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Merge pull request #638 from jdevemy/master 

Mods for extra/special/per/atom and add toluene
This commit is contained in:
Steve Plimpton 2017-09-05 10:05:49 -06:00 committed by GitHub
parent 2b9646097c a5b65c1af4
commit 65b295e826
12 changed files with 25916 additions and 47 deletions
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4
doc/src/Section_howto.txt
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@ -2859,8 +2859,8 @@ The nature of the atoms (core, Drude particle or non-polarizable) is
specified via the "fix drude"_fix_drude.html command. The special
list of neighbors is automatically refactored to account for the
equivalence of core and Drude particles as regards special 1-2 to 1-4
screening. It may be necessary to use the {extra} keyword of the
"special_bonds"_special_bonds.html command. If using "fix
screening. It may be necessary to use the {extra/special/per/atom}
keyword of the "read_data"_read_data.html command. If using "fix
shake"_fix_shake.html, make sure no Drude particle is in this fix
group.

5
examples/USER/drude/README
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@ -6,8 +6,11 @@ Nosé-Hoover or Langevin thermostats.
* `butane` -- simulation in NVT ensemble with Thole damping
* `toluene` -- simulation in NVT ensemble with Thole damping and
use of the `extra/special/per/atom` keyword
* `ethanol` -- simulation in NpT ensemble with Thole damping
* `swm4-ndp` -- 4-site rigid water model in NpT ensemble (no Thole
* `swm4-ndp` -- 4-site rigid water model in NpT ensemble (no Thole
damping)

24601
examples/USER/drude/toluene/data.toluene Normal file
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116
examples/USER/drude/toluene/in.toluene.lang Normal file
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@ -0,0 +1,116 @@
# 250 toluene system for drude polarizability example (Langevin)
units real
boundary p p p
atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style opls
improper_style opls
special_bonds lj/coul 0.0 0.0 0.5
pair_style lj/cut/thole/long 2.600 8.0 8.0
pair_modify mix geometric tail yes
kspace_style pppm 1.0e-4
read_data data.toluene extra/special/per/atom 1
comm_modify vel yes
group gTOLUENE molecule 1:250
group gCORES type 1 2 3 4 5 6 7
group gDRUDES type 8 9 10 11 12
pair_coeff 1 1 0.069998 3.550000 1.620000 # CAT CAT
pair_coeff 1 2 0.069998 3.550000 1.620000 # CAT CAO
pair_coeff 1 3 0.069998 3.550000 1.620000 # CAT CAM
pair_coeff 1 4 0.069998 3.550000 1.620000 # CAT CAP
pair_coeff 1 5 0.067968 3.524911 1.620000 # CAT CTT
pair_coeff 1 6 0.045825 2.931041 0.000000 # CAT HAT
pair_coeff 1 7 0.045825 2.931041 0.000000 # CAT HT
pair_coeff 2 2 0.069998 3.550000 1.620000 # CAO CAO
pair_coeff 2 3 0.069998 3.550000 1.620000 # CAO CAM
pair_coeff 2 4 0.069998 3.550000 1.620000 # CAO CAP
pair_coeff 2 5 0.067968 3.524911 1.620000 # CAO CTT
pair_coeff 2 6 0.045825 2.931041 0.000000 # CAO HAT
pair_coeff 2 7 0.045825 2.931041 0.000000 # CAO HT
pair_coeff 3 3 0.069998 3.550000 1.620000 # CAM CAM
pair_coeff 3 4 0.069998 3.550000 1.620000 # CAM CAP
pair_coeff 3 5 0.067968 3.524911 1.620000 # CAM CTT
pair_coeff 3 6 0.045825 2.931041 0.000000 # CAM HAT
pair_coeff 3 7 0.045825 2.931041 0.000000 # CAM HT
pair_coeff 4 4 0.069998 3.550000 1.620000 # CAP CAP
pair_coeff 4 5 0.067968 3.524911 1.620000 # CAP CTT
pair_coeff 4 6 0.045825 2.931041 0.000000 # CAP HAT
pair_coeff 4 7 0.045825 2.931041 0.000000 # CAP HT
pair_coeff 5 5 0.065997 3.500000 1.620000 # CTT CTT
pair_coeff 5 6 0.044496 2.910326 0.000000 # CTT HAT
pair_coeff 5 7 0.044496 2.910326 0.000000 # CTT HT
pair_coeff 6 6 0.029999 2.420000 0.000000 # HAT HAT
pair_coeff 6 7 0.029999 2.420000 0.000000 # HAT HT
pair_coeff 7 7 0.029999 2.420000 0.000000 # HT HT
pair_coeff 1 8 0.000000 0.000000 1.620000 # CAT D_CAT
pair_coeff 1 9 0.000000 0.000000 1.620000 # CAT D_CAO
pair_coeff 1 10 0.000000 0.000000 1.620000 # CAT D_CAM
pair_coeff 1 11 0.000000 0.000000 1.620000 # CAT D_CAP
pair_coeff 1 12 0.000000 0.000000 1.620000 # CAT D_CTT
pair_coeff 2 8 0.000000 0.000000 1.620000 # CAO D_CAT
pair_coeff 2 9 0.000000 0.000000 1.620000 # CAO D_CAO
pair_coeff 2 10 0.000000 0.000000 1.620000 # CAO D_CAM
pair_coeff 2 11 0.000000 0.000000 1.620000 # CAO D_CAP
pair_coeff 2 12 0.000000 0.000000 1.620000 # CAO D_CTT
pair_coeff 3 8 0.000000 0.000000 1.620000 # CAM D_CAT
pair_coeff 3 9 0.000000 0.000000 1.620000 # CAM D_CAO
pair_coeff 3 10 0.000000 0.000000 1.620000 # CAM D_CAM
pair_coeff 3 11 0.000000 0.000000 1.620000 # CAM D_CAP
pair_coeff 3 12 0.000000 0.000000 1.620000 # CAM D_CTT
pair_coeff 4 8 0.000000 0.000000 1.620000 # CAP D_CAT
pair_coeff 4 9 0.000000 0.000000 1.620000 # CAP D_CAO
pair_coeff 4 10 0.000000 0.000000 1.620000 # CAP D_CAM
pair_coeff 4 11 0.000000 0.000000 1.620000 # CAP D_CAP
pair_coeff 4 12 0.000000 0.000000 1.620000 # CAP D_CTT
pair_coeff 5 8 0.000000 0.000000 1.620000 # CTT D_CAT
pair_coeff 5 9 0.000000 0.000000 1.620000 # CTT D_CAO
pair_coeff 5 10 0.000000 0.000000 1.620000 # CTT D_CAM
pair_coeff 5 11 0.000000 0.000000 1.620000 # CTT D_CAP
pair_coeff 5 12 0.000000 0.000000 1.620000 # CTT D_CTT
pair_coeff 8 8 0.000000 0.000000 1.620000 # D_CAT D_CAT
pair_coeff 8 9 0.000000 0.000000 1.620000 # D_CAT D_CAO
pair_coeff 8 10 0.000000 0.000000 1.620000 # D_CAT D_CAM
pair_coeff 8 11 0.000000 0.000000 1.620000 # D_CAT D_CAP
pair_coeff 8 12 0.000000 0.000000 1.620000 # D_CAT D_CTT
pair_coeff 9 9 0.000000 0.000000 1.620000 # D_CAO D_CAO
pair_coeff 9 10 0.000000 0.000000 1.620000 # D_CAO D_CAM
pair_coeff 9 11 0.000000 0.000000 1.620000 # D_CAO D_CAP
pair_coeff 9 12 0.000000 0.000000 1.620000 # D_CAO D_CTT
pair_coeff 10 10 0.000000 0.000000 1.620000 # D_CAM D_CAM
pair_coeff 10 11 0.000000 0.000000 1.620000 # D_CAM D_CAP
pair_coeff 10 12 0.000000 0.000000 1.620000 # D_CAM D_CTT
pair_coeff 11 11 0.000000 0.000000 1.620000 # D_CAP D_CAP
pair_coeff 11 12 0.000000 0.000000 1.620000 # D_CAP D_CTT
pair_coeff 12 12 0.000000 0.000000 1.620000 # D_CTT D_CTT
neighbor 2.0 bin
variable vTEMP equal 260.0
variable vTEMP_D equal 1.0
variable vPRESS equal 1.0
velocity gCORES create ${vTEMP} 12345
velocity gDRUDES create ${vTEMP_D} 12345
fix fDRUDE all drude C C C C C N N D D D D D
fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8
fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
fix fNPH all nve
compute cTEMP all temp/drude
thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
thermo 50
timestep 0.5
run 2000

