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more work on LATTE interface

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This commit is contained in:
Steve Plimpton
2023-02-01 10:53:08 -07:00
parent 2b5ef8d93e
commit a81e6693cd
19 changed files with 164 additions and 45332 deletions
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36
examples/QUANTUM/LATTE/TBparam/bondints.nonortho Normal file
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@ -0,0 +1,36 @@
Noints= 34
Element1 Element2 Kind H0 B1 B2 B3 B4 B5 R1 Rcut H0 B1 B2 B3 B4 B5 R1 Rcut
N O sss -11.430028 -2.257346 -1.152844 0.000000 0.000000 1.200000 3.500000 4.000000 0.340064 -1.703613 -0.622348 0.036738 -0.040158 1.200000 3.500000 4.000000
N O sps 11.597479 -1.382001 -0.765170 0.000000 0.000000 1.200000 3.500000 4.000000 -0.370946 -1.040947 -0.931097 0.252441 -0.115450 1.200000 3.500000 4.000000
O N sps 12.143744 -0.822913 -0.676127 0.000000 0.000000 1.200000 3.500000 4.000000 -0.420014 -1.107918 -0.905594 0.188424 -0.088365 1.200000 3.500000 4.000000
N O pps 9.465191 -1.082032 -0.769214 0.000000 0.000000 1.200000 3.500000 4.000000 -0.314073 0.499050 -2.914288 2.067657 -0.738439 1.200000 3.500000 4.000000
N O ppp -4.676789 -2.171480 -0.288002 0.000000 0.000000 1.200000 3.500000 4.000000 0.223937 -1.991867 -0.537630 -0.081270 -0.004130 1.200000 3.500000 4.000000
C O sss -14.369472 -2.077439 -0.875471 0.000000 0.000000 1.200000 3.500000 4.000000 0.375339 -1.547372 -0.642492 0.020614 -0.026699 1.200000 3.500000 4.000000
C O sps 9.576296 -1.156217 -0.494803 0.000000 0.000000 1.200000 3.500000 4.000000 -0.373027 -0.776043 -1.019920 0.257539 -0.102838 1.200000 3.500000 4.000000
O C sps 14.037374 -1.192632 -0.654572 0.000000 0.000000 1.200000 3.500000 4.000000 -0.458068 -1.035067 -0.937868 0.190562 -0.077841 1.200000 3.500000 4.000000
C O pps 9.331152 -0.718120 -0.822100 0.000000 0.000000 1.200000 3.500000 4.000000 -0.322293 0.795473 -3.476601 2.589965 -0.897800 1.200000 3.500000 4.000000
C O ppp -5.334367 -2.263939 -0.204910 0.000000 0.000000 1.200000 3.500000 4.000000 0.244570 -1.922717 -0.573671 -0.057280 -0.004108 1.200000 3.500000 4.000000
C N sss -7.010061 -1.730597 -0.575559 0.000000 0.000000 1.500000 3.500000 4.000000 0.263438 -1.754525 -0.584215 -0.007801 -0.021729 1.500000 3.500000 4.000000
C N sps 7.543283 -1.293768 -0.624363 0.000000 0.000000 1.500000 3.500000 4.000000 -0.326609 -1.197485 -0.807786 0.134891 -0.084373 1.500000 3.500000 4.000000
N C sps 9.090970 -1.494255 -0.616711 0.000000 0.000000 1.500000 3.500000 4.000000 -0.337943 -1.335442 -0.769693 0.119373 -0.079493 1.500000 3.500000 4.000000
C N pps 6.892240 -0.931920 -0.769164 0.000000 0.000000 1.500000 3.500000 4.000000 -0.350240 -0.467439 -1.849316 1.854403 -0.988471 1.500000 3.500000 4.000000
C N ppp -2.903346 -2.149349 -0.253006 0.000000 0.000000 1.500000 3.500000 4.000000 0.158424 -2.114409 -0.582346 -0.051076 -0.006183 1.500000 3.500000 4.000000
