	1.86 7.03 12.37
+188	2	1.08 9.16 10.59
+189	2	10.19 12.39 8.15
+190	2	0.92 2.56 3.28
+191	2	9.34 3.01 4.17
+192	2	1.11 10.09 7.21

executables/deepmd/dp_lmp.yml

@@ -0,0 +1,15 @@
+isDefault: false
+monitors:
+  - standard_output
+results: []
+flavors:
+  dp_lmp:
+    input:
+      - name:
+        - in.lammps
+        - structure.lmp
+    results: []
+    monitors:
+      - standard_output
+    applicationName: deepmd
+    executableName: dp_lmp  # mpirun -np $NP lmp -in in.lammps

templates/deepmd/dp_lmp.yml

@@ -0,0 +1,11 @@
+- content: !readFile 'assets/deepmd/in.lammps'
+  name: in.lammps
+  contextProviders: []
+  applicationName: deepmd
+  executableName: dp_lmp
+
+- content: !readFile 'assets/deepmd/structure.lmp'
+  name: structure.lmp
+  contextProviders: []
+  applicationName: deepmd
+  executableName: dp_lmp