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examples/USER/drude/toluene/in.toluene.nh Normal file
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@ -0,0 +1,122 @@
# 250 toluene system for drude polarizability example (Nose-Hoover)
units real
boundary p p p
atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style opls
improper_style opls
special_bonds lj/coul 0.0 0.0 0.5
pair_style lj/cut/thole/long 2.600 8.0 8.0
pair_modify mix geometric tail yes
kspace_style pppm 1.0e-4
read_data data.toluene extra/special/per/atom 1
comm_modify vel yes
group gTOLUENE molecule 1:250
group gCORES type 1 2 3 4 5 6 7
group gDRUDES type 8 9 10 11 12
pair_coeff 1 1 0.069998 3.550000 1.620000 # CAT CAT
pair_coeff 1 2 0.069998 3.550000 1.620000 # CAT CAO
pair_coeff 1 3 0.069998 3.550000 1.620000 # CAT CAM
pair_coeff 1 4 0.069998 3.550000 1.620000 # CAT CAP
pair_coeff 1 5 0.067968 3.524911 1.620000 # CAT CTT
pair_coeff 1 6 0.045825 2.931041 0.000000 # CAT HAT
pair_coeff 1 7 0.045825 2.931041 0.000000 # CAT HT
pair_coeff 2 2 0.069998 3.550000 1.620000 # CAO CAO
pair_coeff 2 3 0.069998 3.550000 1.620000 # CAO CAM
pair_coeff 2 4 0.069998 3.550000 1.620000 # CAO CAP
pair_coeff 2 5 0.067968 3.524911 1.620000 # CAO CTT
pair_coeff 2 6 0.045825 2.931041 0.000000 # CAO HAT
pair_coeff 2 7 0.045825 2.931041 0.000000 # CAO HT
pair_coeff 3 3 0.069998 3.550000 1.620000 # CAM CAM
pair_coeff 3 4 0.069998 3.550000 1.620000 # CAM CAP
pair_coeff 3 5 0.067968 3.524911 1.620000 # CAM CTT
pair_coeff 3 6 0.045825 2.931041 0.000000 # CAM HAT
pair_coeff 3 7 0.045825 2.931041 0.000000 # CAM HT
pair_coeff 4 4 0.069998 3.550000 1.620000 # CAP CAP
pair_coeff 4 5 0.067968 3.524911 1.620000 # CAP CTT
pair_coeff 4 6 0.045825 2.931041 0.000000 # CAP HAT
pair_coeff 4 7 0.045825 2.931041 0.000000 # CAP HT
pair_coeff 5 5 0.065997 3.500000 1.620000 # CTT CTT
pair_coeff 5 6 0.044496 2.910326 0.000000 # CTT HAT
pair_coeff 5 7 0.044496 2.910326 0.000000 # CTT HT
pair_coeff 6 6 0.029999 2.420000 0.000000 # HAT HAT
pair_coeff 6 7 0.029999 2.420000 0.000000 # HAT HT
pair_coeff 7 7 0.029999 2.420000 0.000000 # HT HT
pair_coeff 1 8 0.000000 0.000000 1.620000 # CAT D_CAT
pair_coeff 1 9 0.000000 0.000000 1.620000 # CAT D_CAO
pair_coeff 1 10 0.000000 0.000000 1.620000 # CAT D_CAM
pair_coeff 1 11 0.000000 0.000000 1.620000 # CAT D_CAP
pair_coeff 1 12 0.000000 0.000000 1.620000 # CAT D_CTT
pair_coeff 2 8 0.000000 0.000000 1.620000 # CAO D_CAT
pair_coeff 2 9 0.000000 0.000000 1.620000 # CAO D_CAO
pair_coeff 2 10 0.000000 0.000000 1.620000 # CAO D_CAM
pair_coeff 2 11 0.000000 0.000000 1.620000 # CAO D_CAP
pair_coeff 2 12 0.000000 0.000000 1.620000 # CAO D_CTT
pair_coeff 3 8 0.000000 0.000000 1.620000 # CAM D_CAT
pair_coeff 3 9 0.000000 0.000000 1.620000 # CAM D_CAO
pair_coeff 3 10 0.000000 0.000000 1.620000 # CAM D_CAM
pair_coeff 3 11 0.000000 0.000000 1.620000 # CAM D_CAP
pair_coeff 3 12 0.000000 0.000000 1.620000 # CAM D_CTT
pair_coeff 4 8 0.000000 0.000000 1.620000 # CAP D_CAT
pair_coeff 4 9 0.000000 0.000000 1.620000 # CAP D_CAO
pair_coeff 4 10 0.000000 0.000000 1.620000 # CAP D_CAM
pair_coeff 4 11 0.000000 0.000000 1.620000 # CAP D_CAP
pair_coeff 4 12 0.000000 0.000000 1.620000 # CAP D_CTT
pair_coeff 5 8 0.000000 0.000000 1.620000 # CTT D_CAT
pair_coeff 5 9 0.000000 0.000000 1.620000 # CTT D_CAO
pair_coeff 5 10 0.000000 0.000000 1.620000 # CTT D_CAM
pair_coeff 5 11 0.000000 0.000000 1.620000 # CTT D_CAP
pair_coeff 5 12 0.000000 0.000000 1.620000 # CTT D_CTT
pair_coeff 8 8 0.000000 0.000000 1.620000 # D_CAT D_CAT
pair_coeff 8 9 0.000000 0.000000 1.620000 # D_CAT D_CAO
pair_coeff 8 10 0.000000 0.000000 1.620000 # D_CAT D_CAM
pair_coeff 8 11 0.000000 0.000000 1.620000 # D_CAT D_CAP
pair_coeff 8 12 0.000000 0.000000 1.620000 # D_CAT D_CTT
pair_coeff 9 9 0.000000 0.000000 1.620000 # D_CAO D_CAO
pair_coeff 9 10 0.000000 0.000000 1.620000 # D_CAO D_CAM
pair_coeff 9 11 0.000000 0.000000 1.620000 # D_CAO D_CAP
pair_coeff 9 12 0.000000 0.000000 1.620000 # D_CAO D_CTT
pair_coeff 10 10 0.000000 0.000000 1.620000 # D_CAM D_CAM
pair_coeff 10 11 0.000000 0.000000 1.620000 # D_CAM D_CAP
pair_coeff 10 12 0.000000 0.000000 1.620000 # D_CAM D_CTT
pair_coeff 11 11 0.000000 0.000000 1.620000 # D_CAP D_CAP
pair_coeff 11 12 0.000000 0.000000 1.620000 # D_CAP D_CTT
pair_coeff 12 12 0.000000 0.000000 1.620000 # D_CTT D_CTT
neighbor 2.0 bin
variable vTEMP equal 260.0
variable vTEMP_D equal 1.0
variable vPRESS equal 1.0
velocity gCORES create ${vTEMP} 12345
velocity gDRUDES create ${vTEMP_D} 12345
fix fDRUDE all drude C C C C C N N D D D D D
fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8
compute cTEMP_CORE gCORES temp/com
compute cTEMP all temp/drude
fix fDIRECT all drude/transform/direct
fix fNVT1 gCORES nvt temp ${vTEMP} ${vTEMP} 100.0
fix fNVT2 gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 20.0
fix fINVERSE all drude/transform/inverse
fix fMOMENTUM all momentum 100 linear 1 1 1
thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
thermo 50
timestep 0.5
run 2000

251
examples/USER/drude/toluene/log.toluene.lang.11Aug17.linux.1 Normal file
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@ -0,0 +1,251 @@
LAMMPS (11 Aug 2017)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# 250 toluene system for drude polarizability example (Langevin)
units real
boundary p p p
atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style opls
improper_style opls
special_bonds lj/coul 0.0 0.0 0.5
pair_style lj/cut/thole/long 2.600 8.0 8.0
pair_modify mix geometric tail yes
kspace_style pppm 1.0e-4
read_data data.toluene extra/special/per/atom 1
orthogonal box = (-18.2908 -18.1636 -18.223) to (18.3357 18.1621 18.3287)
1 by 1 by 1 MPI processor grid
reading atoms ...
5500 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
8 = max dihedrals/atom
scanning impropers ...
2 = max impropers/atom
reading bonds ...
5500 bonds
reading angles ...
6000 angles
reading dihedrals ...
6000 dihedrals
reading impropers ...
1500 impropers
5 = max # of 1-2 neighbors
10 = max # of 1-3 neighbors
16 = max # of 1-4 neighbors
20 = max # of special neighbors
comm_modify vel yes
group gTOLUENE molecule 1:250
5500 atoms in group gTOLUENE
group gCORES type 1 2 3 4 5 6 7
3750 atoms in group gCORES
group gDRUDES type 8 9 10 11 12
1750 atoms in group gDRUDES
pair_coeff 1 1 0.069998 3.550000 1.620000 # CAT CAT
pair_coeff 1 2 0.069998 3.550000 1.620000 # CAT CAO
pair_coeff 1 3 0.069998 3.550000 1.620000 # CAT CAM
pair_coeff 1 4 0.069998 3.550000 1.620000 # CAT CAP
pair_coeff 1 5 0.067968 3.524911 1.620000 # CAT CTT
pair_coeff 1 6 0.045825 2.931041 0.000000 # CAT HAT
pair_coeff 1 7 0.045825 2.931041 0.000000 # CAT HT
pair_coeff 2 2 0.069998 3.550000 1.620000 # CAO CAO
pair_coeff 2 3 0.069998 3.550000 1.620000 # CAO CAM
pair_coeff 2 4 0.069998 3.550000 1.620000 # CAO CAP
pair_coeff 2 5 0.067968 3.524911 1.620000 # CAO CTT
pair_coeff 2 6 0.045825 2.931041 0.000000 # CAO HAT
pair_coeff 2 7 0.045825 2.931041 0.000000 # CAO HT
pair_coeff 3 3 0.069998 3.550000 1.620000 # CAM CAM
pair_coeff 3 4 0.069998 3.550000 1.620000 # CAM CAP
pair_coeff 3 5 0.067968 3.524911 1.620000 # CAM CTT
pair_coeff 3 6 0.045825 2.931041 0.000000 # CAM HAT
pair_coeff 3 7 0.045825 2.931041 0.000000 # CAM HT
pair_coeff 4 4 0.069998 3.550000 1.620000 # CAP CAP
pair_coeff 4 5 0.067968 3.524911 1.620000 # CAP CTT
pair_coeff 4 6 0.045825 2.931041 0.000000 # CAP HAT
pair_coeff 4 7 0.045825 2.931041 0.000000 # CAP HT
pair_coeff 5 5 0.065997 3.500000 1.620000 # CTT CTT
pair_coeff 5 6 0.044496 2.910326 0.000000 # CTT HAT
pair_coeff 5 7 0.044496 2.910326 0.000000 # CTT HT
pair_coeff 6 6 0.029999 2.420000 0.000000 # HAT HAT
pair_coeff 6 7 0.029999 2.420000 0.000000 # HAT HT
pair_coeff 7 7 0.029999 2.420000 0.000000 # HT HT
pair_coeff 1 8 0.000000 0.000000 1.620000 # CAT D_CAT
pair_coeff 1 9 0.000000 0.000000 1.620000 # CAT D_CAO
pair_coeff 1 10 0.000000 0.000000 1.620000 # CAT D_CAM
pair_coeff 1 11 0.000000 0.000000 1.620000 # CAT D_CAP
pair_coeff 1 12 0.000000 0.000000 1.620000 # CAT D_CTT
pair_coeff 2 8 0.000000 0.000000 1.620000 # CAO D_CAT
pair_coeff 2 9 0.000000 0.000000 1.620000 # CAO D_CAO
pair_coeff 2 10 0.000000 0.000000 1.620000 # CAO D_CAM
pair_coeff 2 11 0.000000 0.000000 1.620000 # CAO D_CAP
pair_coeff 2 12 0.000000 0.000000 1.620000 # CAO D_CTT
pair_coeff 3 8 0.000000 0.000000 1.620000 # CAM D_CAT
pair_coeff 3 9 0.000000 0.000000 1.620000 # CAM D_CAO
pair_coeff 3 10 0.000000 0.000000 1.620000 # CAM D_CAM
pair_coeff 3 11 0.000000 0.000000 1.620000 # CAM D_CAP
pair_coeff 3 12 0.000000 0.000000 1.620000 # CAM D_CTT
pair_coeff 4 8 0.000000 0.000000 1.620000 # CAP D_CAT
pair_coeff 4 9 0.000000 0.000000 1.620000 # CAP D_CAO
pair_coeff 4 10 0.000000 0.000000 1.620000 # CAP D_CAM
pair_coeff 4 11 0.000000 0.000000 1.620000 # CAP D_CAP
pair_coeff 4 12 0.000000 0.000000 1.620000 # CAP D_CTT
pair_coeff 5 8 0.000000 0.000000 1.620000 # CTT D_CAT
pair_coeff 5 9 0.000000 0.000000 1.620000 # CTT D_CAO
pair_coeff 5 10 0.000000 0.000000 1.620000 # CTT D_CAM
pair_coeff 5 11 0.000000 0.000000 1.620000 # CTT D_CAP
pair_coeff 5 12 0.000000 0.000000 1.620000 # CTT D_CTT
pair_coeff 8 8 0.000000 0.000000 1.620000 # D_CAT D_CAT
pair_coeff 8 9 0.000000 0.000000 1.620000 # D_CAT D_CAO
pair_coeff 8 10 0.000000 0.000000 1.620000 # D_CAT D_CAM
pair_coeff 8 11 0.000000 0.000000 1.620000 # D_CAT D_CAP
pair_coeff 8 12 0.000000 0.000000 1.620000 # D_CAT D_CTT
pair_coeff 9 9 0.000000 0.000000 1.620000 # D_CAO D_CAO
pair_coeff 9 10 0.000000 0.000000 1.620000 # D_CAO D_CAM
pair_coeff 9 11 0.000000 0.000000 1.620000 # D_CAO D_CAP
pair_coeff 9 12 0.000000 0.000000 1.620000 # D_CAO D_CTT
pair_coeff 10 10 0.000000 0.000000 1.620000 # D_CAM D_CAM
pair_coeff 10 11 0.000000 0.000000 1.620000 # D_CAM D_CAP
pair_coeff 10 12 0.000000 0.000000 1.620000 # D_CAM D_CTT
pair_coeff 11 11 0.000000 0.000000 1.620000 # D_CAP D_CAP
pair_coeff 11 12 0.000000 0.000000 1.620000 # D_CAP D_CTT
pair_coeff 12 12 0.000000 0.000000 1.620000 # D_CTT D_CTT
neighbor 2.0 bin
variable vTEMP equal 260.0
variable vTEMP_D equal 1.0
variable vPRESS equal 1.0
velocity gCORES create ${vTEMP} 12345
velocity gCORES create 260 12345
velocity gDRUDES create ${vTEMP_D} 12345
velocity gDRUDES create 1 12345
fix fDRUDE all drude C C C C C N N D D D D D
fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8
1250 = # of size 2 clusters
0 = # of size 3 clusters
250 = # of size 4 clusters
0 = # of frozen angles
fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
fix fLANG all langevin/drude 260 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
fix fLANG all langevin/drude 260 100.0 200611 1 20.0 260514 zero yes
fix fNPH all nve
compute cTEMP all temp/drude
thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
thermo 50
timestep 0.5
run 2000
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.382011
grid = 40 40 40
stencil order = 5
estimated absolute RMS force accuracy = 0.0325934
estimated relative force accuracy = 9.8154e-05
using double precision FFTs
3d grid and FFT values/proc = 103823 64000
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 19
New max number of 1-2 to 1-4 neighbors: 20 (+1)
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10
ghost atom cutoff = 10
binsize = 5, bins = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/thole/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 42.06 | 42.06 | 42.06 Mbytes
Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2]
0 0 14386.197 2910.7282 202.07402 11475.469 6565.4851 20.333365 1.0706727e-06 1.3894617e-07 4972.8631 1306116.6 -1306199.8 40273.68 48631.318 314.89553 3.1777821
50 4.311986 8083.3901 4729.9995 328.37487 3353.3906 1812.5186 685.40417 646.10358 50.083281 804.80656 1305984.8 -1306630.3 16960.287 48631.318 448.67988 116.22125
100 8.756623 6206.7865 3683.944 255.75365 2522.8425 977.52675 777.45439 838.58809 68.086914 471.97862 1306097.1 -1306707.9 15657.142 48631.318 380.53159 35.760643
150 13.134938 5386.0219 3582.482 248.70976 1803.5399 752.25928 803.04832 643.43249 49.76684 131.97853 1306139.2 -1306716.2 15140.102 48631.318 383.61303 10.880935
200 17.508189 4846.4097 3254.3932 225.93257 1592.0166 700.43329 812.26722 657.52279 51.044716 -64.045174 1306160.5 -1306725.7 13844.277 48631.318 351.90677 3.8489009
250 21.871676 4473.215 3091.5333 214.6262 1381.6817 688.24707 842.63267 590.45999 48.22798 -214.02425 1306156.6 -1306730.5 8808.7402 48631.318 335.32872 1.8372171
300 26.226064 4191.8834 2883.8468 200.2078 1308.0367 734.36657 856.15482 584.87904 47.590787 -343.44615 1306163.4 -1306734.9 3389.3777 48631.318 313.03581 1.3011826
350 30.568716 3972.0739 2756.8392 191.39044 1215.2347 664.4688 866.06348 580.13632 48.515297 -378.8729 1306173.3 -1306738.3 8458.1149 48631.318 299.31146 1.1345329
400 34.845648 3838.3528 2731.3975 189.62419 1106.9552 684.0318 870.67752 548.93014 44.038787 -460.1537 1306160.4 -1306741 6697.9188 48631.318 296.54405 1.1332149
450 39.17477 3731.18 2607.8585 181.04762 1123.3216 719.57572 894.99915 571.99504 47.625227 -537.60494 1306171.9 -1306745.2 2450.4224 48631.318 283.13713 1.0721818
500 43.497489 3607.0055 2565.9469 178.13796 1041.0586 717.36452 841.34375 551.39834 45.985413 -542.47313 1306170.9 -1306743.4 3077.1849 48631.318 278.59462 1.0410963
550 47.812038 3513.8132 2548.7259 176.94241 965.08736 673.81272 852.38161 522.99297 44.276434 -552.27379 1306171.2 -1306747.4 4659.7275 48631.318 276.70124 1.0757459
600 52.124423 3386.9627 2471.0692 171.55118 915.89348 689.99732 833.61298 517.49343 43.023588 -594.96363 1306170.6 -1306743.8 2159.7328 48631.318 268.27854 1.0287605
650 56.370068 3374.3191 2413.6719 167.56644 960.64717 703.32428 874.12028 535.41271 43.256032 -617.25815 1306168.6 -1306746.8 1262.4757 48631.318 261.99584 1.0950976
700 60.667476 3342.9467 2412.9563 167.51676 929.99042 683.70355 882.22521 527.03932 43.661355 -616.70117 1306161 -1306751 2950.9009 48631.318 261.92814 1.0771869
750 64.964696 3327.7938 2414.3547 167.61385 913.43902 695.12778 863.48248 542.99202 46.408369 -639.60076 1306160.7 -1306755.6 1583.0277 48631.318 262.09771 1.0464936
800 69.256916 3391.689 2452.2049 170.24155 939.48407 694.2176 892.61592 557.53726 45.495129 -654.56675 1306155.2 -1306751 1232.1671 48631.318 266.20601 1.0640309
850 73.527972 3386.8618 2486.6928 172.63584 900.16902 696.7684 880.27643 545.11446 46.474227 -665.90464 1306154.7 -1306757.3 1129.2062 48631.318 269.97945 1.027015
900 77.775993 3368.0724 2416.7145 167.77767 951.35789 718.66654 893.18396 537.79136 46.404626 -641.29596 1306152.9 -1306756.3 1673.0743 48631.318 262.34697 1.0597091
950 82.028341 3300.4793 2409.5613 167.28107 890.918 728.06888 890.51193 515.08456 44.36547 -671.13741 1306142.3 -1306758.2 1038.6579 48631.318 261.57036 1.0567234
1000 86.189789 3333.2955 2452.2486 170.24458 881.04692 699.8414 915.33862 506.83261 41.77374 -665.68264 1306141.6 -1306758.7 467.42142 48631.318 266.19104 1.0987814
1050 90.384168 3303.87 2376.9713 165.01854 926.89875 706.12941 930.65844 524.73304 42.644613 -657.19573 1306139.3 -1306759.4 1737.6624 48631.318 258.00246 1.0954432
1100 94.549452 3367.668 2454.9154 170.42973 912.75259 715.68494 935.8363 516.52205 43.261761 -671.86101 1306137.9 -1306764.6 961.79199 48631.318 266.492 1.0797548
1150 98.65493 3350.0898 2485.3993 172.54604 864.69051 699.23072 933.76405 510.60424 42.381362 -684.53513 1306127.1 -1306763.8 -272.48178 48631.318 269.82496 1.0512421
1200 102.82045 3309.6871 2398.9577 166.54492 910.72944 705.58979 934.53183 531.90967 45.872142 -664.58495 1306126.9 -1306769.5 627.31931 48631.318 260.41866 1.0531639
1250 106.9899 3304.504 2491.6998 172.98344 812.80426 710.83366 881.33764 494.90045 41.71618 -672.49264 1306123.8 -1306767.3 136.11723 48631.318 270.51026 1.0516137
1300 111.16224 3318.9543 2462.0621 170.92588 856.89219 709.17314 932.87209 503.80373 43.426006 -680.2474 1306121.2 -1306773.3 1276.2503 48631.318 267.28591 1.0510113
1350 115.27184 3314.8515 2434.8483 169.03659 880.00316 710.91641 922.28347 540.40795 44.753548 -686.09335 1306124.5 -1306776.7 -438.87694 48631.318 264.31236 1.0731666
1400 119.44228 3349.0785 2457.7697 170.62788 891.30875 711.28064 936.58607 516.63511 42.396287 -653.09763 1306113.8 -1306776.3 350.79618 48631.318 266.80555 1.0745043
1450 123.61267 3364.1486 2459.8741 170.77397 904.27455 696.57265 946.32098 538.55368 44.69075 -652.75091 1306111 -1306780.1 502.47466 48631.318 267.03201 1.0789056
1500 127.72962 3341.9369 2454.3302 170.3891 887.60672 726.46979 903.40815 557.73064 47.536125 -667.65025 1306100.7 -1306780.6 -248.0975 48631.318 266.44821 1.044725
1550 131.91041 3270.4282 2437.7916 169.24093 832.63655 691.49462 910.83807 523.17366 44.83093 -654.48655 1306100.5 -1306783.7 490.32965 48631.318 264.63652 1.0662604
1600 136.0834 3252.0725 2429.6805 168.67782 822.39196 689.68155 898.22828 535.31963 43.84399 -660.93277 1306100.1 -1306783.9 1729.5956 48631.318 263.74523 1.0817172
1650 140.26444 3239.748 2442.6258 169.57653 797.12222 671.1832 907.1659 507.03947 43.048028 -648.14001 1306103.3 -1306786.5 970.43988 48631.318 265.15987 1.0708872
1700 144.3855 3202.9157 2410.267 167.33006 792.64869 686.40974 882.40791 527.02899 43.819792 -656.82001 1306096 -1306786.2 -107.50166 48631.318 261.64368 1.062837
1750 148.56592 3214.6107 2366.3264 164.27953 848.28434 696.38228 915.58636 538.2236 47.852688 -652.7697 1306093.6 -1306790.6 -164.14366 48631.318 256.84519 1.0937744
1800 152.74611 3209.5771 2421.4089 168.10357 788.16819 683.61816 869.45802 532.77927 45.708374 -658.39221 1306103.1 -1306788.1 277.61781 48631.318 262.83282 1.1036154
1850 156.86567 3146.3973 2362.3333 164.00232 784.064 697.87032 875.8451 523.54452 43.851379 -665.83106 1306101.5 -1306792.7 497.88657 48631.318 256.42683 1.0654271
1900 161.0419 3141.5496 2367.1077 164.33378 774.44186 693.39945 878.97447 515.65653 44.619392 -668.11692 1306103.8 -1306793.9 -1427.3998 48631.318 256.94212 1.0727903
1950 165.22235 3134.6473 2295.577 159.36784 839.07025 699.62719 905.76937 519.32307 46.109334 -645.08933 1306104.9 -1306791.6 1744.2846 48631.318 249.19694 1.0064565
2000 169.4 3146.866 2361.3821 163.93628 785.48386 682.24124 889.6864 534.94877 46.855983 -678.1614 1306104 -1306794.1 699.8735 48631.318 256.32873 1.0559143
Loop time of 169.4 on 1 procs for 2000 steps with 5500 atoms
Performance: 0.510 ns/day, 47.056 hours/ns, 11.806 timesteps/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 | 107.93 | 107.93 | 107.93 | 0.0 | 63.71
Bond | 19.76 | 19.76 | 19.76 | 0.0 | 11.66
Kspace | 34.926 | 34.926 | 34.926 | 0.0 | 20.62
Neigh | 1.9932 | 1.9932 | 1.9932 | 0.0 | 1.18
Comm | 0.73555 | 0.73555 | 0.73555 | 0.0 | 0.43
Output | 0.0065863 | 0.0065863 | 0.0065863 | 0.0 | 0.00
Modify | 3.9135 | 3.9135 | 3.9135 | 0.0 | 2.31
Other | | 0.133 | | | 0.08
Nlocal: 5500 ave 5500 max 5500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 13219 ave 13219 max 13219 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.33739e+06 ave 1.33739e+06 max 1.33739e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1337388
Ave neighs/atom = 243.161
Ave special neighs/atom = 15.6364
Neighbor list builds = 32
Dangerous builds = 0
Total wall time: 0:02:49

251
examples/USER/drude/toluene/log.toluene.lang.11Aug17.linux.4 Normal file
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LAMMPS (11 Aug 2017)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# 250 toluene system for drude polarizability example (Langevin)
units real
boundary p p p
atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style opls
improper_style opls
special_bonds lj/coul 0.0 0.0 0.5
pair_style lj/cut/thole/long 2.600 8.0 8.0
pair_modify mix geometric tail yes
kspace_style pppm 1.0e-4
read_data data.toluene extra/special/per/atom 1
orthogonal box = (-18.2908 -18.1636 -18.223) to (18.3357 18.1621 18.3287)
2 by 1 by 2 MPI processor grid
reading atoms ...
5500 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
8 = max dihedrals/atom
scanning impropers ...
2 = max impropers/atom
reading bonds ...
5500 bonds
reading angles ...
6000 angles
reading dihedrals ...
6000 dihedrals
reading impropers ...
1500 impropers
5 = max # of 1-2 neighbors
10 = max # of 1-3 neighbors
16 = max # of 1-4 neighbors
20 = max # of special neighbors
comm_modify vel yes
group gTOLUENE molecule 1:250
5500 atoms in group gTOLUENE
group gCORES type 1 2 3 4 5 6 7
3750 atoms in group gCORES
group gDRUDES type 8 9 10 11 12
1750 atoms in group gDRUDES
pair_coeff 1 1 0.069998 3.550000 1.620000 # CAT CAT
pair_coeff 1 2 0.069998 3.550000 1.620000 # CAT CAO
pair_coeff 1 3 0.069998 3.550000 1.620000 # CAT CAM
pair_coeff 1 4 0.069998 3.550000 1.620000 # CAT CAP
pair_coeff 1 5 0.067968 3.524911 1.620000 # CAT CTT
pair_coeff 1 6 0.045825 2.931041 0.000000 # CAT HAT
pair_coeff 1 7 0.045825 2.931041 0.000000 # CAT HT
pair_coeff 2 2 0.069998 3.550000 1.620000 # CAO CAO
pair_coeff 2 3 0.069998 3.550000 1.620000 # CAO CAM
pair_coeff 2 4 0.069998 3.550000 1.620000 # CAO CAP
pair_coeff 2 5 0.067968 3.524911 1.620000 # CAO CTT
pair_coeff 2 6 0.045825 2.931041 0.000000 # CAO HAT
pair_coeff 2 7 0.045825 2.931041 0.000000 # CAO HT
pair_coeff 3 3 0.069998 3.550000 1.620000 # CAM CAM
pair_coeff 3 4 0.069998 3.550000 1.620000 # CAM CAP
pair_coeff 3 5 0.067968 3.524911 1.620000 # CAM CTT
pair_coeff 3 6 0.045825 2.931041 0.000000 # CAM HAT
pair_coeff 3 7 0.045825 2.931041 0.000000 # CAM HT
pair_coeff 4 4 0.069998 3.550000 1.620000 # CAP CAP
pair_coeff 4 5 0.067968 3.524911 1.620000 # CAP CTT
pair_coeff 4 6 0.045825 2.931041 0.000000 # CAP HAT
pair_coeff 4 7 0.045825 2.931041 0.000000 # CAP HT
pair_coeff 5 5 0.065997 3.500000 1.620000 # CTT CTT
pair_coeff 5 6 0.044496 2.910326 0.000000 # CTT HAT
pair_coeff 5 7 0.044496 2.910326 0.000000 # CTT HT
pair_coeff 6 6 0.029999 2.420000 0.000000 # HAT HAT
pair_coeff 6 7 0.029999 2.420000 0.000000 # HAT HT
pair_coeff 7 7 0.029999 2.420000 0.000000 # HT HT
pair_coeff 1 8 0.000000 0.000000 1.620000 # CAT D_CAT
pair_coeff 1 9 0.000000 0.000000 1.620000 # CAT D_CAO
pair_coeff 1 10 0.000000 0.000000 1.620000 # CAT D_CAM
pair_coeff 1 11 0.000000 0.000000 1.620000 # CAT D_CAP
pair_coeff 1 12 0.000000 0.000000 1.620000 # CAT D_CTT
pair_coeff 2 8 0.000000 0.000000 1.620000 # CAO D_CAT
pair_coeff 2 9 0.000000 0.000000 1.620000 # CAO D_CAO
pair_coeff 2 10 0.000000 0.000000 1.620000 # CAO D_CAM
pair_coeff 2 11 0.000000 0.000000 1.620000 # CAO D_CAP
pair_coeff 2 12 0.000000 0.000000 1.620000 # CAO D_CTT
pair_coeff 3 8 0.000000 0.000000 1.620000 # CAM D_CAT
pair_coeff 3 9 0.000000 0.000000 1.620000 # CAM D_CAO
pair_coeff 3 10 0.000000 0.000000 1.620000 # CAM D_CAM
pair_coeff 3 11 0.000000 0.000000 1.620000 # CAM D_CAP
pair_coeff 3 12 0.000000 0.000000 1.620000 # CAM D_CTT
pair_coeff 4 8 0.000000 0.000000 1.620000 # CAP D_CAT
pair_coeff 4 9 0.000000 0.000000 1.620000 # CAP D_CAO
pair_coeff 4 10 0.000000 0.000000 1.620000 # CAP D_CAM
pair_coeff 4 11 0.000000 0.000000 1.620000 # CAP D_CAP
pair_coeff 4 12 0.000000 0.000000 1.620000 # CAP D_CTT
pair_coeff 5 8 0.000000 0.000000 1.620000 # CTT D_CAT
pair_coeff 5 9 0.000000 0.000000 1.620000 # CTT D_CAO
pair_coeff 5 10 0.000000 0.000000 1.620000 # CTT D_CAM
pair_coeff 5 11 0.000000 0.000000 1.620000 # CTT D_CAP
pair_coeff 5 12 0.000000 0.000000 1.620000 # CTT D_CTT
pair_coeff 8 8 0.000000 0.000000 1.620000 # D_CAT D_CAT
pair_coeff 8 9 0.000000 0.000000 1.620000 # D_CAT D_CAO
pair_coeff 8 10 0.000000 0.000000 1.620000 # D_CAT D_CAM
pair_coeff 8 11 0.000000 0.000000 1.620000 # D_CAT D_CAP
pair_coeff 8 12 0.000000 0.000000 1.620000 # D_CAT D_CTT
pair_coeff 9 9 0.000000 0.000000 1.620000 # D_CAO D_CAO
pair_coeff 9 10 0.000000 0.000000 1.620000 # D_CAO D_CAM
pair_coeff 9 11 0.000000 0.000000 1.620000 # D_CAO D_CAP
pair_coeff 9 12 0.000000 0.000000 1.620000 # D_CAO D_CTT
pair_coeff 10 10 0.000000 0.000000 1.620000 # D_CAM D_CAM
pair_coeff 10 11 0.000000 0.000000 1.620000 # D_CAM D_CAP
pair_coeff 10 12 0.000000 0.000000 1.620000 # D_CAM D_CTT
pair_coeff 11 11 0.000000 0.000000 1.620000 # D_CAP D_CAP
pair_coeff 11 12 0.000000 0.000000 1.620000 # D_CAP D_CTT
pair_coeff 12 12 0.000000 0.000000 1.620000 # D_CTT D_CTT
neighbor 2.0 bin
variable vTEMP equal 260.0
variable vTEMP_D equal 1.0
variable vPRESS equal 1.0
velocity gCORES create ${vTEMP} 12345
velocity gCORES create 260 12345
velocity gDRUDES create ${vTEMP_D} 12345
velocity gDRUDES create 1 12345
fix fDRUDE all drude C C C C C N N D D D D D
fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8
1250 = # of size 2 clusters
0 = # of size 3 clusters
250 = # of size 4 clusters
0 = # of frozen angles
fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
fix fLANG all langevin/drude 260 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
fix fLANG all langevin/drude 260 100.0 200611 1 20.0 260514 zero yes
fix fNPH all nve
compute cTEMP all temp/drude
thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
thermo 50
timestep 0.5
run 2000
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.382011
grid = 40 40 40
stencil order = 5
estimated absolute RMS force accuracy = 0.0325934
estimated relative force accuracy = 9.8154e-05
using double precision FFTs
3d grid and FFT values/proc = 34263 16000
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 19
New max number of 1-2 to 1-4 neighbors: 20 (+1)
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10
ghost atom cutoff = 10
binsize = 5, bins = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/thole/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 18 | 18 | 18 Mbytes
Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2]
0 0 14386.197 2910.7282 202.07402 11475.469 6565.4851 20.333365 1.0706727e-06 1.3894617e-07 4972.8631 1306116.6 -1306199.8 40273.68 48631.318 314.89553 3.1777821
50 1.0658228 8014.6879 4671.7498 324.33095 3342.9381 1798.7991 670.22837 651.99307 50.352024 819.34616 1305984.9 -1306632.7 17255.952 48631.318 442.52888 116.12397
100 2.136163 6185.5007 3697.0414 256.66292 2488.4593 974.42931 774.88353 840.46625 66.896007 427.27085 1306105.5 -1306701 15044.739 48631.318 381.93582 35.802658
150 3.202647 5418.0644 3628.2714 251.88864 1789.7929 764.02696 804.61034 641.14915 47.995428 108.05084 1306138.9 -1306714.9 15258.194 48631.318 388.65363 10.777816
200 4.2728949 4838.4235 3303.8964 229.36927 1534.5271 702.10438 772.85348 625.99718 52.299187 -63.792745 1306166.5 -1306721.4 13487.722 48631.318 357.35337 3.7423617
250 5.3275268 4461.2438 3084.8973 214.16551 1376.3465 693.85145 823.23815 599.85313 48.280277 -230.56822 1306167.8 -1306726.1 8779.0061 48631.318 334.59262 1.8620294
300 6.3794398 4179.6462 2885.0738 200.29299 1294.5724 739.337 868.84011 555.04912 44.838819 -354.73738 1306171.3 -1306730 4410.8735 48631.318 313.17473 1.2892347
350 7.427706 3934.3968 2756.2421 191.34899 1178.1546 666.16877 877.32996 548.99846 45.087026 -404.32209 1306179 -1306734.1 8477.8828 48631.318 299.22663 1.1698531
400 8.4820418 3800.4769 2674.8317 185.69716 1125.6452 693.29433 841.29833 579.61438 48.325361 -470.18802 1306170.5 -1306737.2 6265.7532 48631.318 290.39105 1.1303952
450 9.528651 3685.28 2616.9074 181.67583 1068.3726 702.68328 886.66644 555.74511 46.160811 -557.70651 1306176.6 -1306741.7 2701.7737 48631.318 284.11064 1.091646
500 10.579133 3582.6591 2517.6443 174.78461 1065.0148 701.82101 894.9429 554.06012 46.074357 -570.49878 1306181.8 -1306743.2 3643.7426 48631.318 273.31525 1.0831346
550 11.629649 3542.0402 2527.0386 175.4368 1015.0016 688.73877 916.2381 521.69932 44.014375 -580.05437 1306171 -1306746.6 2928.6632 48631.318 274.34257 1.0740018
600 12.684143 3507.0443 2519.9749 174.94641 987.06936 711.58734 894.63276 525.57884 42.944226 -603.24423 1306161.2 -1306745.7 2082.9907 48631.318 273.57124 1.0784841
650 13.737965 3416.2001 2445.9361 169.80635 970.26394 706.95207 891.76446 540.90369 45.970985 -626.32832 1306160.2 -1306749.2 1912.8783 48631.318 265.5023 1.1021764
700 14.777375 3419.7572 2446.117 169.81891 973.64019 664.17579 936.51992 551.67148 45.696531 -634.70926 1306159.6 -1306749.4 2215.7085 48631.318 265.53614 1.0774684
750 15.795347 3418.6537 2449.343 170.04287 969.31069 706.12432 899.61553 553.21874 45.793213 -642.75298 1306158.1 -1306750.8 1022.2516 48631.318 265.89304 1.0681488
800 16.835794 3385.2449 2465.4963 171.16429 919.74864 692.34918 888.91243 530.24204 45.132243 -638.54787 1306154.6 -1306753 1601.1391 48631.318 267.64361 1.0797553
850 17.87536 3397.1124 2426.3129 168.44403 970.79951 717.48898 878.71057 580.26487 46.675101 -646.96926 1306150.9 -1306756.3 1048.7905 48631.318 263.38063 1.0785255
900 18.899639 3324.2064 2447.5004 169.91495 876.70599 683.62339 881.77789 531.98758 43.646731 -648.59248 1306144.4 -1306760.2 2221.5859 48631.318 265.69596 1.0608373
950 19.938468 3316.6329 2398.6988 166.52695 917.93405 702.84237 885.96473 540.35376 45.671318 -638.80334 1306144.4 -1306762.5 1955.2237 48631.318 260.38167 1.0687233
1000 20.973543 3287.4205 2384.191 165.51976 903.22949 705.56988 889.96387 535.23674 44.902139 -661.28175 1306150.4 -1306761.6 90.200683 48631.318 258.81506 1.0477545
1050 21.990961 3297.7806 2392.0372 166.06448 905.74339 697.33157 889.75086 537.2395 46.319713 -636.03286 1306135.9 -1306764.8 1893.8234 48631.318 259.67633 1.0344207
1100 23.006456 3240.651 2370.2217 164.54996 870.42931 693.87289 897.0846 526.89184 43.778979 -657.83716 1306132.1 -1306765.5 799.62979 48631.318 257.28711 1.0618941
1150 24.014558 3232.457 2377.9797 165.08855 854.47728 692.51558 897.77048 520.3269 43.903959 -657.38369 1306126.9 -1306769.6 178.21408 48631.318 258.13876 1.0479172
1200 25.010178 3238.4266 2392.0623 166.06622 846.36427 695.98996 887.237 522.01974 42.355716 -660.92843 1306124.7 -1306765 1006.1877 48631.318 259.66037 1.0698925
1250 26.01949 3198.3364 2332.7551 161.94888 865.58134 690.81786 897.35028 524.47996 44.421121 -640.92419 1306116.3 -1306766.8 2073.9672 48631.318 253.227 1.0326937
1300 27.026911 3237.6809 2386.3739 165.67131 851.30706 672.11785 901.04813 530.2964 44.020263 -655.33033 1306125.7 -1306766.5 579.46013 48631.318 259.05838 1.0374113
1350 28.033721 3285.9536 2371.155 164.61476 914.79862 718.12968 928.41764 524.02349 43.89896 -657.10221 1306127.3 -1306769.9 518.88041 48631.318 257.36737 1.0993197
1400 29.026742 3272.2173 2391.4158 166.02134 880.80147 712.59883 896.13616 532.95785 45.989768 -658.37495 1306125.6 -1306774.1 961.2067 48631.318 259.5968 1.0557033
1450 30.032566 3244.2627 2356.0955 163.56926 888.16727 714.72692 901.18382 534.59787 45.517573 -655.58258 1306124.5 -1306776.8 596.10558 48631.318 255.75173 1.058657
1500 31.03878 3244.8598 2408.5382 167.21004 836.32161 695.63105 867.27743 527.37333 44.496971 -648.96393 1306125.2 -1306774.7 443.71088 48631.318 261.45495 1.0648973
1550 32.041435 3239.3658 2367.1336 164.33557 872.23223 704.16965 884.5938 544.41685 46.110791 -654.61963 1306124.1 -1306776.5 -446.5562 48631.318 256.96289 1.0409003
1600 33.058977 3221.4258 2334.2656 162.05375 887.1602 713.8296 885.80472 533.86753 45.413663 -633.58824 1306119.6 -1306777.8 1527.9489 48631.318 253.36367 1.0817678
1650 34.080875 3224.4472 2385.9055 165.63879 838.54168 681.01628 879.88017 536.75983 43.884394 -643.24788 1306114 -1306773.8 1314.2208 48631.318 258.97106 1.1033457
1700 35.095047 3178.6575 2352.4294 163.31475 826.2281 700.79494 854.06687 549.39826 46.155483 -662.57181 1306115.2 -1306776.9 -187.36898 48631.318 255.35015 1.0638209
1750 36.093828 3219.473 2371.9421 164.6694 847.53093 699.44953 891.26068 541.91687 45.714235 -679.13432 1306120.3 -1306771.9 -618.32924 48631.318 257.48034 1.0512601
1800 37.110101 3202.0094 2371.8909 164.66585 830.11842 698.44522 858.38216 550.82008 46.315893 -667.77838 1306119.2 -1306775.3 -9.4963278 48631.318 257.46873 1.0619052
1850 38.121337 3202.0111 2366.6984 164.30536 835.31277 714.69988 849.6778 553.24258 46.502994 -667.44162 1306114.9 -1306776.3 131.11108 48631.318 256.90165 1.0656162
1900 39.132607 3228.7805 2365.934 164.25229 862.84648 720.68418 890.65533 554.75943 45.736726 -685.52803 1306115.1 -1306778.5 -82.525994 48631.318 256.81451 1.0726218
1950 40.127507 3218.4068 2443.0023 169.60267 775.40452 673.40001 874.63022 529.69964 43.166847 -680.57322 1306115.4 -1306780.3 622.76654 48631.318 265.20173 1.0693092
2000 41.138176 3257.463 2375.6246 164.92505 881.83842 677.60747 933.47776 547.01076 46.507189 -665.56273 1306123.7 -1306780.9 1829.3477 48631.318 257.88171 1.0500311
Loop time of 41.1383 on 4 procs for 2000 steps with 5500 atoms
Performance: 2.100 ns/day, 11.427 hours/ns, 48.617 timesteps/s
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 21.082 | 22.483 | 24.145 | 26.6 | 54.65
Bond | 4.9992 | 5.0781 | 5.1544 | 2.7 | 12.34
Kspace | 9.1202 | 10.806 | 12.272 | 39.7 | 26.27
Neigh | 0.45045 | 0.45076 | 0.45094 | 0.0 | 1.10
Comm | 0.85982 | 0.87287 | 0.88725 | 1.2 | 2.12
Output | 0.0036495 | 0.004005 | 0.0049655 | 0.9 | 0.01
Modify | 1.4009 | 1.401 | 1.4013 | 0.0 | 3.41
Other | | 0.04245 | | | 0.10
Nlocal: 1375 ave 1398 max 1361 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Nghost: 7745.75 ave 7788 max 7697 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Neighs: 334374 ave 348629 max 319495 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 1337494
Ave neighs/atom = 243.181
Ave special neighs/atom = 15.6364
Neighbor list builds = 31
Dangerous builds = 0
Total wall time: 0:00:41

259
examples/USER/drude/toluene/log.toluene.nh.11Aug17.linux.1 Normal file
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@ -0,0 +1,259 @@
LAMMPS (11 Aug 2017)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# 250 toluene system for drude polarizability example (Nose-Hoover)
units real
boundary p p p
atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style opls
improper_style opls
special_bonds lj/coul 0.0 0.0 0.5
pair_style lj/cut/thole/long 2.600 8.0 8.0
pair_modify mix geometric tail yes
kspace_style pppm 1.0e-4
read_data data.toluene extra/special/per/atom 1
orthogonal box = (-18.2908 -18.1636 -18.223) to (18.3357 18.1621 18.3287)
1 by 1 by 1 MPI processor grid
reading atoms ...
5500 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
8 = max dihedrals/atom
scanning impropers ...
2 = max impropers/atom
reading bonds ...
5500 bonds
reading angles ...
6000 angles
reading dihedrals ...
6000 dihedrals
reading impropers ...
1500 impropers
5 = max # of 1-2 neighbors
10 = max # of 1-3 neighbors
16 = max # of 1-4 neighbors
20 = max # of special neighbors
comm_modify vel yes
group gTOLUENE molecule 1:250
5500 atoms in group gTOLUENE
group gCORES type 1 2 3 4 5 6 7
3750 atoms in group gCORES
group gDRUDES type 8 9 10 11 12
1750 atoms in group gDRUDES
pair_coeff 1 1 0.069998 3.550000 1.620000 # CAT CAT
pair_coeff 1 2 0.069998 3.550000 1.620000 # CAT CAO
pair_coeff 1 3 0.069998 3.550000 1.620000 # CAT CAM
pair_coeff 1 4 0.069998 3.550000 1.620000 # CAT CAP
pair_coeff 1 5 0.067968 3.524911 1.620000 # CAT CTT
pair_coeff 1 6 0.045825 2.931041 0.000000 # CAT HAT
pair_coeff 1 7 0.045825 2.931041 0.000000 # CAT HT
pair_coeff 2 2 0.069998 3.550000 1.620000 # CAO CAO
pair_coeff 2 3 0.069998 3.550000 1.620000 # CAO CAM
pair_coeff 2 4 0.069998 3.550000 1.620000 # CAO CAP
pair_coeff 2 5 0.067968 3.524911 1.620000 # CAO CTT
pair_coeff 2 6 0.045825 2.931041 0.000000 # CAO HAT
pair_coeff 2 7 0.045825 2.931041 0.000000 # CAO HT
pair_coeff 3 3 0.069998 3.550000 1.620000 # CAM CAM
pair_coeff 3 4 0.069998 3.550000 1.620000 # CAM CAP
pair_coeff 3 5 0.067968 3.524911 1.620000 # CAM CTT
pair_coeff 3 6 0.045825 2.931041 0.000000 # CAM HAT
pair_coeff 3 7 0.045825 2.931041 0.000000 # CAM HT
pair_coeff 4 4 0.069998 3.550000 1.620000 # CAP CAP
pair_coeff 4 5 0.067968 3.524911 1.620000 # CAP CTT
pair_coeff 4 6 0.045825 2.931041 0.000000 # CAP HAT
pair_coeff 4 7 0.045825 2.931041 0.000000 # CAP HT
pair_coeff 5 5 0.065997 3.500000 1.620000 # CTT CTT
pair_coeff 5 6 0.044496 2.910326 0.000000 # CTT HAT
pair_coeff 5 7 0.044496 2.910326 0.000000 # CTT HT
pair_coeff 6 6 0.029999 2.420000 0.000000 # HAT HAT
pair_coeff 6 7 0.029999 2.420000 0.000000 # HAT HT
pair_coeff 7 7 0.029999 2.420000 0.000000 # HT HT
pair_coeff 1 8 0.000000 0.000000 1.620000 # CAT D_CAT
pair_coeff 1 9 0.000000 0.000000 1.620000 # CAT D_CAO
pair_coeff 1 10 0.000000 0.000000 1.620000 # CAT D_CAM
pair_coeff 1 11 0.000000 0.000000 1.620000 # CAT D_CAP
pair_coeff 1 12 0.000000 0.000000 1.620000 # CAT D_CTT
pair_coeff 2 8 0.000000 0.000000 1.620000 # CAO D_CAT
pair_coeff 2 9 0.000000 0.000000 1.620000 # CAO D_CAO
pair_coeff 2 10 0.000000 0.000000 1.620000 # CAO D_CAM
pair_coeff 2 11 0.000000 0.000000 1.620000 # CAO D_CAP
pair_coeff 2 12 0.000000 0.000000 1.620000 # CAO D_CTT
pair_coeff 3 8 0.000000 0.000000 1.620000 # CAM D_CAT
pair_coeff 3 9 0.000000 0.000000 1.620000 # CAM D_CAO
pair_coeff 3 10 0.000000 0.000000 1.620000 # CAM D_CAM
pair_coeff 3 11 0.000000 0.000000 1.620000 # CAM D_CAP
pair_coeff 3 12 0.000000 0.000000 1.620000 # CAM D_CTT
pair_coeff 4 8 0.000000 0.000000 1.620000 # CAP D_CAT
pair_coeff 4 9 0.000000 0.000000 1.620000 # CAP D_CAO
pair_coeff 4 10 0.000000 0.000000 1.620000 # CAP D_CAM
pair_coeff 4 11 0.000000 0.000000 1.620000 # CAP D_CAP
pair_coeff 4 12 0.000000 0.000000 1.620000 # CAP D_CTT
pair_coeff 5 8 0.000000 0.000000 1.620000 # CTT D_CAT
pair_coeff 5 9 0.000000 0.000000 1.620000 # CTT D_CAO
pair_coeff 5 10 0.000000 0.000000 1.620000 # CTT D_CAM
pair_coeff 5 11 0.000000 0.000000 1.620000 # CTT D_CAP
pair_coeff 5 12 0.000000 0.000000 1.620000 # CTT D_CTT
pair_coeff 8 8 0.000000 0.000000 1.620000 # D_CAT D_CAT
pair_coeff 8 9 0.000000 0.000000 1.620000 # D_CAT D_CAO
pair_coeff 8 10 0.000000 0.000000 1.620000 # D_CAT D_CAM
pair_coeff 8 11 0.000000 0.000000 1.620000 # D_CAT D_CAP
pair_coeff 8 12 0.000000 0.000000 1.620000 # D_CAT D_CTT
pair_coeff 9 9 0.000000 0.000000 1.620000 # D_CAO D_CAO
pair_coeff 9 10 0.000000 0.000000 1.620000 # D_CAO D_CAM
pair_coeff 9 11 0.000000 0.000000 1.620000 # D_CAO D_CAP
pair_coeff 9 12 0.000000 0.000000 1.620000 # D_CAO D_CTT
pair_coeff 10 10 0.000000 0.000000 1.620000 # D_CAM D_CAM
pair_coeff 10 11 0.000000 0.000000 1.620000 # D_CAM D_CAP
pair_coeff 10 12 0.000000 0.000000 1.620000 # D_CAM D_CTT
pair_coeff 11 11 0.000000 0.000000 1.620000 # D_CAP D_CAP
pair_coeff 11 12 0.000000 0.000000 1.620000 # D_CAP D_CTT
pair_coeff 12 12 0.000000 0.000000 1.620000 # D_CTT D_CTT
neighbor 2.0 bin
variable vTEMP equal 260.0
variable vTEMP_D equal 1.0
variable vPRESS equal 1.0
velocity gCORES create ${vTEMP} 12345
velocity gCORES create 260 12345
velocity gDRUDES create ${vTEMP_D} 12345
velocity gDRUDES create 1 12345
fix fDRUDE all drude C C C C C N N D D D D D
fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8
1250 = # of size 2 clusters
0 = # of size 3 clusters
250 = # of size 4 clusters
0 = # of frozen angles
compute cTEMP_CORE gCORES temp/com
compute cTEMP all temp/drude
fix fDIRECT all drude/transform/direct
fix fNVT1 gCORES nvt temp ${vTEMP} ${vTEMP} 100.0
fix fNVT1 gCORES nvt temp 260 ${vTEMP} 100.0
fix fNVT1 gCORES nvt temp 260 260 100.0
fix fNVT2 gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 20.0
fix fNVT2 gDRUDES nvt temp 1 ${vTEMP_D} 20.0
fix fNVT2 gDRUDES nvt temp 1 1 20.0
fix fINVERSE all drude/transform/inverse
fix fMOMENTUM all momentum 100 linear 1 1 1
thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
thermo 50
timestep 0.5
run 2000
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.382011
grid = 40 40 40
stencil order = 5
estimated absolute RMS force accuracy = 0.0325934
estimated relative force accuracy = 9.8154e-05
using double precision FFTs
3d grid and FFT values/proc = 103823 64000
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 19
New max number of 1-2 to 1-4 neighbors: 20 (+1)
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10
ghost atom cutoff = 10
binsize = 5, bins = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/thole/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 42.06 | 42.06 | 42.06 Mbytes
Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2]
0 0 14386.197 2910.7282 202.07402 11475.469 6565.4851 20.333365 1.0706727e-06 1.3894617e-07 4972.8631 1306116.6 -1306199.8 40273.68 48631.318 314.89553 3.1777821
50 4.462481 6863.642 4633.9267 321.70512 2229.7153 735.2547 604.6946 648.35773 49.039129 824.06033 1306091.3 -1306722.9 17914.827 48631.318 504.18525 0.0086839843
100 8.8666639 6628.0722 4376.1868 303.81182 2251.8853 598.11249 651.43051 919.41359 74.216826 589.6504 1306135.1 -1306716 17450.721 48631.318 476.14276 0.0075129702
150 13.323556 6336.1884 4726.0692 328.10201 1610.1192 560.01225 621.30109 640.32475 45.531175 288.99128 1306173.9 -1306720 18303.624 48631.318 514.21215 0.0061921467
200 17.710109 5997.6194 4565.6288 316.96362 1431.9906 524.2765 591.79843 718.11015 56.374558 88.660843 1306183 -1306730.3 17986.182 48631.318 496.75522 0.00681205
250 22.154451 5648.1758 4433.1558 307.76682 1215.02 502.13687 578.85369 665.27326 49.096119 -19.019967 1306179.2 -1306740.5 11771.328 48631.318 482.34141 0.0071619539
300 26.524393 5317.8584 4075.2077 282.91669 1242.6506 602.55113 637.40817 647.27074 44.769726 -123.22347 1306183.3 -1306749.5 3571.1867 48631.318 443.3952 0.0071733829
350 30.881443 4996.709 3935.7988 273.23838 1060.9102 455.75196 634.36552 638.77826 45.831053 -157.6304 1306198.1 -1306754.3 13525.264 48631.318 428.22739 0.0063722044
400 35.218285 4695.9297 3742.6585 259.82983 953.27122 457.49584 620.73047 591.94411 42.495713 -183.91838 1306186.7 -1306762.2 10901.217 48631.318 407.21326 0.005787501
450 39.545502 4417.8027 3513.6374 243.9303 904.16528 519.61263 580.76003 624.06933 45.631271 -286.60025 1306184.3 -1306763.6 2956.9012 48631.318 382.29486 0.0057536613
500 43.868895 4165.0012 3333.7203 231.43976 831.28089 465.5234 579.36085 580.60005 42.34515 -254.82269 1306183.9 -1306765.6 5818.5565 48631.318 362.71904 0.0059224891
550 48.242395 3934.5209 3211.9362 222.98504 722.58462 431.14864 581.46511 517.2025 39.188196 -265.47041 1306182.7 -1306763.6 8537.9404 48631.318 349.46863 0.0055762504
600 52.542171 3714.8655 3121.0494 216.67532 593.81611 425.12998 539.89496 490.30508 34.564566 -305.82069 1306175.2 -1306765.5 7402.7677 48631.318 339.57967 0.0057486673
650 56.830079 3516.2452 2930.7498 203.46399 585.49537 511.91461 512.48859 521.40636 37.766801 -391.65392 1306163.5 -1306770 381.72879 48631.318 318.87447 0.0054629243
700 61.119511 3342.7694 2864.1576 198.8409 478.6118 451.54683 498.82407 489.17207 35.23127 -375.78886 1306153.8 -1306774.2 3691.2716 48631.318 311.62801 0.0071278731
750 65.401576 3181.7673 2786.7104 193.46422 395.05691 409.83192 508.19542 454.56182 32.890716 -379.80692 1306149 -1306779.6 7428.3698 48631.318 303.20195 0.006233194
800 69.680899 3032.4158 2699.8707 187.43547 332.54509 453.40673 486.16575 441.1235 32.847786 -437.39338 1306144.4 -1306788 1701.7652 48631.318 293.75377 0.0056528223
850 73.96463 2898.4928 2563.6959 177.98169 334.7969 463.66637 486.19929 453.38803 34.062233 -455.86062 1306144.2 -1306790.9 -285.03665 48631.318 278.9376 0.0052777781
900 78.229548 2780.3555 2528.3241 175.52604 252.03136 396.92692 451.76463 435.59744 33.035257 -413.46176 1306142.9 -1306794.7 3836.4341 48631.318 275.08801 0.0070306435
950 82.482848 2679.3417 2456.8817 170.56624 222.45998 385.66656 434.6516 418.37977 32.156722 -387.2201 1306136.9 -1306798.1 5510.2309 48631.318 267.31515 0.0064042654
1000 86.722726 2593.4365 2367.4477 164.35738 225.98882 427.8524 453.27435 415.48809 31.097577 -436.62051 1306131.8 -1306796.9 1166.3909 48631.318 257.58464 0.0059160543
1050 90.888482 2524.7788 2305.0253 160.02377 219.75349 432.90807 438.86657 412.79356 30.892593 -414.29436 1306119.4 -1306800.8 1698.2687 48631.318 250.79245 0.0065593259
1100 95.024656 2471.8176 2311.0953 160.44518 160.72227 378.43572 453.3435 392.48525 29.012472 -409.64374 1306119.6 -1306802.5 4190.91 48631.318 251.45323 0.0059713432
1150 99.165724 2433.9279 2279.0766 158.22231 154.8513 395.30434 436.87933 414.39389 31.118973 -428.90902 1306110.2 -1306804.2 3274.8924 48631.318 247.96893 0.0069039065
1200 103.31062 2411.3777 2238.4638 155.40282 172.91381 453.61551 460.27693 408.59237 31.237062 -482.78549 1306110.2 -1306808.2 -523.10179 48631.318 243.55012 0.0068754631
1250 107.40149 2402.1932 2286.0576 158.70696 116.13565 416.44979 462.75875 391.75373 29.446705 -477.67214 1306102.2 -1306808.8 484.04837 48631.318 248.72579 0.011679749
1300 111.55448 2406.5029 2261.2729 156.98631 145.23005 408.68043 437.74725 400.4567 30.448106 -418.44274 1306096.8 -1306810.5 4490.4165 48631.318 245.99228 0.076574936
1350 115.71244 2459.1398 2317.5855 160.89575 141.55434 651.84862 447.40877 400.66793 29.060967 -461.45124 1305884.3 -1306810.3 693.59782 48631.318 250.14098 3.5622064
1400 119.88515 2479.5991 2285.6701 158.68006 193.929 582.54021 457.54475 430.29254 30.183876 -449.49979 1305955.6 -1306812.8 930.31169 48631.318 247.21826 2.5935077
1450 124.05689 2498.3537 2286.4924 158.73715 211.86128 434.79588 477.9598 402.79356 31.070492 -406.60813 1306086.4 -1306814.5 2933.4418 48631.318 248.74646 0.058608522
1500 128.29115 2546.66 2423.6257 168.25747 123.03432 392.07474 456.01536 385.97457 29.255586 -417.92459 1306089.9 -1306812.3 3333.3497 48631.318 263.694 0.011243575
1550 132.46344 2596.5481 2325.2227 161.42596 271.32542 462.52464 469.53612 461.20308 34.616094 -423.51186 1306080.4 -1306813.4 2155.0566 48631.318 252.98739 0.011191115
1600 136.64497 2646.7844 2387.8797 165.77585 258.90469 424.6071 484.95314 449.56642 33.318144 -395.67454 1306077 -1306814.8 1291.5449 48631.318 259.80403 0.012426122
1650 140.83234 2700.2847 2387.3033 165.73584 312.98138 431.00741 496.39504 455.52303 32.724808 -357.63815 1306070.3 -1306815.3 5007.2365 48631.318 259.70198 0.081729799
1700 145.02103 2777.9556 2386.7756 165.6992 391.18003 636.61544 523.12627 482.84847 35.186128 -391.10505 1305919.7 -1306815.2 2192.7076 48631.318 258.14043 2.7318649
1750 149.22218 2829.5998 2559.2796 177.67509 270.32019 684.587 479.93609 446.30457 31.888933 -385.84966 1305832.5 -1306819.1 1683.1471 48631.318 276.95798 2.6465587
1800 153.41978 2835.768 2465.6959 171.17815 370.07208 470.05934 508.38934 479.71489 37.826868 -369.0767 1306062.8 -1306819.6 3023.0762 48631.318 268.22249 0.097440318
1850 157.62632 2857.7601 2504.3893 173.86439 353.37083 436.06841 516.10132 487.71301 36.514956 -385.43181 1306078.9 -1306816.5 2950.5189 48631.318 272.47825 0.016816883
1900 161.8372 2867.791 2528.8957 175.56572 338.89527 446.38065 509.27013 485.03036 37.283587 -402.68445 1306076.6 -1306812.9 3161.5045 48631.318 275.1476 0.011615474
1950 166.10858 2861.34 2513.9103 174.52538 347.4297 470.9855 536.84666 467.9604 36.049051 -430.05716 1306079.3 -1306813.6 738.77866 48631.318 273.51233 0.020075246
2000 170.32286 2838.0367 2530.4481 175.6735 307.58858 423.18694 516.91384 454.72628 35.048394 -387.67176 1306074.6 -1306809.3 4321.7103 48631.318 275.24492 0.13775419
Loop time of 170.323 on 1 procs for 2000 steps with 5500 atoms
Performance: 0.507 ns/day, 47.312 hours/ns, 11.742 timesteps/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 | 105.66 | 105.66 | 105.66 | 0.0 | 62.04
Bond | 19.802 | 19.802 | 19.802 | 0.0 | 11.63
Kspace | 35.029 | 35.029 | 35.029 | 0.0 | 20.57
Neigh | 2.7502 | 2.7502 | 2.7502 | 0.0 | 1.61
Comm | 0.62654 | 0.62654 | 0.62654 | 0.0 | 0.37
Output | 0.006705 | 0.006705 | 0.006705 | 0.0 | 0.00
Modify | 6.3072 | 6.3072 | 6.3072 | 0.0 | 3.70
Other | | 0.1366 | | | 0.08
Nlocal: 5500 ave 5500 max 5500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 15407 ave 15407 max 15407 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.30509e+06 ave 1.30509e+06 max 1.30509e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1305088
Ave neighs/atom = 237.289
Ave special neighs/atom = 15.6364
Neighbor list builds = 44
Dangerous builds = 0
Total wall time: 0:02:50

259
examples/USER/drude/toluene/log.toluene.nh.11Aug17.linux.4 Normal file
View File

@ -0,0 +1,259 @@
LAMMPS (11 Aug 2017)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# 250 toluene system for drude polarizability example (Nose-Hoover)
units real
boundary p p p
atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style opls
improper_style opls
special_bonds lj/coul 0.0 0.0 0.5
pair_style lj/cut/thole/long 2.600 8.0 8.0
pair_modify mix geometric tail yes
kspace_style pppm 1.0e-4
read_data data.toluene extra/special/per/atom 1
orthogonal box = (-18.2908 -18.1636 -18.223) to (18.3357 18.1621 18.3287)
2 by 1 by 2 MPI processor grid
reading atoms ...
5500 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
8 = max dihedrals/atom
scanning impropers ...
2 = max impropers/atom
reading bonds ...
5500 bonds
reading angles ...
6000 angles
reading dihedrals ...
6000 dihedrals
reading impropers ...
1500 impropers
5 = max # of 1-2 neighbors
10 = max # of 1-3 neighbors
16 = max # of 1-4 neighbors
20 = max # of special neighbors
comm_modify vel yes
group gTOLUENE molecule 1:250
5500 atoms in group gTOLUENE
group gCORES type 1 2 3 4 5 6 7
3750 atoms in group gCORES
group gDRUDES type 8 9 10 11 12
1750 atoms in group gDRUDES
pair_coeff 1 1 0.069998 3.550000 1.620000 # CAT CAT
pair_coeff 1 2 0.069998 3.550000 1.620000 # CAT CAO
pair_coeff 1 3 0.069998 3.550000 1.620000 # CAT CAM
pair_coeff 1 4 0.069998 3.550000 1.620000 # CAT CAP
pair_coeff 1 5 0.067968 3.524911 1.620000 # CAT CTT
pair_coeff 1 6 0.045825 2.931041 0.000000 # CAT HAT
pair_coeff 1 7 0.045825 2.931041 0.000000 # CAT HT
pair_coeff 2 2 0.069998 3.550000 1.620000 # CAO CAO
pair_coeff 2 3 0.069998 3.550000 1.620000 # CAO CAM
pair_coeff 2 4 0.069998 3.550000 1.620000 # CAO CAP
pair_coeff 2 5 0.067968 3.524911 1.620000 # CAO CTT
pair_coeff 2 6 0.045825 2.931041 0.000000 # CAO HAT
pair_coeff 2 7 0.045825 2.931041 0.000000 # CAO HT
pair_coeff 3 3 0.069998 3.550000 1.620000 # CAM CAM
pair_coeff 3 4 0.069998 3.550000 1.620000 # CAM CAP
pair_coeff 3 5 0.067968 3.524911 1.620000 # CAM CTT
pair_coeff 3 6 0.045825 2.931041 0.000000 # CAM HAT
pair_coeff 3 7 0.045825 2.931041 0.000000 # CAM HT
pair_coeff 4 4 0.069998 3.550000 1.620000 # CAP CAP
pair_coeff 4 5 0.067968 3.524911 1.620000 # CAP CTT
pair_coeff 4 6 0.045825 2.931041 0.000000 # CAP HAT
pair_coeff 4 7 0.045825 2.931041 0.000000 # CAP HT
pair_coeff 5 5 0.065997 3.500000 1.620000 # CTT CTT
pair_coeff 5 6 0.044496 2.910326 0.000000 # CTT HAT
pair_coeff 5 7 0.044496 2.910326 0.000000 # CTT HT
pair_coeff 6 6 0.029999 2.420000 0.000000 # HAT HAT
pair_coeff 6 7 0.029999 2.420000 0.000000 # HAT HT
pair_coeff 7 7 0.029999 2.420000 0.000000 # HT HT
pair_coeff 1 8 0.000000 0.000000 1.620000 # CAT D_CAT
pair_coeff 1 9 0.000000 0.000000 1.620000 # CAT D_CAO
pair_coeff 1 10 0.000000 0.000000 1.620000 # CAT D_CAM
pair_coeff 1 11 0.000000 0.000000 1.620000 # CAT D_CAP
pair_coeff 1 12 0.000000 0.000000 1.620000 # CAT D_CTT
pair_coeff 2 8 0.000000 0.000000 1.620000 # CAO D_CAT
pair_coeff 2 9 0.000000 0.000000 1.620000 # CAO D_CAO
pair_coeff 2 10 0.000000 0.000000 1.620000 # CAO D_CAM
pair_coeff 2 11 0.000000 0.000000 1.620000 # CAO D_CAP
pair_coeff 2 12 0.000000 0.000000 1.620000 # CAO D_CTT
pair_coeff 3 8 0.000000 0.000000 1.620000 # CAM D_CAT
pair_coeff 3 9 0.000000 0.000000 1.620000 # CAM D_CAO
pair_coeff 3 10 0.000000 0.000000 1.620000 # CAM D_CAM
pair_coeff 3 11 0.000000 0.000000 1.620000 # CAM D_CAP
pair_coeff 3 12 0.000000 0.000000 1.620000 # CAM D_CTT
pair_coeff 4 8 0.000000 0.000000 1.620000 # CAP D_CAT
pair_coeff 4 9 0.000000 0.000000 1.620000 # CAP D_CAO
pair_coeff 4 10 0.000000 0.000000 1.620000 # CAP D_CAM
pair_coeff 4 11 0.000000 0.000000 1.620000 # CAP D_CAP
pair_coeff 4 12 0.000000 0.000000 1.620000 # CAP D_CTT
pair_coeff 5 8 0.000000 0.000000 1.620000 # CTT D_CAT
pair_coeff 5 9 0.000000 0.000000 1.620000 # CTT D_CAO
pair_coeff 5 10 0.000000 0.000000 1.620000 # CTT D_CAM
pair_coeff 5 11 0.000000 0.000000 1.620000 # CTT D_CAP
pair_coeff 5 12 0.000000 0.000000 1.620000 # CTT D_CTT
pair_coeff 8 8 0.000000 0.000000 1.620000 # D_CAT D_CAT
pair_coeff 8 9 0.000000 0.000000 1.620000 # D_CAT D_CAO
pair_coeff 8 10 0.000000 0.000000 1.620000 # D_CAT D_CAM
pair_coeff 8 11 0.000000 0.000000 1.620000 # D_CAT D_CAP
pair_coeff 8 12 0.000000 0.000000 1.620000 # D_CAT D_CTT
pair_coeff 9 9 0.000000 0.000000 1.620000 # D_CAO D_CAO
pair_coeff 9 10 0.000000 0.000000 1.620000 # D_CAO D_CAM
pair_coeff 9 11 0.000000 0.000000 1.620000 # D_CAO D_CAP
pair_coeff 9 12 0.000000 0.000000 1.620000 # D_CAO D_CTT
pair_coeff 10 10 0.000000 0.000000 1.620000 # D_CAM D_CAM
pair_coeff 10 11 0.000000 0.000000 1.620000 # D_CAM D_CAP
pair_coeff 10 12 0.000000 0.000000 1.620000 # D_CAM D_CTT
pair_coeff 11 11 0.000000 0.000000 1.620000 # D_CAP D_CAP
pair_coeff 11 12 0.000000 0.000000 1.620000 # D_CAP D_CTT
pair_coeff 12 12 0.000000 0.000000 1.620000 # D_CTT D_CTT
neighbor 2.0 bin
variable vTEMP equal 260.0
variable vTEMP_D equal 1.0
variable vPRESS equal 1.0
velocity gCORES create ${vTEMP} 12345
velocity gCORES create 260 12345
velocity gDRUDES create ${vTEMP_D} 12345
velocity gDRUDES create 1 12345
fix fDRUDE all drude C C C C C N N D D D D D
fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8
1250 = # of size 2 clusters
0 = # of size 3 clusters
250 = # of size 4 clusters
0 = # of frozen angles
compute cTEMP_CORE gCORES temp/com
compute cTEMP all temp/drude
fix fDIRECT all drude/transform/direct
fix fNVT1 gCORES nvt temp ${vTEMP} ${vTEMP} 100.0
fix fNVT1 gCORES nvt temp 260 ${vTEMP} 100.0
fix fNVT1 gCORES nvt temp 260 260 100.0
fix fNVT2 gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 20.0
fix fNVT2 gDRUDES nvt temp 1 ${vTEMP_D} 20.0
fix fNVT2 gDRUDES nvt temp 1 1 20.0
fix fINVERSE all drude/transform/inverse
fix fMOMENTUM all momentum 100 linear 1 1 1
thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
thermo 50
timestep 0.5
run 2000
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.382011
grid = 40 40 40
stencil order = 5
estimated absolute RMS force accuracy = 0.0325934
estimated relative force accuracy = 9.8154e-05
using double precision FFTs
3d grid and FFT values/proc = 34263 16000
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 19
New max number of 1-2 to 1-4 neighbors: 20 (+1)
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10
ghost atom cutoff = 10
binsize = 5, bins = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/thole/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 18 | 18 | 18 Mbytes
Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2]
0 0 14386.197 2910.7282 202.07402 11475.469 6565.4851 20.333365 1.0706727e-06 1.3894617e-07 4972.8631 1306116.6 -1306199.8 40273.68 48631.318 314.89553 3.1777821
50 1.1419601 6863.6417 4633.9267 321.70512 2229.715 735.2547 604.69459 648.35773 49.039129 824.06033 1306091.3 -1306722.9 17914.827 48631.318 504.18525 0.0086839775
100 2.3001912 6628.0719 4376.1868 303.81182 2251.8851 598.11248 651.43051 919.41359 74.216825 589.6504 1306135.1 -1306716 17450.721 48631.318 476.14276 0.0075129701
150 3.473469 6336.1884 4726.0692 328.10201 1610.1192 560.01225 621.30109 640.32474 45.531174 288.99129 1306173.9 -1306720 18303.624 48631.318 514.21215 0.006192153