C C sss -9.404207 -1.363297 -0.507128 0.000000 0.000000 1.400000 3.500000 4.000000 0.346977 -1.519820 -0.570812 -0.013518 -0.015829 1.400000 3.500000 4.000000
C C sps 8.662429 -1.047410 -0.661999 0.000000 0.000000 1.400000 3.500000 4.000000 -0.400467 -0.984048 -0.853949 0.157178 -0.073381 1.400000 3.500000 4.000000
C C pps 6.811512 -0.552299 -0.776890 0.000000 0.000000 1.400000 3.500000 4.000000 -0.382417 0.102889 -2.786680 2.646356 -1.134320 1.400000 3.500000 4.000000
C C ppp -3.550127 -1.925572 -0.132715 0.000000 0.000000 1.400000 3.500000 4.000000 0.214357 -1.948923 -0.578323 -0.034356 -0.007257 1.400000 3.500000 4.000000
H C sss -9.072577 -1.393093 -0.430611 0.000000 0.000000 1.100000 3.500000 4.000000 0.416003 -1.459596 -0.654874 0.009140 -0.012658 1.100000 3.500000 4.000000
H C sps 8.176008 -0.985177 -0.427403 0.000000 0.000000 1.100000 3.500000 4.000000 -0.495695 -0.901626 -1.007214 0.189808 -0.057087 1.100000 3.500000 4.000000
H H sss -9.340000 -1.145903 -0.391777 0.000000 0.000000 0.750000 3.500000 4.000000 0.575007 -1.391261 -0.778831 0.080209 -0.017759 0.750000 3.500000 4.000000
O O sss -12.737687 -1.851608 -0.666621 0.000000 0.000000 1.200000 3.500000 4.000000 0.296445 -1.911896 -0.663451 0.038054 -0.046608 1.200000 3.500000 4.000000
O O sps 13.683050 -1.684554 -0.468349 0.000000 0.000000 1.200000 3.500000 4.000000 -0.362143 -1.285274 -0.939591 0.204641 -0.106438 1.200000 3.500000 4.000000
O O pps 9.460772 -1.211748 -0.581016 0.000000 0.000000 1.200000 3.500000 4.000000 -0.312044 0.121814 -2.519352 1.681266 -0.644566 1.200000 3.500000 4.000000
O O ppp -4.494595 -2.709223 -0.284124 0.000000 0.000000 1.200000 3.500000 4.000000 0.193010 -2.168462 -0.580629 -0.105104 0.004891 1.200000 3.500000 4.000000
H O sss -12.230931 -1.808632 -0.421164 0.000000 0.000000 1.000000 3.500000 4.000000 0.404725 -1.702546 -0.707938 0.074904 -0.039922 1.000000 3.500000 4.000000
H O sps 9.466088 -1.321262 -0.386336 0.000000 0.000000 1.000000 3.500000 4.000000 -0.447660 -0.952979 -1.163537 0.400616 -0.156965 1.000000 3.500000 4.000000
N N sss -7.710330 -2.365312 -0.525527 0.000000 0.000000 1.500000 3.500000 4.000000 0.231654 -1.879002 -0.572765 -0.004579 -0.031106 1.500000 3.500000 4.000000
N N sps 8.222314 -1.612118 -0.690081 0.000000 0.000000 1.500000 3.500000 4.000000 -0.305271 -1.385158 -0.751032 0.114531 -0.090839 1.500000 3.500000 4.000000
N N pps 7.178570 -1.176467 -0.571049 0.000000 0.000000 1.500000 3.500000 4.000000 -0.324668 -0.547805 -1.638658 1.495168 -0.827868 1.500000 3.500000 4.000000
N N ppp -2.829344 -2.408049 -0.387709 0.000000 0.000000 1.500000 3.500000 4.000000 0.142909 -2.162036 -0.571942 -0.071640 -0.004682 1.500000 3.500000 4.000000
H N sss -12.095890 -1.519057 -0.277247 0.000000 0.000000 1.000000 3.500000 4.000000 0.446693 -1.500463 -0.657448 0.065741 -0.037004 1.000000 3.500000 4.000000
H N sps 9.851338 -1.231616 -0.370836 0.000000 0.000000 1.000000 3.500000 4.000000 -0.501530 -0.785734 -1.123232 0.394878 -0.148501 1.000000 3.500000 4.000000

7
examples/QUANTUM/LATTE/TBparam/electrons.dat Normal file
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@ -0,0 +1,7 @@
Noelem= 5
Element basis Numel Es Ep Ed Ef Mass HubbardU Wss Wpp Wdd Wff
N sp 5.0 -18.58 -7.09 0.0 0.0 14.0067 15.93 0.0 -0.6950 0.0 0.0
O sp 6.0 -23.96 -9.02 0.0 0.0 15.9994 12.15 0.0 -0.7577 0.0 0.0
H s 1.0 -6.35 0.0 0.0 0.0 1.0079 12.85 -1.7937 0.0 0.0 0.0
C sp 4.0 -13.75 -5.28 0.0 0.0 12.01 10.0 0.0 -0.621 0.0 0.0
Ti sd 4.0 -5.5 0.0 -3.0 0.0 47.867 10.0 0.0 0.0 0.0 0.0

12
examples/QUANTUM/LATTE/TBparam/ppots.nonortho Normal file
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@ -0,0 +1,12 @@
Nopps= 10
Ele1 Ele2 A0 A1 A2 A3 A4 A5 A6 C R1 Rcut
N O 13.182426 20.050322 -46.806321 38.206953 -12.319656 0.000000 0.000000 0.000000 1.600000 1.700000
C N 88.953762 10.294988 -27.706877 22.101434 -6.836438 0.000000 0.000000 0.000000 1.600000 1.700000
C O 0.944093 30.116337 -59.608215 45.107654 -13.178839 0.000000 0.000000 0.000000 1.600000 1.700000
C H 104.889589 3.971095 -23.823043 26.408093 -11.317522 0.000000 0.000000 0.000000 1.200000 1.300000
C C 3.962931 24.467772 -51.156024 39.031644 -11.342979 0.000000 0.000000 0.000000 1.600000 1.700000
H H 38.512100 3.887860 -37.769100 57.083500 -34.512200 0.000000 0.000000 0.000000 0.900000 1.000000
N N 43.228899 15.004605 -36.621777 29.234888 -8.912743 0.000000 0.000000 0.000000 1.600000 1.700000
N H 0.625470 28.081241 -63.414297 53.286361 -17.352234 0.000000 0.000000 0.000000 1.300000 1.400000
O O 10.999870 19.303033 -45.747853 37.946431 -11.935755 0.000000 0.000000 0.000000 1.500000 1.600000
O H 0.481176 33.175383 -81.158683 74.935408 -26.792315 0.000000 0.000000 0.000000 1.200000 1.300000

0
examples/QUANTUM/LATTE/data.water → examples/QUANTUM/LATTE/data.water.latte.aimd
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40
examples/QUANTUM/LATTE/in.latte.water.md Normal file
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@ -0,0 +1,40 @@
# simple water model with LATTE
units metal
atom_style full
atom_modify sort 0 0.0 # turn off sorting of the coordinates
read_data data.water
# replicate system if requested
variable x index 1
variable y index 1
variable z index 1
variable nrep equal v_x*v_y*v_z
if "${nrep} > 1" then "replicate $x $y $z"
# initialize system
velocity all create 0.0 87287 loop geom
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
timestep 0.00025
fix 1 all nve
fix 2 all latte
fix_modify 2 energy yes
thermo_style custom step temp pe etotal press
# dynamics
thermo 10
run 100

2
examples/QUANTUM/LATTE/in.water.latte.aimd
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@ -4,7 +4,7 @@ units metal
atom_style full
atom_modify sort 0 0.0 # turn off sorting of the coordinates
read_data data.water
read_data data.water.latte.aimd
# replicate system if requested

2
examples/QUANTUM/LATTE/in.water.latte.aimd.plugin
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@ -29,7 +29,7 @@ timestep 0.00025
fix 1 all nve
fix 2 qm mdi/qm elements 8 1
fix 2 all mdi/qm elements 8 1
fix_modify 2 energy yes
thermo_style custom step temp pe etotal press

78
examples/QUANTUM/LATTE/latte_mdi.py
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@ -454,7 +454,7 @@ def evaluate():
vflag_global = 1
vflag_atom = 0
flags_latte = 7*[0]
flags_latte = 6*[0]
flags_latte[0] = pbcflag; # 1 for fully periodic, 0 for fully non-periodic
flags_latte[1] = coulombflag; # 1 for LAMMPS computes Coulombics, 0 for LATTE
flags_latte[2] = eflag_atom; # 1 to return per-atom energies, 0 for no
@ -479,15 +479,70 @@ def evaluate():
# AIMD with only QM atoms
elif mode == AIMD:
c_flags_latte = (c_int*6)(*flags_latte)
c_qm_natoms = c_int(qm_natoms)
qm_ntypes = 2
c_qm_ntypes = c_int(qm_ntypes)
c_xy = c_double(xy)
c_xz = c_double(xz)
c_yz = c_double(yz)
c_maxiter = c_int(maxiter)
c_qm_pe = c_double(qm_pe)
c_new_system = c_int(new_system)
qm_types = np.empty(qm_natoms,dtype=np.int32)
for i in range(0,qm_natoms,3): qm_types[i] = 1
for i in range(1,qm_natoms,3): qm_types[i] = 2
for i in range(2,qm_natoms,3): qm_types[i] = 2
qm_mass = [15.995, 1.008]
c_qm_mass = (c_double*qm_ntypes)(*qm_mass)
c_boxlo = (c_double*3)(*boxlo)
c_boxhi = (c_double*3)(*boxhi)
qm_velocity = np.empty((qm_natoms,3))
qm_velocity.fill(0.0)
timestep = 0.00025
c_timestep = c_double(timestep)
latte_error = 0
c_latte_error = c_bool(latte_error)
print("Calling LATTE ...")
time1 = time.time()
print("flags_latte",c_flags_latte[0:6])
print("qm_natoms",c_qm_natoms.value)
print("qm_coords",qm_coords)
print("qm_types",qm_types)
print("qm_ntypes",c_qm_ntypes.value)
print("qm_mass",c_qm_mass[0:2])
print("boxlo",c_boxlo[0:3])
print("boxhi",c_boxhi[0:3])
print("xy",c_xy.value)
print("xz",c_xz.value)
print("yz",c_yz.value)
print("maxiter",c_maxiter.value)
print("timestep",c_timestep.value)
print("new_system",c_new_system.value)
liblatte.\
latte(flags_latte,byref(qm_natoms),qm_coords,
qm_types,byref(qm_ntypes),qm_mass,
boxlo,boxhi,byref(xy),byref(xz),byref(yz),forces,
byref(maxiter),byref(qm_energy),
qm_velocity,byref(timestep),qm_stress,
byref(new_system),byref(latte_error))
latte(c_flags_latte,byref(c_qm_natoms),qm_coords,
qm_types,byref(c_qm_ntypes),c_qm_mass,
c_boxlo,c_boxhi,byref(c_xy),byref(c_xz),byref(c_yz),qm_forces,
byref(c_maxiter),byref(c_qm_pe),
qm_velocity,byref(c_timestep),qm_stress,
byref(c_new_system),byref(c_latte_error))
# NOTE: check latte_error return?
latte_error = c_latte_error.value
qm_pe = c_qm_pe.value
time2 = time.time()
print("DONE LATTE",latte_error,time2-time1)
print("PE",qm_pe)
print("FORCE",qm_forces)
# clear flags for all MDI commands for next QM evaluation
@ -510,15 +565,16 @@ def latte_load():
nparray = np.ctypeslib.ndpointer(dtype=np.float64,ndim=2,flags="C_CONTIGUOUS")
npvector_double = np.ctypeslib.ndpointer(dtype=np.float64,ndim=1,flags="C_CONTIGUOUS")
npvector_int = np.ctypeslib.ndpointer(dtype=np.int8,ndim=1,flags="C_CONTIGUOUS")
npvector_int = np.ctypeslib.ndpointer(dtype=np.int32,ndim=1,flags="C_CONTIGUOUS")
liblatte.latte_abiversion.restype = None
liblatte.latte_abiversion.argtypes = None
liblatte.latte.restype = None
liblatte.latte.argtypes = \
[POINTER(c_int), POINTER(c_int), nparray, npvector_int, POINTER(c_int),
POINTER(c_double), POINTER(c_double), POINTER(c_double), POINTER(c_double), POINTER(c_double),
[POINTER(c_int), POINTER(c_int), nparray, npvector_int, POINTER(c_int), POINTER(c_double),
POINTER(c_double), POINTER(c_double), POINTER(c_double),
POINTER(c_double), POINTER(c_double),
nparray, POINTER(c_int), POINTER(c_double), nparray,
POINTER(c_double), npvector_double, POINTER(c_int), POINTER(c_bool)]
@ -527,7 +583,7 @@ def latte_load():
# only when it invokes pyscf_mdi.py as a plugin
# --------------------------------------------
def MDI_Plugin_init_nwchem_mdi(plugin_state):
def MDI_Plugin_init_latte_mdi(plugin_state):
# other_options = all non-MDI args
# -mdi arg is processed and stripped internally by MDI

102
examples/QUANTUM/LATTE/log.8Sep22.aimd.lammps.mpi.1
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@ -1,102 +0,0 @@
LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# AIMD test of two UO2 molecules with LATTE in MDI stand-alone mode
units metal
atom_style full
atom_modify sort 0 0.0
read_data 2uo2.lmp
Reading data file ...
triclinic box = (0 0 0) to (10.8 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
1 by 1 by 1 MPI processor grid
reading atoms ...
6 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.003 seconds
velocity all create 300.0 87287 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
timestep 0.00025
fix 1 all nve
fix 2 all mdi/qm virial yes elements 92 8
thermo_style custom step temp pe etotal press
thermo 1
dump 1 all custom 1 dump.aimd.mpi id type x y z vx vy vz fx fy fz
run 20
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0
ghost atom cutoff = 0
binsize = 10.8, bins = 1 1 1
0 neighbor lists, perpetual/occasional/extra = 0 0 0
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 6.489 | 6.489 | 6.489 Mbytes
Step Temp PotEng TotEng Press
0 300 -50.539035 -50.345145 -120197.6
1 307.57345 -50.544722 -50.345937 -120123.27
2 316.3757 -50.551342 -50.346868 -120035.12
3 326.39203 -50.558885 -50.347938 -119933.11
4 337.60559 -50.567341 -50.349146 -119817.17
5 349.99734 -50.576697 -50.350493 -119687.24
6 363.54606 -50.586939 -50.351979 -119543.23
7 378.22834 -50.598054 -50.353605 -119385.07
8 394.0186 -50.610024 -50.355369 -119212.67
9 410.88903 -50.622831 -50.357273 -119025.94
10 428.80963 -50.636457 -50.359317 -118824.77
11 447.74819 -50.65088 -50.3615 -118609.06
12 467.67027 -50.666079 -50.363823 -118378.7
13 488.53922 -50.68203 -50.366287 -118133.58
14 510.31617 -50.698708 -50.36889 -117873.58
15 532.96002 -50.716086 -50.371633 -117598.57
16 556.42747 -50.734137 -50.374517 -117308.44
17 580.67298 -50.75283 -50.377541 -117003.05
18 605.64879 -50.772136 -50.380705 -116682.27
19 631.30497 -50.792023 -50.38401 -116345.95
20 657.58937 -50.812455 -50.387454 -115993.97
Loop time of 3.40001 on 1 procs for 20 steps with 6 atoms
Performance: 0.127 ns/day, 188.889 hours/ns, 5.882 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 1.2223e-05 | 1.2223e-05 | 1.2223e-05 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 6.0971e-05 | 6.0971e-05 | 6.0971e-05 | 0.0 | 0.00
Output | 0.0009257 | 0.0009257 | 0.0009257 | 0.0 | 0.03
Modify | 3.3989 | 3.3989 | 3.3989 | 0.0 | 99.97
Other | | 6.824e-05 | | | 0.00
Nlocal: 6 ave 6 max 6 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2 ave 2 max 2 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:03

102
examples/QUANTUM/LATTE/log.8Sep22.aimd.lammps.mpi.2
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@ -1,102 +0,0 @@
LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# AIMD test of two UO2 molecules with LATTE in MDI stand-alone mode
units metal
atom_style full
atom_modify sort 0 0.0
read_data 2uo2.lmp
Reading data file ...
triclinic box = (0 0 0) to (10.8 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
2 by 1 by 1 MPI processor grid
reading atoms ...
6 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.005 seconds
velocity all create 300.0 87287 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
timestep 0.00025
fix 1 all nve
fix 2 all mdi/qm virial yes elements 92 8
thermo_style custom step temp pe etotal press
thermo 1
dump 1 all custom 1 dump.aimd.mpi id type x y z vx vy vz fx fy fz
run 20
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0
ghost atom cutoff = 0
binsize = 10.8, bins = 1 1 1
0 neighbor lists, perpetual/occasional/extra = 0 0 0
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 5.485 | 5.987 | 6.489 Mbytes
Step Temp PotEng TotEng Press
0 300 -50.539035 -50.345145 -120197.6
1 307.57345 -50.544722 -50.345937 -120123.27
2 316.3757 -50.551342 -50.346868 -120035.12
3 326.39203 -50.558885 -50.347938 -119933.11
4 337.60559 -50.567341 -50.349146 -119817.17
5 349.99734 -50.576697 -50.350493 -119687.24
6 363.54606 -50.586939 -50.351979 -119543.23
7 378.22834 -50.598054 -50.353605 -119385.07
8 394.0186 -50.610024 -50.355369 -119212.67
9 410.88903 -50.622831 -50.357273 -119025.94
10 428.80963 -50.636457 -50.359317 -118824.77
11 447.74819 -50.65088 -50.3615 -118609.06
12 467.67027 -50.666079 -50.363823 -118378.7
13 488.53922 -50.68203 -50.366287 -118133.58
14 510.31617 -50.698708 -50.36889 -117873.58
15 532.96002 -50.716086 -50.371633 -117598.57
16 556.42747 -50.734137 -50.374517 -117308.44
17 580.67298 -50.75283 -50.377541 -117003.05
18 605.64879 -50.772136 -50.380705 -116682.27
19 631.30497 -50.792023 -50.38401 -116345.95
20 657.58937 -50.812455 -50.387454 -115993.97
Loop time of 25.2055 on 2 procs for 20 steps with 6 atoms
Performance: 0.017 ns/day, 1400.306 hours/ns, 0.793 timesteps/s
99.9% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 1.746e-05 | 2.5213e-05 | 3.2966e-05 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 4.3862e-05 | 5.4267e-05 | 6.4671e-05 | 0.0 | 0.00
Output | 0.001642 | 0.0018189 | 0.0019957 | 0.4 | 0.01
Modify | 25.203 | 25.203 | 25.203 | 0.0 | 99.99
Other | | 0.000307 | | | 0.00
Nlocal: 3 ave 6 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 1 ave 2 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:26

103
examples/QUANTUM/LATTE/log.8Sep22.aimd.lammps.plugin
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@ -1,103 +0,0 @@
LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# AIMD test of two UO2 molecules with LATTE in MDI plugin mode
units metal
atom_style full
atom_modify sort 0 0.0
read_data 2uo2.lmp
Reading data file ...
triclinic box = (0 0 0) to (10.8 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
1 by 1 by 1 MPI processor grid
reading atoms ...
6 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.004 seconds
velocity all create 300.0 87287 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
timestep 0.00025
fix 1 all nve
fix 2 all mdi/qm virial yes elements 92 8
thermo_style custom step temp pe etotal press
thermo 1
dump 1 all custom 1 dump.aimd.plugin id type x y z vx vy vz fx fy fz
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" command "run 20"
run 20
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0
ghost atom cutoff = 0
binsize = 10.8, bins = 1 1 1
0 neighbor lists, perpetual/occasional/extra = 0 0 0
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 6.489 | 6.489 | 6.489 Mbytes
Step Temp PotEng TotEng Press
0 300 -50.539035 -50.345145 -120197.6
1 307.57345 -50.544722 -50.345937 -120123.27
2 316.3757 -50.551342 -50.346868 -120035.12
3 326.39203 -50.558885 -50.347938 -119933.11
4 337.60559 -50.567341 -50.349146 -119817.17
5 349.99734 -50.576697 -50.350493 -119687.24
6 363.54606 -50.586939 -50.351979 -119543.23
7 378.22834 -50.598054 -50.353605 -119385.07
8 394.0186 -50.610024 -50.355369 -119212.67
9 410.88903 -50.622831 -50.357273 -119025.94
10 428.80963 -50.636457 -50.359317 -118824.77
11 447.74819 -50.65088 -50.3615 -118609.06
12 467.67027 -50.666079 -50.363823 -118378.7
13 488.53922 -50.68203 -50.366287 -118133.58
14 510.31617 -50.698708 -50.36889 -117873.58
15 532.96002 -50.716086 -50.371633 -117598.57
16 556.42747 -50.734137 -50.374517 -117308.44
17 580.67298 -50.75283 -50.377541 -117003.05
18 605.64879 -50.772136 -50.380705 -116682.27
19 631.30497 -50.792023 -50.38401 -116345.95
20 657.58937 -50.812455 -50.387454 -115993.97
Loop time of 2.74435 on 1 procs for 20 steps with 6 atoms
Performance: 0.157 ns/day, 152.464 hours/ns, 7.288 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 1.299e-05 | 1.299e-05 | 1.299e-05 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 7.9198e-05 | 7.9198e-05 | 7.9198e-05 | 0.0 | 0.00
Output | 0.001118 | 0.001118 | 0.001118 | 0.0 | 0.04
Modify | 2.743 | 2.743 | 2.743 | 0.0 | 99.95
Other | | 0.0001456 | | | 0.01
Nlocal: 6 ave 6 max 6 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2 ave 2 max 2 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:03

12604
examples/QUANTUM/LATTE/log.8Sep22.aimd.latte.1
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12604
examples/QUANTUM/LATTE/log.8Sep22.aimd.latte.2
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12604
examples/QUANTUM/LATTE/log.8Sep22.aimd.latte.plugin
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263
examples/QUANTUM/LATTE/log.8Sep22.series.lammps.mpi.1
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@ -1,263 +0,0 @@
LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Series of single-point calcs of 2,3,4 UO2 molecules
# with LATTE in MDI stand-alone mode
variable files index 2uo2 3uo2 4uo2
mdi connect
label LOOP
units metal
atom_style full
atom_modify sort 0 0.0
read_data ${files}.lmp
read_data 2uo2.lmp
Reading data file ...
triclinic box = (0 0 0) to (10.8 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
1 by 1 by 1 MPI processor grid
reading atoms ...
6 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.003 seconds
neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
timestep 0.001
fix 1 all mdi/qm virial yes elements 92 8 connect no
thermo_style custom step temp pe etotal press
thermo 1
run 0
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0
ghost atom cutoff = 0
binsize = 10.8, bins = 1 1 1
0 neighbor lists, perpetual/occasional/extra = 0 0 0
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 5.238 | 5.238 | 5.238 Mbytes
Step Temp PotEng TotEng Press
0 0 -50.539035 -50.539035 -120855.2
Loop time of 1.397e-06 on 1 procs for 0 steps with 6 atoms
71.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.397e-06 | | |100.00
Nlocal: 6 ave 6 max 6 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2 ave 2 max 2 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
write_dump all custom dump.series.mpi.${files} id type x y z fx fy fz modify sort id
write_dump all custom dump.series.mpi.2uo2 id type x y z fx fy fz modify sort id
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
next files
jump SELF LOOP
units metal
atom_style full
atom_modify sort 0 0.0
read_data ${files}.lmp
read_data 3uo2.lmp
Reading data file ...
triclinic box = (0 0 0) to (16.2 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
1 by 1 by 1 MPI processor grid
reading atoms ...
9 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.002 seconds
neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
timestep 0.001
fix 1 all mdi/qm virial yes elements 92 8 connect no
thermo_style custom step temp pe etotal press
thermo 1
run 0
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0
ghost atom cutoff = 0
binsize = 16.2, bins = 1 1 1
0 neighbor lists, perpetual/occasional/extra = 0 0 0
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 5.238 | 5.238 | 5.238 Mbytes
Step Temp PotEng TotEng Press
0 0 -78.155679 -78.155679 -99931.431
Loop time of 1.117e-06 on 1 procs for 0 steps with 9 atoms
89.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.117e-06 | | |100.00
Nlocal: 9 ave 9 max 9 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3 ave 3 max 3 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
write_dump all custom dump.series.mpi.${files} id type x y z fx fy fz modify sort id
write_dump all custom dump.series.mpi.3uo2 id type x y z fx fy fz modify sort id
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
next files
jump SELF LOOP
units metal
atom_style full
atom_modify sort 0 0.0
read_data ${files}.lmp
read_data 4uo2.lmp
Reading data file ...
triclinic box = (0 0 0) to (10.8 10.8 5.4) with tilt (6.6130927e-16 3.3065464e-16 3.3065464e-16)
1 by 1 by 1 MPI processor grid
reading atoms ...
12 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.001 seconds
neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
timestep 0.001
fix 1 all mdi/qm virial yes elements 92 8 connect no
thermo_style custom step temp pe etotal press
thermo 1
run 0
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0
ghost atom cutoff = 0
binsize = 10.8, bins = 1 1 1
0 neighbor lists, perpetual/occasional/extra = 0 0 0
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 5.238 | 5.238 | 5.238 Mbytes
Step Temp PotEng TotEng Press
0 0 -102.35713 -102.35713 -31036.168
Loop time of 1.466e-06 on 1 procs for 0 steps with 12 atoms
136.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.466e-06 | | |100.00
Nlocal: 12 ave 12 max 12 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5 ave 5 max 5 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
write_dump all custom dump.series.mpi.${files} id type x y z fx fy fz modify sort id
write_dump all custom dump.series.mpi.4uo2 id type x y z fx fy fz modify sort id
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
next files
jump SELF LOOP
mdi exit
Total wall time: 0:00:02

