Commit e4b14213 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
Browse files

delete old log files. new log files are approved by @athomps

parent adbc75ca

examples/gcmc/log.6Jul17.gcmc.co2.g++.1

deleted100644 → 0
+0 −193
Original line number Diff line number Diff line 
LAMMPS (22 Sep 2017)

OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)

  using 1 OpenMP thread(s) per MPI task

# GCMC for CO2 molecular fluid, rigid/small/nvt dynamics

# Rigid CO2 TraPPE model

# [Potoff and J.I. Siepmann, Vapor-liquid equilibria of

# mixtures containing alkanes, carbon dioxide and

# nitrogen AIChE J., 47,1676-1682 (2001)].



# variables available on command line



variable        mu index -8.1

variable	disp index 0.5

variable        temp index 338.0

variable        lbox index 10.0

variable        spacing index 5.0



# global model settings



units           real

atom_style      full

boundary        p p p

pair_style      lj/cut/coul/long  14

pair_modify     mix arithmetic tail yes

kspace_style    ewald 0.0001

bond_style      harmonic

angle_style     harmonic



# box, start molecules on simple cubic lattice



lattice 	sc ${spacing}

lattice 	sc 5.0

Lattice spacing in x,y,z = 5 5 5

region          box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box

region          box block 0 10.0 0 ${lbox} 0 ${lbox} units box

region          box block 0 10.0 0 10.0 0 ${lbox} units box

region          box block 0 10.0 0 10.0 0 10.0 units box

create_box      2 box                                       bond/types 1                                angle/types 1                               extra/bond/per/atom 2                       extra/angle/per/atom 1                      extra/special/per/atom 2

Created orthogonal box = (0 0 0) to (10 10 10)

  1 by 1 by 1 MPI processor grid

molecule        co2mol CO2.txt

Read molecule co2mol:

  3 atoms with 2 types

  2 bonds with 1 types

  1 angles with 1 types

  0 dihedrals with 0 types

  0 impropers with 0 types

create_atoms   	0 box mol co2mol 464563 units box

Created 24 atoms

  Time spent = 0.00136113 secs



# rigid CO2 TraPPE model



pair_coeff      1   1  0.053649   2.8

pair_coeff      2   2  0.156973   3.05

bond_coeff      1       0       1.16

angle_coeff     1       0       180



# masses



mass 1 12.0107

mass 2 15.9994



# MD settings



group           co2 type 1 2

24 atoms in group co2

neighbor        2.0 bin

neigh_modify    every 1 delay 10 check yes

velocity       	all create ${temp} 54654

velocity       	all create 338.0 54654

timestep        1.0



# rigid constraints with thermostat



fix             myrigidnvt all rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol

fix             myrigidnvt all rigid/nvt/small molecule temp 338.0 ${temp} 100 mol co2mol

fix             myrigidnvt all rigid/nvt/small molecule temp 338.0 338.0 100 mol co2mol

8 rigid bodies with 24 atoms

  1.16 = max distance from body owner to body atom

fix_modify	myrigidnvt dynamic/dof no



# gcmc



variable        tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)

fix             mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol                 co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt

fix             mygcmc all gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol                 co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt

fix             mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol                 co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt

fix             mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol                 co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt

fix             mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol                 co2mol tfac_insert 1.66666666666667 group co2 rigid myrigidnvt



# atom counts



variable 	carbon atom "type==1"

variable        oxygen atom "type==2"

group 		carbon dynamic all var carbon

dynamic group carbon defined

group 	        oxygen dynamic all var oxygen

dynamic group oxygen defined

variable        nC equal count(carbon)

variable        nO equal count(oxygen)



# output



variable	tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)

variable	iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)

variable	dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)

variable	racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)

compute_modify  thermo_temp dynamic/dof yes

thermo_style    custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO

thermo          1000



# run



run             20000

Ewald initialization ...

WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)

  G vector (1/distance) = 0.164636

  estimated absolute RMS force accuracy = 0.0332064

  estimated relative force accuracy = 0.0001

  KSpace vectors: actual max1d max3d = 16 2 62

                  kxmax kymax kzmax  = 2 2 2

WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:445)

0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc

0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc

WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:476)

Neighbor list info ...

  update every 1 steps, delay 10 steps, check yes

  max neighbors/atom: 2000, page size: 100000

  master list distance cutoff = 16

  ghost atom cutoff = 16

  binsize = 8, bins = 2 2 2

  1 neighbor lists, perpetual/occasional/extra = 1 0 0

  (1) pair lj/cut/coul/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) = 15.62 | 15.62 | 15.62 Mbytes

Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO 

       0    364.27579    4238.8631   -9.6809388    13.391989    0.5846359       24            0            0            0            0            8           16 

WARNING: Using kspace solver on system with no charge (../kspace.cpp:289)

    1000    420.43475    1722.4052   -9.6956122    15.456579    0.5846359       24   0.20879341   0.20713005            0            0            8           16 

    2000    302.29516   -547.83642   -22.017674     14.11699   0.73079488       30    0.1742478    0.1678018            0            0           10           20 

    3000     316.6934   -1080.2673   -8.2218902    10.069364   0.51155641       21   0.13544917   0.13720634            0            0            7           14 

    4000    246.81614   -679.83628    -14.57724    10.299968   0.65771539       27    0.1568939   0.15860229            0            0            9           18 

    5000    260.23291   -896.27949   -16.097524    10.859868   0.65771539       27   0.13138744   0.13547049            0            0            9           18 

    6000    291.64889   -1524.1007   -22.306243    13.619816   0.73079488       30   0.12615476   0.12717694            0            0           10           20 

    7000    235.90417   -565.40879   -27.600934    13.360525   0.87695385       36     0.119703   0.12145398            0            0           12           24 

    8000      483.381    2017.6258   -7.1315833    15.369247   0.51155641       21   0.10942279   0.11082908            0            0            7           14 

    9000    468.87446   -285.22545  -0.22330095   0.93175047  0.073079488        3   0.13029748   0.13349433            0            0            1            2 

   10000    245.34708   -254.65444   -16.192443    11.457551   0.73079488       30   0.15023549   0.15176828            0            0           10           20 

   11000    233.27704    523.81197    -24.29051    12.052812   0.80387436       33    0.1438083   0.14547187            0            0           11           22 

   12000    230.75966   -2161.9134   -23.812352    11.922746   0.80387436       33    0.1338274   0.13534617            0            0           11           22 

   13000    216.09982   -930.72014   -23.138263     11.16531   0.80387436       33   0.12480714   0.12612138            0            0           11           22 

   14000    343.12403   -327.36241   -16.995149    16.023672   0.73079488       30   0.12006081   0.12108416            0            0           10           20 

   15000    369.60805    581.40471   -11.495738    13.588021    0.5846359       24   0.11372814   0.11534691            0            0            8           16 

   16000    221.23125   -918.58249   -30.702491    12.529519   0.87695385       36   0.11489536   0.11560548            0            0           12           24 

   17000    301.82269   -450.56586   -14.373996    12.595466   0.65771539       27   0.11226626   0.11350321            0            0            9           18 

   18000    1065.1385    474.31881  -0.45476519    7.4082761   0.14615898        6   0.11419593   0.11580815            0            0            2            4 

   19000    217.29422   -1111.0114   -12.048289     7.988458    0.5846359       24   0.12564213    0.1261457            0            0            8           16 

   20000    353.35515    465.29269   -6.8428553    9.4795613   0.43847693       18   0.12529827   0.12590018            0            0            6           12 

Loop time of 14.604 on 1 procs for 20000 steps with 18 atoms



Performance: 118.323 ns/day, 0.203 hours/ns, 1369.484 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    | 1.8966     | 1.8966     | 1.8966     |   0.0 | 12.99

Bond    | 0.019538   | 0.019538   | 0.019538   |   0.0 |  0.13

Kspace  | 0.14784    | 0.14784    | 0.14784    |   0.0 |  1.01

Neigh   | 0.070002   | 0.070002   | 0.070002   |   0.0 |  0.48

Comm    | 0.15055    | 0.15055    | 0.15055    |   0.0 |  1.03

Output  | 0.0017672  | 0.0017672  | 0.0017672  |   0.0 |  0.01

Modify  | 12.287     | 12.287     | 12.287     |   0.0 | 84.13

Other   |            | 0.03089    |            |       |  0.21



Nlocal:    18 ave 18 max 18 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Nghost:    1335 ave 1335 max 1335 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Neighs:    2797 ave 2797 max 2797 min

Histogram: 1 0 0 0 0 0 0 0 0 0



Total # of neighbors = 2797

Ave neighs/atom = 155.389

Ave special neighs/atom = 2

Neighbor list builds = 20401

Dangerous builds = 0



Total wall time: 0:00:14

examples/gcmc/log.6Jul17.gcmc.co2.g++.4

deleted100644 → 0
+0 −193
Original line number Diff line number Diff line 
LAMMPS (22 Sep 2017)

OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)

  using 1 OpenMP thread(s) per MPI task

# GCMC for CO2 molecular fluid, rigid/small/nvt dynamics

# Rigid CO2 TraPPE model

# [Potoff and J.I. Siepmann, Vapor-liquid equilibria of

# mixtures containing alkanes, carbon dioxide and

# nitrogen AIChE J., 47,1676-1682 (2001)].



# variables available on command line



variable        mu index -8.1

variable	disp index 0.5

variable        temp index 338.0

variable        lbox index 10.0

variable        spacing index 5.0



# global model settings



units           real

atom_style      full

boundary        p p p

pair_style      lj/cut/coul/long  14

pair_modify     mix arithmetic tail yes

kspace_style    ewald 0.0001

bond_style      harmonic

angle_style     harmonic



# box, start molecules on simple cubic lattice



lattice 	sc ${spacing}

lattice 	sc 5.0

Lattice spacing in x,y,z = 5 5 5

region          box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box

region          box block 0 10.0 0 ${lbox} 0 ${lbox} units box

region          box block 0 10.0 0 10.0 0 ${lbox} units box

region          box block 0 10.0 0 10.0 0 10.0 units box

create_box      2 box                                       bond/types 1                                angle/types 1                               extra/bond/per/atom 2                       extra/angle/per/atom 1                      extra/special/per/atom 2

Created orthogonal box = (0 0 0) to (10 10 10)

  1 by 2 by 2 MPI processor grid

molecule        co2mol CO2.txt

Read molecule co2mol:

  3 atoms with 2 types

  2 bonds with 1 types

  1 angles with 1 types

  0 dihedrals with 0 types

  0 impropers with 0 types

create_atoms   	0 box mol co2mol 464563 units box

Created 24 atoms

  Time spent = 0.00223303 secs



# rigid CO2 TraPPE model



pair_coeff      1   1  0.053649   2.8

pair_coeff      2   2  0.156973   3.05

bond_coeff      1       0       1.16

angle_coeff     1       0       180



# masses



mass 1 12.0107

mass 2 15.9994



# MD settings



group           co2 type 1 2

24 atoms in group co2

neighbor        2.0 bin

neigh_modify    every 1 delay 10 check yes

velocity       	all create ${temp} 54654

velocity       	all create 338.0 54654

timestep        1.0



# rigid constraints with thermostat



fix             myrigidnvt all rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol

fix             myrigidnvt all rigid/nvt/small molecule temp 338.0 ${temp} 100 mol co2mol

fix             myrigidnvt all rigid/nvt/small molecule temp 338.0 338.0 100 mol co2mol

8 rigid bodies with 24 atoms

  1.16 = max distance from body owner to body atom

fix_modify	myrigidnvt dynamic/dof no



# gcmc



variable        tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)

fix             mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol                 co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt

fix             mygcmc all gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol                 co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt

fix             mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol                 co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt

fix             mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol                 co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt

fix             mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol                 co2mol tfac_insert 1.66666666666667 group co2 rigid myrigidnvt



# atom counts



variable 	carbon atom "type==1"

variable        oxygen atom "type==2"

group 		carbon dynamic all var carbon

dynamic group carbon defined

group 	        oxygen dynamic all var oxygen

dynamic group oxygen defined

variable        nC equal count(carbon)

variable        nO equal count(oxygen)



# output



variable	tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)

variable	iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)

variable	dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)

variable	racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)

compute_modify  thermo_temp dynamic/dof yes

thermo_style    custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO

thermo          1000



# run



run             20000

Ewald initialization ...

WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)

  G vector (1/distance) = 0.164636

  estimated absolute RMS force accuracy = 0.0332064

  estimated relative force accuracy = 0.0001

  KSpace vectors: actual max1d max3d = 16 2 62

                  kxmax kymax kzmax  = 2 2 2

WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:445)

0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc

0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc

WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:476)

Neighbor list info ...

  update every 1 steps, delay 10 steps, check yes

  max neighbors/atom: 2000, page size: 100000

  master list distance cutoff = 16

  ghost atom cutoff = 16

  binsize = 8, bins = 2 2 2

  1 neighbor lists, perpetual/occasional/extra = 1 0 0

  (1) pair lj/cut/coul/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) = 15.41 | 15.41 | 15.41 Mbytes

Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO 

       0    386.52184    23582.465   -3.2433417    14.209828    0.5846359       24            0            0            0            0            8           16 

WARNING: Using kspace solver on system with no charge (../kspace.cpp:289)

    1000    335.66829   -3.7743052   -4.6268612    7.3374649   0.36539744       15   0.20601899   0.20787963            0            0            5           10 

    2000    459.73529    238.91592  -0.42937831    5.4815343   0.21923846        9   0.30392058   0.30105616            0            0            3            6 

    3000    255.47773   -479.67802   -36.850434    15.738299   0.95003334       39   0.22220744    0.2197582            0            0           13           26 

    4000    182.70803   -1059.2265    -43.04484    12.163134    1.0231128       42   0.16781689   0.16716177            0            0           14           28 

    5000    234.00901   -1821.0459   -46.047939    15.578313    1.0231128       42   0.13498091   0.13704201            0            0           14           28 

    6000    163.42358   -774.64962   -49.686149    11.691232    1.0961923       45   0.11401677   0.11296973            0            0           15           30 

    7000    171.36765   -359.28792    -49.34022    12.259546    1.0961923       45  0.098302308  0.098552065            0            0           15           30 

    8000     215.2905   -905.73479   -38.206404    13.262629   0.95003334       39  0.086608098  0.086135456            0            0           13           26 

    9000    185.19905   -2320.8255   -52.964346    13.249037    1.0961923       45  0.077379246  0.077059206            0            0           15           30 

   10000     241.5783   -1410.8134    -51.37248    17.282377    1.0961923       45  0.069600048  0.069395413            0            0           15           30 

   11000    153.38332   -2647.9572   -53.967244    10.972957    1.0961923       45  0.063207938   0.06315287            0            0           15           30 

   12000    188.93059   -1639.9304   -52.218219    13.515989    1.0961923       45   0.05816163  0.058001715            0            0           15           30 

   13000    243.39974   -1127.2881    -44.54519    16.203468    1.0231128       42  0.053682268  0.053700858            0            0           14           28 

   14000    200.88474   -272.11992   -41.725507    13.373183    1.0231128       42  0.050212054  0.050071222            0            0           14           28 

   15000     204.6505   -1616.9057   -44.631997    13.623875    1.0231128       42  0.046944632  0.046920585            0            0           14           28 

   16000    169.22546    105.40991    -42.46103     11.26558    1.0231128       42  0.044460451  0.044287314            0            0           14           28 

   17000    163.55389   -783.34837   -36.841459    10.075477   0.95003334       39  0.042304052  0.042283048            0            0           13           26 

   18000    499.48334   -503.24838     -8.94456    15.881226   0.51155641       21   0.04035334  0.040870565            0            0            7           14 

   19000    658.81004    391.68747   -2.6979013     11.12813   0.29231795       12  0.055391781  0.056188676            0            0            4            8 

   20000    489.87356   -122.40743   -13.636951     18.00938    0.5846359       24  0.061378424  0.061821941            0            0            8           16 

Loop time of 17.1274 on 4 procs for 20000 steps with 24 atoms



Performance: 100.891 ns/day, 0.238 hours/ns, 1167.718 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    | 0.81646    | 1.1504     | 1.4937     |  23.0 |  6.72

Bond    | 0.011878   | 0.012255   | 0.013296   |   0.5 |  0.07

Kspace  | 0.23802    | 0.58086    | 0.91304    |  32.3 |  3.39

Neigh   | 0.04321    | 0.043291   | 0.043372   |   0.0 |  0.25

Comm    | 0.90855    | 0.90959    | 0.91112    |   0.1 |  5.31

Output  | 0.0011697  | 0.0012506  | 0.001482   |   0.4 |  0.01

Modify  | 14.362     | 14.365     | 14.367     |   0.1 | 83.87

Other   |            | 0.06436    |            |       |  0.38



Nlocal:    6 ave 8 max 4 min

Histogram: 1 0 1 0 0 0 0 1 0 1

Nghost:    1465.25 ave 1556 max 1376 min

Histogram: 1 0 1 0 0 0 0 1 0 1

Neighs:    1243.5 ave 1726 max 748 min

Histogram: 1 0 0 1 0 0 1 0 0 1



Total # of neighbors = 4974

Ave neighs/atom = 207.25

Ave special neighs/atom = 2

Neighbor list builds = 20375

Dangerous builds = 0



Total wall time: 0:00:17

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