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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11411 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2014-01-30 22:50:33 +00:00
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examples/dreiding/log.dreiding.1Feb14.linux.1 Normal file
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LAMMPS (1 Feb 2014)
units real
atom_style full
boundary p p p
dielectric 1
special_bonds lj/coul 0.0 0.0 1.0
pair_style hybrid/overlay hbond/dreiding/lj 2 6 6.5 90 lj/cut/coul/long 8.50000 11.5
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
improper_style none
kspace_style pppm 0.001
read_data data.dreiding
orthogonal box = (0 0 0) to (19.9969 19.1282 19.4697)
1 by 1 by 1 MPI processor grid
reading atoms ...
384 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
3 = max dihedrals/atom
reading bonds ...
320 bonds
reading angles ...
448 angles
reading dihedrals ...
192 dihedrals
4 = max # of 1-2 neighbors
3 = max # of 1-3 neighbors
5 = max # of special neighbors
pair_coeff 1 1 lj/cut/coul/long 0.015200000256300 2.846421344984478
pair_coeff 1 2 lj/cut/coul/long 0.001232882795416 2.846421344984478
pair_coeff 1 3 lj/cut/coul/long 0.038019995160237 3.159705878878677
pair_coeff 1 4 lj/cut/coul/long 0.038139744011598 2.939787518071103
pair_coeff 2 2 lj/cut/coul/long 9.99999974737875e-05 2.846421344984478
pair_coeff 2 3 lj/cut/coul/long 0.003083828758188 3.159705878878677
pair_coeff 2 4 lj/cut/coul/long 0.003093541672406 2.939787518071103
pair_coeff 3 3 lj/cut/coul/long 0.095100000500679 3.472990412772877
pair_coeff 3 4 lj/cut/coul/long 0.095399530150179 3.253072051965302
pair_coeff 4 4 lj/cut/coul/long 0.095700003206730 3.033153691157727
pair_coeff 4 4 hbond/dreiding/lj 2 i 0.4000E+01 2.750000000000000 4
pair_modify mix arithmetic
neighbor 2.0 multi
neigh_modify every 2 delay 4 check yes
variable input index in.ch3oh.box.dreiding
variable sname index ch3oh.box.dreiding
compute hb all pair hbond/dreiding/lj
variable C_hbond equal c_hb[1] #number hbonds
variable E_hbond equal c_hb[2] #hbond energy
thermo_style custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong v_E_hbond v_C_hbond press vol
thermo_modify line multi format float %14.6f
run 0
WARNING: No fixes defined, atoms won't move (../verlet.cpp:54)
PPPM initialization ...
WARNING: System is not charge neutral, net charge = -0.00064 (../pppm.cpp:271)
G vector (1/distance) = 0.142073
grid = 3 3 3
stencil order = 5
estimated absolute RMS force accuracy = 0.154715
estimated relative force accuracy = 0.00046592
using double precision FFTs
3d grid and FFT values/proc = 512 27
Memory usage per processor = 7.97163 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = 113.723601 KinEng = 0.000000 Temp = 0.000000
PotEng = 113.723601 E_bond = 0.535673 E_angle = 1.281880
E_dihed = 1.232497 E_impro = 0.000000 E_vdwl = -125.381324
E_coul = 597.219740 E_long = -361.164864 E_hbond = -69.322152
C_hbond = 235.000000 Press = -328.847347 Volume = 7447.236335
Loop time of 2.14577e-06 on 1 procs for 0 steps with 384 atoms
Pair time (%) = 0 (0)
Bond time (%) = 0 (0)
Kspce time (%) = 0 (0)
Neigh time (%) = 0 (0)
Comm time (%) = 0 (0)
Outpt time (%) = 0 (0)
Other time (%) = 2.14577e-06 (100)
FFT time (% of Kspce) = 0 (0)
FFT Gflps 3d (1d only) = 0 0
Nlocal: 384 ave 384 max 384 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4637 ave 4637 max 4637 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 101854 ave 101854 max 101854 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 203708 ave 203708 max 203708 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 203708
Ave neighs/atom = 530.49
Ave special neighs/atom = 4
Neighbor list builds = 0
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation

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LAMMPS (1 Feb 2014)
units real
atom_style full
boundary p p p
dielectric 1
special_bonds lj/coul 0.0 0.0 1.0
pair_style hybrid/overlay hbond/dreiding/lj 2 6 6.5 90 lj/cut/coul/long 8.50000 11.5
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
improper_style none
kspace_style pppm 0.001
read_data data.dreiding
orthogonal box = (0 0 0) to (19.9969 19.1282 19.4697)
2 by 1 by 2 MPI processor grid
reading atoms ...