263
examples/QUANTUM/LATTE/log.8Sep22.series.lammps.mpi.2
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@ -1,263 +0,0 @@
LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Series of single-point calcs of 2,3,4 UO2 molecules
# with LATTE in MDI stand-alone mode
variable files index 2uo2 3uo2 4uo2
mdi connect
label LOOP
units metal
atom_style full
atom_modify sort 0 0.0
read_data ${files}.lmp
read_data 2uo2.lmp
Reading data file ...
triclinic box = (0 0 0) to (10.8 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
2 by 1 by 1 MPI processor grid
reading atoms ...
6 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.004 seconds
neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
timestep 0.001
fix 1 all mdi/qm virial yes elements 92 8 connect no
thermo_style custom step temp pe etotal press
thermo 1
run 0
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0
ghost atom cutoff = 0
binsize = 10.8, bins = 1 1 1
0 neighbor lists, perpetual/occasional/extra = 0 0 0
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 5.234 | 5.236 | 5.238 Mbytes
Step Temp PotEng TotEng Press
0 0 -50.539035 -50.539035 -120855.2
Loop time of 1.956e-06 on 2 procs for 0 steps with 6 atoms
127.8% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.956e-06 | | |100.00
Nlocal: 3 ave 6 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 1 ave 2 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
write_dump all custom dump.series.mpi.${files} id type x y z fx fy fz modify sort id
write_dump all custom dump.series.mpi.2uo2 id type x y z fx fy fz modify sort id
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
next files
jump SELF LOOP
units metal
atom_style full
atom_modify sort 0 0.0
read_data ${files}.lmp
read_data 3uo2.lmp
Reading data file ...
triclinic box = (0 0 0) to (16.2 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
2 by 1 by 1 MPI processor grid
reading atoms ...
9 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.001 seconds
neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
timestep 0.001
fix 1 all mdi/qm virial yes elements 92 8 connect no
thermo_style custom step temp pe etotal press
thermo 1
run 0
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0
ghost atom cutoff = 0
binsize = 16.2, bins = 1 1 1
0 neighbor lists, perpetual/occasional/extra = 0 0 0
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 5.234 | 5.236 | 5.238 Mbytes
Step Temp PotEng TotEng Press
0 0 -78.155679 -78.155679 -99931.431
Loop time of 2.375e-06 on 2 procs for 0 steps with 9 atoms
147.4% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 2.375e-06 | | |100.00
Nlocal: 4.5 ave 9 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 1.5 ave 3 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
write_dump all custom dump.series.mpi.${files} id type x y z fx fy fz modify sort id
write_dump all custom dump.series.mpi.3uo2 id type x y z fx fy fz modify sort id
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
next files
jump SELF LOOP
units metal
atom_style full
atom_modify sort 0 0.0
read_data ${files}.lmp
read_data 4uo2.lmp
Reading data file ...
triclinic box = (0 0 0) to (10.8 10.8 5.4) with tilt (6.6130927e-16 3.3065464e-16 3.3065464e-16)
1 by 2 by 1 MPI processor grid
reading atoms ...
12 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.002 seconds
neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
timestep 0.001
fix 1 all mdi/qm virial yes elements 92 8 connect no
thermo_style custom step temp pe etotal press
thermo 1
run 0
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0
ghost atom cutoff = 0
binsize = 10.8, bins = 1 1 1
0 neighbor lists, perpetual/occasional/extra = 0 0 0
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 5.238 | 5.238 | 5.238 Mbytes
Step Temp PotEng TotEng Press
0 0 -102.35713 -102.35713 -31036.168
Loop time of 2.4445e-06 on 2 procs for 0 steps with 12 atoms
122.7% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 2.444e-06 | | |100.00
Nlocal: 6 ave 6 max 6 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Nghost: 2.5 ave 4 max 1 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
write_dump all custom dump.series.mpi.${files} id type x y z fx fy fz modify sort id
write_dump all custom dump.series.mpi.4uo2 id type x y z fx fy fz modify sort id
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
next files
jump SELF LOOP
mdi exit
Total wall time: 0:00:08

256
examples/QUANTUM/LATTE/log.8Sep22.series.lammps.plugin
View File

@ -1,256 +0,0 @@
LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Series of single-point calcs of 2,3,4 UO2 molecules
# with LATTE in MDI plugin mode
variable files index 2uo2 3uo2 4uo2
label LOOP
units metal
atom_style full
atom_modify sort 0 0.0
read_data ${files}.lmp
read_data 2uo2.lmp
Reading data file ...
triclinic box = (0 0 0) to (10.8 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
1 by 1 by 1 MPI processor grid
reading atoms ...
6 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.004 seconds
neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
fix 1 all mdi/qm virial yes elements 92 8
thermo_style custom step temp pe etotal press
thermo 1
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" command "run 0"
run 0
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0
ghost atom cutoff = 0
binsize = 10.8, bins = 1 1 1
0 neighbor lists, perpetual/occasional/extra = 0 0 0
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 5.238 | 5.238 | 5.238 Mbytes
Step Temp PotEng TotEng Press
0 0 -50.539035 -50.539035 -120855.2
Loop time of 1.396e-06 on 1 procs for 0 steps with 6 atoms
143.3% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.396e-06 | | |100.00
Nlocal: 6 ave 6 max 6 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2 ave 2 max 2 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
write_dump all custom dump.series.plugin.${files} id type x y z fx fy fz modify sort id
write_dump all custom dump.series.plugin.2uo2 id type x y z fx fy fz modify sort id
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
next files
jump SELF LOOP
units metal
atom_style full
atom_modify sort 0 0.0
read_data ${files}.lmp
read_data 3uo2.lmp
Reading data file ...
triclinic box = (0 0 0) to (16.2 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
1 by 1 by 1 MPI processor grid
reading atoms ...
9 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.002 seconds
neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
fix 1 all mdi/qm virial yes elements 92 8
thermo_style custom step temp pe etotal press
thermo 1
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" command "run 0"
run 0
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0
ghost atom cutoff = 0
binsize = 16.2, bins = 1 1 1
0 neighbor lists, perpetual/occasional/extra = 0 0 0
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 5.238 | 5.238 | 5.238 Mbytes
Step Temp PotEng TotEng Press
0 0 -78.155679 -78.155679 -99931.431
Loop time of 1.117e-06 on 1 procs for 0 steps with 9 atoms
89.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.117e-06 | | |100.00
Nlocal: 9 ave 9 max 9 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3 ave 3 max 3 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
write_dump all custom dump.series.plugin.${files} id type x y z fx fy fz modify sort id
write_dump all custom dump.series.plugin.3uo2 id type x y z fx fy fz modify sort id
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
next files
jump SELF LOOP
units metal
atom_style full
atom_modify sort 0 0.0
read_data ${files}.lmp
read_data 4uo2.lmp
Reading data file ...
triclinic box = (0 0 0) to (10.8 10.8 5.4) with tilt (6.6130927e-16 3.3065464e-16 3.3065464e-16)
1 by 1 by 1 MPI processor grid
reading atoms ...
12 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.001 seconds
neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
fix 1 all mdi/qm virial yes elements 92 8
thermo_style custom step temp pe etotal press
thermo 1
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" command "run 0"
run 0
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0
ghost atom cutoff = 0
binsize = 10.8, bins = 1 1 1
0 neighbor lists, perpetual/occasional/extra = 0 0 0
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 5.238 | 5.238 | 5.238 Mbytes
Step Temp PotEng TotEng Press
0 0 -102.35713 -102.35713 -31036.168
Loop time of 1.048e-06 on 1 procs for 0 steps with 12 atoms
190.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.048e-06 | | |100.00
Nlocal: 12 ave 12 max 12 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5 ave 5 max 5 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
write_dump all custom dump.series.plugin.${files} id type x y z fx fy fz modify sort id
write_dump all custom dump.series.plugin.4uo2 id type x y z fx fy fz modify sort id
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
next files
jump SELF LOOP
Total wall time: 0:00:01

3209
examples/QUANTUM/LATTE/log.8Sep22.series.latte.1
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3209
examples/QUANTUM/LATTE/log.8Sep22.series.latte.2
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