200 4.6296241 5997.6192 4565.6288 316.96362 1431.9903 524.27651 591.79844 718.11014 56.374557 88.66084 1306183 -1306730.3 17986.183 48631.318 496.75522 0.0068120542
250 5.7982912 5648.1756 4433.1557 307.76682 1215.0199 502.13686 578.8537 665.27326 49.096119 -19.019961 1306179.2 -1306740.5 11771.328 48631.318 482.34141 0.0071619522
300 6.9468622 5317.8583 4075.2077 282.91669 1242.6505 602.55113 637.40818 647.27073 44.769725 -123.22347 1306183.3 -1306749.5 3571.1872 48631.318 443.3952 0.0071733908
350 8.0925181 4996.7094 3935.7988 273.23838 1060.9106 455.75195 634.3655 638.77824 45.831051 -157.63039 1306198.1 -1306754.3 13525.265 48631.318 428.22739 0.0063722017
400 9.2309761 4695.9294 3742.6584 259.82983 953.27093 457.49585 620.73048 591.94413 42.495714 -183.91838 1306186.7 -1306762.2 10901.217 48631.318 407.21326 0.0057875
450 10.363872 4417.8018 3513.6374 243.9303 904.1644 519.61261 580.76003 624.06933 45.631272 -286.60025 1306184.3 -1306763.6 2956.9021 48631.318 382.29485 0.0057536673
500 11.493601 4165.0005 3333.7203 231.43976 831.28022 465.52341 579.36085 580.60004 42.345149 -254.82269 1306183.9 -1306765.6 5818.5549 48631.318 362.71904 0.0059224858
550 12.636785 3934.5207 3211.9362 222.98504 722.58446 431.14864 581.46511 517.20249 39.188194 -265.4704 1306182.7 -1306763.6 8537.9415 48631.318 349.46863 0.0055762027
600 13.759642 3714.8658 3121.0493 216.67532 593.81649 425.12998 539.89497 490.30506 34.564567 -305.82067 1306175.2 -1306765.5 7402.7688 48631.318 339.57967 0.005748668
650 14.880794 3516.2453 2930.7499 203.464 585.49542 511.91457 512.48857 521.40634 37.766798 -391.65394 1306163.5 -1306770 381.72898 48631.318 318.87448 0.0054629381
700 15.99791 3342.7693 2864.1576 198.8409 478.61174 451.54685 498.82406 489.17206 35.231269 -375.78888 1306153.8 -1306774.2 3691.2706 48631.318 311.62801 0.0071278792
750 17.111346 3181.7665 2786.7104 193.46422 395.05608 409.83191 508.19537 454.56183 32.890719 -379.80694 1306149 -1306779.6 7428.3698 48631.318 303.20196 0.0062331873
800 18.219225 3032.4162 2699.8707 187.43547 332.54543 453.40674 486.16573 441.12346 32.847783 -437.39291 1306144.4 -1306788 1701.7675 48631.318 293.75377 0.0056528077
850 19.320825 2898.4936 2563.6961 177.9817 334.79757 463.66634 486.19928 453.38802 34.062236 -455.86081 1306144.2 -1306790.9 -285.04073 48631.318 278.93762 0.0052778244
900 20.41979 2780.3551 2528.3241 175.52604 252.03099 396.92693 451.7645 435.59756 33.035261 -413.46181 1306142.9 -1306794.7 3836.4347 48631.318 275.08801 0.0070307677
950 21.517533 2679.3418 2456.8821 170.56626 222.45967 385.66649 434.6516 418.37957 32.156706 -387.22039 1306136.9 -1306798.1 5510.2277 48631.318 267.31518 0.0064041284
1000 22.614275 2593.435 2367.4471 164.35734 225.98798 427.85237 453.27432 415.48822 31.097611 -436.61808 1306131.8 -1306796.9 1166.3709 48631.318 257.58457 0.0059160188
1050 23.688642 2524.7784 2305.0257 160.0238 219.75264 432.90797 438.8666 412.79338 30.892595 -414.29467 1306119.4 -1306800.8 1698.2602 48631.318 250.7925 0.0065595368
1100 24.750163 2471.818 2311.095 160.44516 160.72297 378.43554 453.3434 392.485 29.012487 -409.64322 1306119.6 -1306802.5 4190.9174 48631.318 251.4532 0.0059713928
1150 25.813605 2433.9311 2279.0768 158.22233 154.85433 395.30409 436.87935 414.39367 31.118959 -428.90913 1306110.2 -1306804.2 3274.9237 48631.318 247.96895 0.0069037916
1200 26.876952 2411.3772 2238.4639 155.40283 172.91329 453.61525 460.27658 408.59192 31.237007 -482.78468 1306110.2 -1306808.2 -523.10237 48631.318 243.55013 0.0068752641
1250 27.929701 2402.1937 2286.0559 158.70685 116.13778 416.44884 462.75935 391.75448 29.446777 -477.6718 1306102.2 -1306808.8 484.0561 48631.318 248.72561 0.011679662
1300 29.000999 2406.5014 2261.274 156.98639 145.22737 408.678 437.74824 400.45662 30.448139 -418.44472 1306096.8 -1306810.5 4490.4105 48631.318 245.9924 0.076575975
1350 30.07322 2459.141 2317.5852 160.89573 141.55579 651.85736 447.40791 400.66662 29.060882 -461.45016 1305884.3 -1306810.3 693.5247 48631.318 250.14112 3.5619231
1400 31.14859 2479.6103 2285.6714 158.68015 193.93893 582.54135 457.54445 430.29301 30.184026 -449.49877 1305955.6 -1306812.8 930.44669 48631.318 247.21806 2.5941109
1450 32.226914 2498.357 2286.4857 158.73668 211.87137 434.79636 477.95951 402.79572 31.070593 -406.60139 1306086.4 -1306814.5 2933.5045 48631.318 248.74572 0.058613153
1500 33.410717 2546.6608 2423.6247 168.25741 123.03609 392.07322 456.01243 385.97344 29.255562 -417.91413 1306089.9 -1306812.3 3333.391 48631.318 263.6939 0.011242005
1550 34.466176 2596.5534 2325.2208 161.42583 271.33259 462.52172 469.54241 461.20405 34.616224 -423.51068 1306080.4 -1306813.4 2155.1194 48631.318 252.98718 0.011190963
1600 35.524206 2646.7837 2387.8846 165.77619 258.8991 424.60563 484.95051 449.57767 33.318683 -395.68293 1306077 -1306814.8 1291.42 48631.318 259.80456 0.01242131
1650 36.582854 2700.2921 2387.3119 165.73643 312.98026 431.01369 496.39909 455.52591 32.725057 -357.65832 1306070.3 -1306815.3 5006.9348 48631.318 259.70291 0.081728845
1700 37.641527 2777.9572 2386.7777 165.69934 391.1795 636.55763 523.11512 482.8483 35.185863 -391.0955 1305919.8 -1306815.2 2192.6733 48631.318 258.1403 2.7324891
1750 38.722299 2829.6167 2559.2488 177.67295 270.36793 684.60746 479.95058 446.29664 31.887359 -385.83616 1305832.5 -1306819 1683.6061 48631.318 276.955 2.6459088
1800 39.800548 2835.7772 2465.7031 171.17865 370.07414 470.05306 508.38361 479.70121 37.826988 -369.0694 1306062.8 -1306819.6 3022.9801 48631.318 268.22328 0.097437593
1850 40.878327 2857.76 2504.4099 173.86582 353.35016 436.05857 516.10495 487.70907 36.514477 -385.43957 1306078.9 -1306816.5 2950.6415 48631.318 272.48049 0.016822774
1900 41.9583 2867.7843 2528.8424 175.56202 338.94193 446.38058 509.30719 485.04661 37.284135 -402.67104 1306076.5 -1306812.9 3161.5835 48631.318 275.1418 0.011620333
1950 43.058281 2861.3388 2513.8846 174.5236 347.45414 470.99292 536.81741 467.97736 36.047648 -430.00695 1306079.3 -1306813.6 739.25154 48631.318 273.50953 0.020089235
2000 44.142059 2838.068 2530.3189 175.66453 307.74914 423.19157 516.85371 454.76945 35.048253 -387.49234 1306074.6 -1306809.3 4324.0966 48631.318 275.23081 0.13784772
Loop time of 44.1421 on 4 procs for 2000 steps with 5500 atoms
Performance: 1.957 ns/day, 12.262 hours/ns, 45.308 timesteps/s
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 21.008 | 22.592 | 23.892 | 21.7 | 51.18
Bond | 4.8951 | 5.1338 | 5.2542 | 6.4 | 11.63
Kspace | 9.1158 | 10.514 | 12.296 | 35.3 | 23.82
Neigh | 0.63826 | 0.63849 | 0.63875 | 0.0 | 1.45
Comm | 0.78008 | 0.80146 | 0.84186 | 2.7 | 1.82
Output | 0.0036852 | 0.0040929 | 0.0052037 | 1.0 | 0.01
Modify | 4.3966 | 4.4074 | 4.4147 | 0.3 | 9.98
Other | | 0.05088 | | | 0.12
Nlocal: 1375 ave 1415 max 1340 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 8101 ave 8147 max 8056 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 326274 ave 342552 max 306832 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Total # of neighbors = 1305095
Ave neighs/atom = 237.29
Ave special neighs/atom = 15.6364
Neighbor list builds = 44
Dangerous builds = 0
Total wall time: 0:00:44

4
src/USER-DRUDE/README
View File

@ -16,6 +16,6 @@ There are example scripts for using this package in examples/USER/drude.
The person who created this package is Alain Dequidt at the
Chemistry Institute of Clermont-Ferrand, Clermont University, France
(alain.dequidt at univ-bpclermont.fr). Contact him directly if you
have questions. Co-authors: Julien Devémy, Agilio Padua.
(alain.dequidt at uca.fr). Contact him directly if you have questions.
Co-authors: Julien Devémy, Agilio Padua.

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

@ -355,7 +355,7 @@ void FixDrude::rebuild_special(){
}
if (atom->maxspecial < nspecmax) {
char str[1024];
sprintf(str, "Not enough space in special: special_bonds extra should be at least %d", nspecmax - nspecmax_old);
sprintf(str, "Not enough space in special: extra/special/per/atom should be at least %d", nspecmax - nspecmax_old);
error->all(FLERR, str);
}

89
tools/drude/polarizer.py
View File

@ -2,7 +2,7 @@
# polarizer.py - add Drude oscillators to LAMMPS data file.
# Agilio Padua <agilio.padua@univ-bpclermont.fr>
# Alain Dequidt <alain.dequidt@univ-bpclermont.fr>
# version 2017/02/03
# version 2017/02/08
import sys
import argparse
@ -38,9 +38,9 @@ identification of the atom types within the force field database:
This script will add new atom types, new bond types, new atoms and
new bonds to the data file.
It will also print some commands to be included in the LAMMPS input script,
It will also generate some commands to be included in the LAMMPS input script,
which are related to the topology and force field, namely fix drude,
pair_style and pair coeff_commands. For information on thermostating please
pair_style and pair_coeff commands. For information on thermostating please
read the documentation of the USER-DRUDE package.
This tool can also be used to revert a Drude-polarized data file to a
@ -549,6 +549,8 @@ class Data(object):
def lmpscript(self, drude, outfile, thole = 2.6, cutoff = 12.0):
"""print lines for input script, including pair_style thole"""
pairfile = "pair-drude.lmp"
dfound = False
for att in self.atomtypes:
if att['dflag'] == 'd':
@ -564,49 +566,54 @@ class Data(object):
print("pair_style hybrid/overlay ... coul/long/cs {0:.1f} "\
"thole {1:.3f} {0:.1f}\n".format(cutoff, thole))
print("# data file with Drude oscillators added")
print("read_data {0}\n".format(outfile))
print("# add interactions between atoms and Drude particles")
print("pair_coeff * {0:3d}* coul/long/cs".format(att['id']))
print("# pair interactions with Drude particles written to file")
print("# Thole damping recommended if more than 1 Drude per molecule")
print("include {0}\n".format(pairfile))
# Thole parameters for I,J pairs
print("# add Thole damping if more than 1 Drude per molecule")
ifound = False
for atti in self.atomtypes:
itype = atti['type'].split()[0]
for ddt in drude.types:
dtype = ddt['type'].split()[0]
if dtype == itype:
alphai = ddt['alpha']
tholei = ddt['thole']
ifound = True
break
jfound = False
for attj in self.atomtypes:
if attj['id'] < atti['id']:
continue
jtype = attj['type'].split()[0]
with open(pairfile, "w") as f:
f.write("# interactions involving Drude particles\n")
f.write("pair_coeff * {0:3d}* coul/long/cs\n".format(att['id']))
f.write("# Thole damping if more than 1 Drude per molecule\n")
# Thole parameters for I,J pairs
ifound = False
for atti in self.atomtypes:
itype = atti['type'].split()[0]
for ddt in drude.types:
dtype = ddt['type'].split()[0]
if dtype == jtype:
alphaj = ddt['alpha']
tholej = ddt['thole']
jfound = True
if dtype == itype:
alphai = ddt['alpha']
tholei = ddt['thole']
ifound = True
break
if ifound and jfound:
alphaij = (alphai * alphaj)**0.5
tholeij = (tholei + tholej) / 2.0
if tholeij == thole:
print("pair_coeff {0:4} {1:4} thole {2:7.3f}".format(
atti['id'], attj['id'], alphaij))
else:
print("pair_coeff {0:4} {1:4} thole {2:7.3f} "\
"{3:7.3f}".format(atti['id'],attj['id'],
alphaij, tholeij))
jfound = False
ifound = False
print("")
for attj in self.atomtypes:
if attj['id'] < atti['id']:
continue
jtype = attj['type'].split()[0]
for ddt in drude.types:
dtype = ddt['type'].split()[0]
if dtype == jtype:
alphaj = ddt['alpha']
tholej = ddt['thole']
jfound = True
break
if ifound and jfound:
alphaij = (alphai * alphaj)**0.5
tholeij = (tholei + tholej) / 2.0
if tholeij == thole:
f.write("pair_coeff {0:4} {1:4} thole "\
"{2:7.3f}\n".format(atti['id'], attj['id'],
alphaij))
else:
f.write("pair_coeff {0:4} {1:4} thole {2:7.3f} "\
"{3:7.3f}\n".format(atti['id'],attj['id'],
alphaij, tholeij))
jfound = False
ifound = False
print("# atom groups convenient for thermostats (see package "
"documentation), etc.")
@ -631,8 +638,8 @@ class Data(object):
print("")
print("# ATTENTION!")
print("# * special_bonds may need 'extra' keyword, LAMMPS will exit "
"with a message.")
print("# * read_data may need 'extra/special/per/atom' keyword, "
"LAMMPS will exit with a message.")
print("# * If using fix shake the group-ID must not include "
"Drude particles.")
print("# Use group ATOMS for example.")