384 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
3 = max dihedrals/atom
reading bonds ...
320 bonds
reading angles ...
448 angles
reading dihedrals ...
192 dihedrals
4 = max # of 1-2 neighbors
3 = max # of 1-3 neighbors
5 = max # of special neighbors
pair_coeff 1 1 lj/cut/coul/long 0.015200000256300 2.846421344984478
pair_coeff 1 2 lj/cut/coul/long 0.001232882795416 2.846421344984478
pair_coeff 1 3 lj/cut/coul/long 0.038019995160237 3.159705878878677
pair_coeff 1 4 lj/cut/coul/long 0.038139744011598 2.939787518071103
pair_coeff 2 2 lj/cut/coul/long 9.99999974737875e-05 2.846421344984478
pair_coeff 2 3 lj/cut/coul/long 0.003083828758188 3.159705878878677
pair_coeff 2 4 lj/cut/coul/long 0.003093541672406 2.939787518071103
pair_coeff 3 3 lj/cut/coul/long 0.095100000500679 3.472990412772877
pair_coeff 3 4 lj/cut/coul/long 0.095399530150179 3.253072051965302
pair_coeff 4 4 lj/cut/coul/long 0.095700003206730 3.033153691157727
pair_coeff 4 4 hbond/dreiding/lj 2 i 0.4000E+01 2.750000000000000 4
pair_modify mix arithmetic
neighbor 2.0 multi
neigh_modify every 2 delay 4 check yes
variable input index in.ch3oh.box.dreiding
variable sname index ch3oh.box.dreiding
compute hb all pair hbond/dreiding/lj
variable C_hbond equal c_hb[1] #number hbonds
variable E_hbond equal c_hb[2] #hbond energy
thermo_style custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong v_E_hbond v_C_hbond press vol
thermo_modify line multi format float %14.6f
run 0
WARNING: No fixes defined, atoms won't move (../verlet.cpp:54)
PPPM initialization ...
WARNING: System is not charge neutral, net charge = -0.00064 (../pppm.cpp:271)
G vector (1/distance) = 0.142073
grid = 3 3 3
stencil order = 5
estimated absolute RMS force accuracy = 0.154715
estimated relative force accuracy = 0.00046592
using double precision FFTs
3d grid and FFT values/proc = 392 12
Memory usage per processor = 6.52754 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = 113.723601 KinEng = 0.000000 Temp = 0.000000
PotEng = 113.723601 E_bond = 0.535673 E_angle = 1.281880
E_dihed = 1.232497 E_impro = 0.000000 E_vdwl = -125.381324
E_coul = 597.219740 E_long = -361.164864 E_hbond = -69.322152
C_hbond = 235.000000 Press = -328.847347 Volume = 7447.236335
Loop time of 5.24521e-06 on 4 procs for 0 steps with 384 atoms
Pair time (%) = 0 (0)
Bond time (%) = 0 (0)
Kspce time (%) = 0 (0)
Neigh time (%) = 0 (0)
Comm time (%) = 0 (0)
Outpt time (%) = 0 (0)
Other time (%) = 5.24521e-06 (100)
FFT time (% of Kspce) = 0 (0)
FFT Gflps 3d (1d only) = 0 0
Nlocal: 96 ave 104 max 87 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 3063.25 ave 3108 max 3024 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 25463.5 ave 28799 max 22471 min
Histogram: 1 0 0 1 0 1 0 0 0 1
FullNghs: 50927 ave 55516 max 46073 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 203708
Ave neighs/atom = 530.49
Ave special neighs/atom = 4
Neighbor list builds = 0
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation