diff --git a/examples/gcmc/in.gcmc.co2 b/examples/gcmc/in.gcmc.co2
index bb6916fc4847df10707f2712c10955d921878601..b5e11d212dafb99f71acfc0a6870163dc9705723 100644
--- a/examples/gcmc/in.gcmc.co2
+++ b/examples/gcmc/in.gcmc.co2
@@ -59,7 +59,9 @@ timestep 1.0
# rigid constraints with thermostat
fix myrigidnvt co2 rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol
-fix_modify myrigidnvt dynamic/dof no
+
+# dynamically update fix rigid/nvt/small temperature ndof
+fix_modify myrigidnvt dynamic/dof yes
# gcmc
@@ -82,7 +84,10 @@ 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)
+
+# dynamically update default temperature ndof
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
diff --git a/examples/gcmc/in.gcmc.h2o b/examples/gcmc/in.gcmc.h2o
index 2c03b1ab78cc9dad8626ef76241e2dae1ab37955..f689711c2147a621e3937948df7d7bb494135587 100644
--- a/examples/gcmc/in.gcmc.h2o
+++ b/examples/gcmc/in.gcmc.h2o
@@ -30,8 +30,6 @@ create_box 2 box &
extra/angle/per/atom 1 &
extra/special/per/atom 2
-# we can load multiple molecule templates, but don't have to use them all
-molecule co2mol CO2.txt
molecule h2omol H2O.txt
create_atoms 0 box mol h2omol 464563 units box
@@ -58,18 +56,24 @@ timestep 1.0
minimize 0.0 0.0 100 1000
reset_timestep 0
+
# rigid constraints with thermostat
-fix mynvt all nvt temp ${temp} ${temp} 100
-fix wshake all shake 0.0001 50 0 b 1 a 1 mol h2omol
-# gcmc
+fix mynvt h2o nvt temp ${temp} ${temp} 100
+fix wshake h2o shake 0.0001 50 0 b 1 a 1 mol h2omol
+# important to make temperature dofs dynamic
+compute_modify thermo_temp dynamic/dof yes
+compute_modify mynvt_temp dynamic/dof yes
run 1000
+reset_timestep 0
+
+# 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 &
+fix mygcmc h2o gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol &
h2omol tfac_insert ${tfac} group h2o shake wshake
# atom counts
@@ -87,7 +91,6 @@ 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_nO v_nH
thermo 1000
diff --git a/examples/gcmc/log.23Oct17.gcmc.co2.g++.4 b/examples/gcmc/log.23Oct17.gcmc.co2.g++.4
deleted file mode 100644
index b344c7b0685eb0e19deb26e363e9cc43cd292f24..0000000000000000000000000000000000000000
--- a/examples/gcmc/log.23Oct17.gcmc.co2.g++.4
+++ /dev/null
@@ -1,192 +0,0 @@
-LAMMPS (23 Oct 2017)
- 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 = 0.00261331 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:472)
-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 -1059.2262 -43.044833 12.163134 1.0231128 42 0.16781689 0.16716177 0 0 14 28
- 5000 234.00907 -1821.0444 -46.04795 15.578317 1.0231128 42 0.13498091 0.13704201 0 0 14 28
- 6000 163.42759 -774.67294 -49.686261 11.691518 1.0961923 45 0.11401677 0.11296973 0 0 15 30
- 7000 171.64616 -355.23516 -49.323434 12.27947 1.0961923 45 0.098302308 0.098552065 0 0 15 30
- 8000 251.29791 -905.47863 -37.841209 15.480807 0.95003334 39 0.086856972 0.08638658 0 0 13 26
- 9000 143.69498 -849.95393 -49.073188 10.279858 1.0961923 45 0.078261061 0.077955243 0 0 15 30
- 10000 239.35727 -1158.1879 -43.562047 15.934355 1.0231128 42 0.070789792 0.070807529 0 0 14 28
- 11000 169.51213 -1574.7885 -51.125228 12.126803 1.0961923 45 0.065008734 0.06498871 0 0 15 30
- 12000 181.39739 160.11631 -46.850937 12.977068 1.0961923 45 0.059648717 0.059514803 0 0 15 30
- 13000 164.14601 -1107.7629 -50.726722 11.742914 1.0961923 45 0.055207333 0.055097701 0 0 15 30
- 14000 287.26285 418.51463 -41.664766 19.123497 1.0231128 42 0.051346789 0.051222285 0 0 14 28
- 15000 256.94593 -532.36615 -41.651618 17.105257 1.0231128 42 0.047870301 0.047861685 0 0 14 28
- 16000 166.92132 151.15933 -39.957018 11.11219 1.0231128 42 0.045205599 0.045042211 0 0 14 28
- 17000 163.22452 -1299.8119 -42.677558 10.866089 1.0231128 42 0.043122086 0.042993687 0 0 14 28
- 18000 158.01154 475.77329 -48.803162 11.304057 1.0961923 45 0.041016683 0.040647229 0 0 15 30
- 19000 138.49297 -1585.1508 -47.517099 9.9077098 1.0961923 45 0.038929287 0.038436764 0 0 15 30
- 20000 173.84439 -1362.6301 -53.002743 12.436731 1.0961923 45 0.036973919 0.036523816 0 0 15 30
-Loop time of 32.4481 on 4 procs for 20000 steps with 45 atoms
-
-Performance: 53.254 ns/day, 0.451 hours/ns, 616.369 timesteps/s
-98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 1.1687 | 1.6702 | 2.1864 | 30.8 | 5.15
-Bond | 0.018828 | 0.020035 | 0.020975 | 0.6 | 0.06
-Kspace | 0.57506 | 1.0931 | 1.5898 | 37.7 | 3.37
-Neigh | 0.068863 | 0.069524 | 0.070128 | 0.2 | 0.21
-Comm | 2.0735 | 2.0865 | 2.0979 | 0.7 | 6.43
-Output | 0.0025017 | 0.0025966 | 0.0027781 | 0.2 | 0.01
-Modify | 27.335 | 27.344 | 27.363 | 0.2 | 84.27
-Other | | 0.1621 | | | 0.50
-
-Nlocal: 11.25 ave 14 max 8 min
-Histogram: 1 0 0 0 0 1 1 0 0 1
-Nghost: 2639.75 ave 2656 max 2617 min
-Histogram: 1 0 0 0 0 0 2 0 0 1
-Neighs: 4320 ave 5824 max 2201 min
-Histogram: 1 0 0 0 0 0 1 1 0 1
-
-Total # of neighbors = 17280
-Ave neighs/atom = 384
-Ave special neighs/atom = 2
-Neighbor list builds = 20394
-Dangerous builds = 0
-
-Total wall time: 0:00:32
diff --git a/examples/gcmc/log.23Oct17.gcmc.h2o.g++.4 b/examples/gcmc/log.23Oct17.gcmc.h2o.g++.4
deleted file mode 100644
index 4eeab969ddc8c578baf028394c39064f2b57aace..0000000000000000000000000000000000000000
--- a/examples/gcmc/log.23Oct17.gcmc.h2o.g++.4
+++ /dev/null
@@ -1,293 +0,0 @@
-LAMMPS (23 Oct 2017)
- using 1 OpenMP thread(s) per MPI task
-# fix gcmc example with fix shake
-
-# 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
-
-# we can load multiple molecule templates, but don't have to use them all
-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
-molecule h2omol H2O.txt
-Read molecule h2omol:
- 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 h2omol 464563 units box
-Created 24 atoms
- Time spent = 0.00174451 secs
-
-# rigid SPC/E water model
-
-pair_coeff 1 1 0.15535 3.166
-pair_coeff * 2 0.0000 0.0000
-
-bond_coeff 1 1000 1.0
-angle_coeff 1 100 109.47
-
-# masses
-
-mass 1 15.9994
-mass 2 1.0
-
-# MD settings
-
-group h2o type 1 2
-24 atoms in group h2o
-neighbor 2.0 bin
-neigh_modify every 1 delay 1 check yes
-velocity all create ${temp} 54654
-velocity all create 338.0 54654
-timestep 1.0
-
-minimize 0.0 0.0 100 1000
-WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168)
-Ewald initialization ...
-WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
- G vector (1/distance) = 0.170448
- 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
-Neighbor list info ...
- update every 1 steps, delay 0 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) = 11.85 | 11.85 | 11.85 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 338 -4.9610706 9.2628112e-06 18.211756 730.90791
- 100 338 -15.742442 0.14954269 7.579918 -637.49568
-Loop time of 0.0566185 on 4 procs for 100 steps with 24 atoms
-
-98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-Minimization stats:
- Stopping criterion = max iterations
- Energy initial, next-to-last, final =
- -4.96106135393 -15.5388622715 -15.592899346
- Force two-norm initial, final = 15.474 18.1478
- Force max component initial, final = 5.80042 7.56514
- Final line search alpha, max atom move = 0.00151131 0.0114333
- Iterations, force evaluations = 100 328
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.0085177 | 0.016083 | 0.026787 | 5.3 | 28.41
-Bond | 0.00022459 | 0.00031394 | 0.00037575 | 0.0 | 0.55
-Kspace | 0.0049062 | 0.014122 | 0.02044 | 5.0 | 24.94
-Neigh | 0 | 0 | 0 | 0.0 | 0.00
-Comm | 0.018515 | 0.02086 | 0.023246 | 1.2 | 36.84
-Output | 2.4796e-05 | 2.6047e-05 | 2.9802e-05 | 0.0 | 0.05
-Modify | 0 | 0 | 0 | 0.0 | 0.00
-Other | | 0.005213 | | | 9.21
-
-Nlocal: 6 ave 8 max 3 min
-Histogram: 1 0 0 0 1 0 0 0 0 2
-Nghost: 1722 ave 1725 max 1720 min
-Histogram: 2 0 0 0 0 0 1 0 0 1
-Neighs: 1256.75 ave 2101 max 667 min
-Histogram: 1 0 1 0 1 0 0 0 0 1
-
-Total # of neighbors = 5027
-Ave neighs/atom = 209.458
-Ave special neighs/atom = 2
-Neighbor list builds = 0
-Dangerous builds = 0
-reset_timestep 0
-# rigid constraints with thermostat
-
-fix mynvt all nvt temp ${temp} ${temp} 100
-fix mynvt all nvt temp 338.0 ${temp} 100
-fix mynvt all nvt temp 338.0 338.0 100
-fix wshake all shake 0.0001 50 0 b 1 a 1 mol h2omol
- 0 = # of size 2 clusters
- 0 = # of size 3 clusters
- 0 = # of size 4 clusters
- 8 = # of frozen angles
-# gcmc
-
-
-
-run 1000
-Ewald initialization ...
-WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
- G vector (1/distance) = 0.170448
- 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
-Per MPI rank memory allocation (min/avg/max) = 11.6 | 11.6 | 11.6 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 518.26667 -15.742442 0 7.4303753 -613.0781
- 1000 369.81793 -54.202686 0 -37.667331 294.98823
-Loop time of 0.154891 on 4 procs for 1000 steps with 24 atoms
-
-Performance: 557.810 ns/day, 0.043 hours/ns, 6456.135 timesteps/s
-98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.0154 | 0.028993 | 0.040525 | 5.5 | 18.72
-Bond | 0.00016999 | 0.0001902 | 0.00023293 | 0.0 | 0.12
-Kspace | 0.019093 | 0.028112 | 0.038976 | 4.3 | 18.15
-Neigh | 0.0020263 | 0.0022184 | 0.002408 | 0.4 | 1.43
-Comm | 0.04947 | 0.053627 | 0.058009 | 1.4 | 34.62
-Output | 2.5749e-05 | 2.7537e-05 | 3.2187e-05 | 0.0 | 0.02
-Modify | 0.035275 | 0.036815 | 0.038425 | 0.7 | 23.77
-Other | | 0.004909 | | | 3.17
-
-Nlocal: 6 ave 8 max 3 min
-Histogram: 1 0 0 0 0 0 1 0 1 1
-Nghost: 1331.5 ave 1369 max 1290 min
-Histogram: 1 0 0 0 0 2 0 0 0 1
-Neighs: 1259.75 ave 1642 max 428 min
-Histogram: 1 0 0 0 0 0 0 1 0 2
-
-Total # of neighbors = 5039
-Ave neighs/atom = 209.958
-Ave special neighs/atom = 2
-Neighbor list builds = 27
-Dangerous builds = 0
-
-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 h2omol tfac_insert ${tfac} group h2o shake wshake
-fix mygcmc all gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
-fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
-fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert ${tfac} group h2o shake wshake
-fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert 1.66666666666667 group h2o shake wshake
-
-# atom counts
-
-variable oxygen atom "type==1"
-variable hydrogen atom "type==2"
-group oxygen dynamic all var oxygen
-dynamic group oxygen defined
-group hydrogen dynamic all var hydrogen
-dynamic group hydrogen defined
-variable nO equal count(oxygen)
-variable nH equal count(hydrogen)
-
-# 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_nO v_nH
-thermo 1000
-
-# run
-
-run 20000
-Ewald initialization ...
-WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
- G vector (1/distance) = 0.170448
- 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:472)
-Per MPI rank memory allocation (min/avg/max) = 11.6 | 11.6 | 11.6 Mbytes
-Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH
- 1000 369.81793 295.32434 -54.202686 16.535355 0.23910963 24 0 0 0 0 8 16
- 2000 84.544466 -2810.9047 -344.81664 14.364627 0.86677242 87 0.052198354 0.0099581757 0 0 29 58
- 3000 75.188527 -3688.256 -425.02228 14.567977 0.98632724 99 0.030546787 0.0049111089 0 0 33 66
- 4000 75.019396 -5669.3063 -427.69454 14.535207 0.98632724 99 0.019972039 0.0033375609 0 0 33 66
- 5000 90.415371 -2141.7596 -434.65925 17.518218 0.98632724 99 0.014909796 0.002514964 0 0 33 66
- 6000 78.212628 -943.75125 -428.80584 15.153904 0.98632724 99 0.01181521 0.0020316119 0 0 33 66
- 7000 71.754139 -2028.5122 -435.2139 13.902555 0.98632724 99 0.0099466198 0.0016755471 0 0 33 66
- 8000 84.446231 -1969.1657 -428.27313 16.361681 0.98632724 99 0.0084791272 0.0014442102 0 0 33 66
- 9000 70.952348 -2476.9812 -446.33824 14.170197 1.0162159 102 0.0077150892 0.0012556189 0 0 34 68
- 10000 71.418543 -1875.7083 -443.7214 14.263302 1.0162159 102 0.0068355714 0.0011197957 0 0 34 68
- 11000 86.094994 -4508.7581 -444.82687 17.194399 1.0162159 102 0.0061494515 0.0010082475 0 0 34 68
- 12000 81.906091 -1547.8105 -442.36719 16.357815 1.0162159 102 0.0055834729 0.00091775114 0 0 34 68
- 13000 57.221548 -4607.6222 -448.30939 11.42796 1.0162159 102 0.0051230355 0.00084046326 0 0 34 68
- 14000 61.288344 -2518.1779 -445.70636 12.240157 1.0162159 102 0.0047276997 0.00077602396 0 0 34 68
- 15000 85.787669 -2407.7111 -443.3834 17.133022 1.0162159 102 0.0043983485 0.00071920715 0 0 34 68
- 16000 74.845939 -3288.3403 -445.8247 14.947802 1.0162159 102 0.0042321884 0.00080654918 0 0 34 68
- 17000 73.835431 -1926.9566 -445.67476 14.745989 1.0162159 102 0.0039751059 0.00075470749 0 0 34 68
- 18000 72.634985 -3997.552 -447.2351 14.506243 1.0162159 102 0.0037395847 0.00071063946 0 0 34 68
- 19000 96.776472 -714.44132 -453.65552 19.904587 1.0461046 105 0.0036487876 0.00066993446 0 0 35 70
- 20000 75.470786 183.16972 -464.04688 15.522521 1.0461046 105 0.0034630763 0.00063350614 0 0 35 70
- 21000 65.658309 -773.41266 -466.27068 13.504331 1.0461046 105 0.003289113 0.00060198052 0 0 35 70
-Loop time of 84.4085 on 4 procs for 20000 steps with 105 atoms
-
-Performance: 20.472 ns/day, 1.172 hours/ns, 236.943 timesteps/s
-98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 6.3571 | 9.7574 | 13.984 | 90.7 | 11.56
-Bond | 0.026374 | 0.031321 | 0.035482 | 2.1 | 0.04
-Kspace | 0.57402 | 4.7894 | 8.1754 | 129.0 | 5.67
-Neigh | 0.34952 | 0.34987 | 0.35021 | 0.1 | 0.41
-Comm | 2.4028 | 2.4228 | 2.4372 | 0.9 | 2.87
-Output | 0.0012269 | 0.0012826 | 0.0014355 | 0.2 | 0.00
-Modify | 66.819 | 66.828 | 66.837 | 0.1 | 79.17
-Other | | 0.2281 | | | 0.27
-
-Nlocal: 26.25 ave 31 max 22 min
-Histogram: 1 0 1 0 0 0 1 0 0 1
-Nghost: 6049.25 ave 6133 max 5962 min
-Histogram: 1 0 0 0 1 0 1 0 0 1
-Neighs: 23613 ave 35083 max 14025 min
-Histogram: 1 0 0 1 1 0 0 0 0 1
-
-Total # of neighbors = 94452
-Ave neighs/atom = 899.543
-Ave special neighs/atom = 2
-Neighbor list builds = 20428
-Dangerous builds = 0
-
-Total wall time: 0:01:24
diff --git a/examples/gcmc/log.23Oct17.gcmc.co2.g++.1 b/examples/gcmc/log.30Mar18.gcmc.co2.g++.1
similarity index 52%
rename from examples/gcmc/log.23Oct17.gcmc.co2.g++.1
rename to examples/gcmc/log.30Mar18.gcmc.co2.g++.1
index e7b7c6afda0f28e4bb4b7c7dd5aaa5b86635d39d..46afe5ea2ae15af56f9fed995edd9462182f235e 100644
--- a/examples/gcmc/log.23Oct17.gcmc.co2.g++.1
+++ b/examples/gcmc/log.30Mar18.gcmc.co2.g++.1
@@ -1,4 +1,4 @@
-LAMMPS (23 Oct 2017)
+LAMMPS (30 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# GCMC for CO2 molecular fluid, rigid/small/nvt dynamics
# Rigid CO2 TraPPE model
@@ -39,14 +39,14 @@ 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
+ 3 atoms with max type 2
+ 2 bonds with max type 1
+ 1 angles with max type 1
+ 0 dihedrals with max type 0
+ 0 impropers with max type 0
create_atoms 0 box mol co2mol 464563 units box
Created 24 atoms
- Time spent = 0.00196958 secs
+ Time spent = 0.00241756 secs
# rigid CO2 TraPPE model
@@ -72,29 +72,31 @@ 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
+fix myrigidnvt co2 rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol
+fix myrigidnvt co2 rigid/nvt/small molecule temp 338.0 ${temp} 100 mol co2mol
+fix myrigidnvt co2 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
+
+# dynamically update fix rigid/nvt/small temperature ndof
+fix_modify myrigidnvt dynamic/dof yes
# 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
+fix mygcmc co2 gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
+fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
+fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
+fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
+fix mygcmc co2 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
+group carbon dynamic co2 var carbon
dynamic group carbon defined
-group oxygen dynamic all var oxygen
+group oxygen dynamic co2 var oxygen
dynamic group oxygen defined
variable nC equal count(carbon)
variable nO equal count(oxygen)
@@ -105,7 +107,10 @@ 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)
+
+# dynamically update default temperature ndof
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
@@ -113,13 +118,13 @@ thermo 1000
run 20000
Ewald initialization ...
-WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+ 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)
+WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:485)
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:472)
@@ -138,55 +143,54 @@ Neighbor list info ...
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 -9.6956123 15.456579 0.5846359 24 0.20879341 0.20713005 0 0 8 16
- 2000 302.29516 -547.83641 -22.017674 14.11699 0.73079488 30 0.1742478 0.1678018 0 0 10 20
- 3000 316.6934 -1080.2672 -8.2218891 10.069364 0.51155641 21 0.13544917 0.13720634 0 0 7 14
- 4000 246.81618 -679.83642 -14.577244 10.29997 0.65771539 27 0.1568939 0.15860229 0 0 9 18
- 5000 260.22849 -896.29914 -16.097593 10.859684 0.65771539 27 0.13138744 0.13547049 0 0 9 18
- 6000 291.70796 -1521.99 -22.303136 13.622574 0.73079488 30 0.12615476 0.12717694 0 0 10 20
- 7000 236.02638 -599.92186 -27.580831 13.367447 0.87695385 36 0.119703 0.12145398 0 0 12 24
- 8000 321.45341 688.10577 -10.09204 11.817696 0.5846359 24 0.10917411 0.11032646 0 0 8 16
- 9000 502.85382 -302.31056 -0.22330142 0.99927447 0.073079488 3 0.1254105 0.12905828 0 0 1 2
- 10000 249.98239 -510.0091 -32.815145 15.399767 0.95003334 39 0.1274504 0.12875623 0 0 13 26
- 11000 247.59424 -1129.0274 -25.320205 12.792544 0.80387436 33 0.11739076 0.11916784 0 0 11 22
- 12000 0 -20.39554 -0.14872889 -0 0 0 0.1254933 0.12920375 0 0 0 0
- 13000 1272.2738 -474.79484 -0.29450485 8.8489483 0.14615898 6 0.13767133 0.14112496 0 0 2 4
- 14000 516.54246 -36.296516 -5.0012009 11.291243 0.36539744 15 0.15632744 0.15955377 0 0 5 10
- 15000 307.09233 1951.9301 -14.820362 12.815375 0.65771539 27 0.15393544 0.15716192 0 0 9 18
- 16000 198.31989 -559.48443 -30.459487 11.231925 0.87695385 36 0.1482565 0.15025652 0 0 12 24
- 17000 246.99311 657.85683 -18.579206 11.53442 0.73079488 30 0.14143958 0.14375423 0 0 10 20
- 18000 467.13468 167.03738 -1.0945268 5.569759 0.21923846 9 0.13847359 0.14098533 0 0 3 6
- 19000 359.54027 -1413.5407 -12.156233 13.217895 0.5846359 24 0.15169146 0.15294205 0 0 8 16
- 20000 227.79597 -1204.5652 -23.24144 10.637925 0.73079488 30 0.14917199 0.15022946 0 0 10 20
-Loop time of 20.6928 on 1 procs for 20000 steps with 30 atoms
-
-Performance: 83.507 ns/day, 0.287 hours/ns, 966.519 timesteps/s
-99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
+ 1000 330.05964 -376.0111 -13.936335 13.773831 0.65771539 27 0.21142067 0.21453147 0 0 9 18
+ 2000 293.79769 -321.3209 -19.049256 13.720163 0.73079488 30 0.25170944 0.25426294 0 0 10 20
+ 3000 348.9085 259.04079 -0.23347965 2.4267366 0.14615898 6 0.22016906 0.23200597 0 0 2 4
+ 4000 360.54577 -329.12072 -16.584234 15.046059 0.65771539 27 0.19173099 0.19785362 0 0 9 18
+ 5000 275.58628 -58.283006 -12.520856 11.500585 0.65771539 27 0.16490585 0.17329884 0 0 9 18
+ 6000 338.59574 364.93514 -19.866569 17.494353 0.80387436 33 0.17971759 0.18331589 0 0 11 22
+ 7000 286.11586 -1252.5069 -19.588667 13.361427 0.73079488 30 0.15729895 0.16220459 0 0 10 20
+ 8000 454.86786 -642.89382 -20.818357 21.242037 0.73079488 30 0.15500235 0.15802382 0 0 10 20
+ 9000 326.36695 -364.71382 -31.376162 18.48392 0.87695385 36 0.14203985 0.14510714 0 0 12 24
+ 10000 348.46961 -387.75245 -21.068466 18.00451 0.80387436 33 0.14000907 0.14343389 0 0 11 22
+ 11000 409.74257 -15.843895 -20.648252 21.170323 0.80387436 33 0.14689306 0.15117074 0 0 11 22
+ 12000 523.93502 1003.0729 -6.0563102 14.055757 0.43847693 18 0.15337575 0.1580166 0 0 6 12
+ 13000 278.14441 -717.1097 -2.3488496 4.6982087 0.29231795 12 0.15952356 0.16422306 0 0 4 8
+ 14000 367.89375 1239.0841 -11.203323 13.524997 0.5846359 24 0.17002439 0.17460294 0 0 8 16
+ 15000 197.05319 -471.14343 -9.3890758 6.2653668 0.51155641 21 0.17702612 0.18155802 0 0 7 14
+ 16000 138.17147 -935.93437 -2.3846783 2.3338898 0.29231795 12 0.17884346 0.18268758 0 0 4 8
+ 17000 245.61833 -166.1694 -5.0970057 5.3690384 0.36539744 15 0.18909252 0.19317817 0 0 5 10
+ 18000 232.0142 -175.732 -14.320198 9.6822635 0.65771539 27 0.18977089 0.19280537 0 0 9 18
+ 19000 362.01189 864.87258 -6.4515321 9.7117982 0.43847693 18 0.19207244 0.19488984 0 0 6 12
+ 20000 441.19548 186.19779 -18.147268 20.603546 0.73079488 30 0.19713351 0.199073 0 0 10 20
+Loop time of 16.4949 on 1 procs for 20000 steps with 30 atoms
+
+Performance: 104.760 ns/day, 0.229 hours/ns, 1212.498 timesteps/s
+99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 2.5462 | 2.5462 | 2.5462 | 0.0 | 12.30
-Bond | 0.029783 | 0.029783 | 0.029783 | 0.0 | 0.14
-Kspace | 0.26167 | 0.26167 | 0.26167 | 0.0 | 1.26
-Neigh | 0.10705 | 0.10705 | 0.10705 | 0.0 | 0.52
-Comm | 0.23409 | 0.23409 | 0.23409 | 0.0 | 1.13
-Output | 0.0013416 | 0.0013416 | 0.0013416 | 0.0 | 0.01
-Modify | 17.458 | 17.458 | 17.458 | 0.0 | 84.37
-Other | | 0.05433 | | | 0.26
+Pair | 1.8955 | 1.8955 | 1.8955 | 0.0 | 11.49
+Bond | 0.026564 | 0.026564 | 0.026564 | 0.0 | 0.16
+Kspace | 0.21215 | 0.21215 | 0.21215 | 0.0 | 1.29
+Neigh | 0.088336 | 0.088336 | 0.088336 | 0.0 | 0.54
+Comm | 0.19828 | 0.19828 | 0.19828 | 0.0 | 1.20
+Output | 0.001025 | 0.001025 | 0.001025 | 0.0 | 0.01
+Modify | 14.024 | 14.024 | 14.024 | 0.0 | 85.02
+Other | | 0.0491 | | | 0.30
Nlocal: 30 ave 30 max 30 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 2310 ave 2310 max 2310 min
+Nghost: 2094 ave 2094 max 2094 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 7736 ave 7736 max 7736 min
+Neighs: 7664 ave 7664 max 7664 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Total # of neighbors = 7736
-Ave neighs/atom = 257.867
+Total # of neighbors = 7664
+Ave neighs/atom = 255.467
Ave special neighs/atom = 2
-Neighbor list builds = 20349
+Neighbor list builds = 20076
Dangerous builds = 0
-Total wall time: 0:00:20
+Total wall time: 0:00:16
diff --git a/examples/gcmc/log.30Mar18.gcmc.co2.g++.4 b/examples/gcmc/log.30Mar18.gcmc.co2.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..a824945cbfc79b18c8d023c8d9d766ae3abd439a
--- /dev/null
+++ b/examples/gcmc/log.30Mar18.gcmc.co2.g++.4
@@ -0,0 +1,131 @@
+LAMMPS (30 Mar 2018)
+ 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 max type 2
+ 2 bonds with max type 1
+ 1 angles with max type 1
+ 0 dihedrals with max type 0
+ 0 impropers with max type 0
+create_atoms 0 box mol co2mol 464563 units box
+Created 24 atoms
+ Time spent = 0.00257635 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 co2 rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol
+fix myrigidnvt co2 rigid/nvt/small molecule temp 338.0 ${temp} 100 mol co2mol
+fix myrigidnvt co2 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
+
+# dynamically update fix rigid/nvt/small temperature ndof
+fix_modify myrigidnvt dynamic/dof yes
+
+# gcmc
+
+variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
+fix mygcmc co2 gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
+fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
+fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
+fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
+fix mygcmc co2 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 co2 var carbon
+dynamic group carbon defined
+group oxygen dynamic co2 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)
+
+# dynamically update default temperature ndof
+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 ...
+ 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:485)
+0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc
+0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
+ERROR: fix gcmc does currently not support full_energy option with molecules on more than 1 MPI process. (../fix_gcmc.cpp:721)
+Last command: run 20000
diff --git a/examples/gcmc/log.23Oct17.gcmc.h2o.g++.1 b/examples/gcmc/log.30Mar18.gcmc.h2o.g++.1
similarity index 54%
rename from examples/gcmc/log.23Oct17.gcmc.h2o.g++.1
rename to examples/gcmc/log.30Mar18.gcmc.h2o.g++.1
index bc7c3af4541e58dea45b6d917d2645a2fb64683c..2f11cb116e0df82c40d7fa8797bf3c559df1265e 100644
--- a/examples/gcmc/log.23Oct17.gcmc.h2o.g++.1
+++ b/examples/gcmc/log.30Mar18.gcmc.h2o.g++.1
@@ -1,4 +1,4 @@
-LAMMPS (23 Oct 2017)
+LAMMPS (30 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# fix gcmc example with fix shake
@@ -34,24 +34,16 @@ create_box 2 box bond/types 1
Created orthogonal box = (0 0 0) to (10 10 10)
1 by 1 by 1 MPI processor grid
-# we can load multiple molecule templates, but don't have to use them all
-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
molecule h2omol H2O.txt
Read molecule h2omol:
- 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
+ 3 atoms with max type 2
+ 2 bonds with max type 1
+ 1 angles with max type 1
+ 0 dihedrals with max type 0
+ 0 impropers with max type 0
create_atoms 0 box mol h2omol 464563 units box
Created 24 atoms
- Time spent = 0.00201297 secs
+ Time spent = 0.00204968 secs
# rigid SPC/E water model
@@ -79,7 +71,7 @@ timestep 1.0
minimize 0.0 0.0 100 1000
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168)
Ewald initialization ...
-WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+ using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.170448
estimated absolute RMS force accuracy = 0.0332064
estimated relative force accuracy = 0.0001
@@ -101,9 +93,9 @@ Per MPI rank memory allocation (min/avg/max) = 11.88 | 11.88 | 11.88 Mbytes
Step Temp E_pair E_mol TotEng Press
0 338 -4.1890564 9.2628112e-06 18.98377 739.06991
100 338 -30.182886 0.85607237 -6.1539961 -2535.3207
-Loop time of 0.0507543 on 1 procs for 100 steps with 24 atoms
+Loop time of 0.0512006 on 1 procs for 100 steps with 24 atoms
-99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max iterations
@@ -117,14 +109,14 @@ Minimization stats:
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.042597 | 0.042597 | 0.042597 | 0.0 | 83.93
-Bond | 0.00047708 | 0.00047708 | 0.00047708 | 0.0 | 0.94
-Kspace | 0.0031135 | 0.0031135 | 0.0031135 | 0.0 | 6.13
+Pair | 0.04303 | 0.04303 | 0.04303 | 0.0 | 84.04
+Bond | 0.00047088 | 0.00047088 | 0.00047088 | 0.0 | 0.92
+Kspace | 0.0029728 | 0.0029728 | 0.0029728 | 0.0 | 5.81
Neigh | 0.00045919 | 0.00045919 | 0.00045919 | 0.0 | 0.90
-Comm | 0.0032997 | 0.0032997 | 0.0032997 | 0.0 | 6.50
-Output | 1.359e-05 | 1.359e-05 | 1.359e-05 | 0.0 | 0.03
+Comm | 0.003406 | 0.003406 | 0.003406 | 0.0 | 6.65
+Output | 2.265e-05 | 2.265e-05 | 2.265e-05 | 0.0 | 0.04
Modify | 0 | 0 | 0 | 0.0 | 0.00
-Other | | 0.0007946 | | | 1.57
+Other | | 0.0008392 | | | 1.64
Nlocal: 24 ave 24 max 24 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -139,23 +131,26 @@ Ave special neighs/atom = 2
Neighbor list builds = 2
Dangerous builds = 0
reset_timestep 0
+
# rigid constraints with thermostat
-fix mynvt all nvt temp ${temp} ${temp} 100
-fix mynvt all nvt temp 338.0 ${temp} 100
-fix mynvt all nvt temp 338.0 338.0 100
-fix wshake all shake 0.0001 50 0 b 1 a 1 mol h2omol
+fix mynvt h2o nvt temp ${temp} ${temp} 100
+fix mynvt h2o nvt temp 338.0 ${temp} 100
+fix mynvt h2o nvt temp 338.0 338.0 100
+fix wshake h2o shake 0.0001 50 0 b 1 a 1 mol h2omol
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
8 = # of frozen angles
-# gcmc
+# important to make temperature dofs dynamic
+compute_modify thermo_temp dynamic/dof yes
+compute_modify mynvt_temp dynamic/dof yes
run 1000
Ewald initialization ...
-WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+ using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.170448
estimated absolute RMS force accuracy = 0.0332064
estimated relative force accuracy = 0.0001
@@ -164,23 +159,23 @@ WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
Per MPI rank memory allocation (min/avg/max) = 11.63 | 11.63 | 11.63 Mbytes
Step Temp E_pair E_mol TotEng Press
0 518.26667 -30.182886 0 -7.0100684 993.1985
- 1000 326.9865 -62.258445 0 -47.638175 -5.3440813
-Loop time of 0.141449 on 1 procs for 1000 steps with 24 atoms
+ 1000 326.9865 -62.258443 0 -47.638173 -5.3439918
+Loop time of 0.139436 on 1 procs for 1000 steps with 24 atoms
-Performance: 610.819 ns/day, 0.039 hours/ns, 7069.663 timesteps/s
-99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
+Performance: 619.641 ns/day, 0.039 hours/ns, 7171.773 timesteps/s
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.10788 | 0.10788 | 0.10788 | 0.0 | 76.27
-Bond | 0.00018954 | 0.00018954 | 0.00018954 | 0.0 | 0.13
-Kspace | 0.011867 | 0.011867 | 0.011867 | 0.0 | 8.39
-Neigh | 0.0045254 | 0.0045254 | 0.0045254 | 0.0 | 3.20
-Comm | 0.011277 | 0.011277 | 0.011277 | 0.0 | 7.97
-Output | 1.5497e-05 | 1.5497e-05 | 1.5497e-05 | 0.0 | 0.01
-Modify | 0.00383 | 0.00383 | 0.00383 | 0.0 | 2.71
-Other | | 0.001868 | | | 1.32
+Pair | 0.10588 | 0.10588 | 0.10588 | 0.0 | 75.94
+Bond | 0.00015759 | 0.00015759 | 0.00015759 | 0.0 | 0.11
+Kspace | 0.011144 | 0.011144 | 0.011144 | 0.0 | 7.99
+Neigh | 0.00459 | 0.00459 | 0.00459 | 0.0 | 3.29
+Comm | 0.011396 | 0.011396 | 0.011396 | 0.0 | 8.17
+Output | 1.7166e-05 | 1.7166e-05 | 1.7166e-05 | 0.0 | 0.01
+Modify | 0.0043328 | 0.0043328 | 0.0043328 | 0.0 | 3.11
+Other | | 0.001914 | | | 1.37
Nlocal: 24 ave 24 max 24 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -194,13 +189,16 @@ Ave neighs/atom = 213
Ave special neighs/atom = 2
Neighbor list builds = 25
Dangerous builds = 0
+reset_timestep 0
+
+# 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 h2omol tfac_insert ${tfac} group h2o shake wshake
-fix mygcmc all gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
-fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
-fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert ${tfac} group h2o shake wshake
-fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert 1.66666666666667 group h2o shake wshake
+fix mygcmc h2o gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
+fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
+fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
+fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert ${tfac} group h2o shake wshake
+fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert 1.66666666666667 group h2o shake wshake
# atom counts
@@ -219,7 +217,6 @@ 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_nO v_nH
thermo 1000
@@ -227,67 +224,67 @@ thermo 1000
run 20000
Ewald initialization ...
-WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+ using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.170448
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)
+WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:485)
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:472)
Per MPI rank memory allocation (min/avg/max) = 11.63 | 11.63 | 11.63 Mbytes
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH
- 1000 326.9865 -4.3509713 -62.258445 14.62027 0.23910963 24 0 0 0 0 8 16
- 2000 116.99793 -5344.1527 -286.61595 17.088682 0.74721761 75 0.048183096 0.013941446 0 0 25 50
- 3000 106.86746 -3920.4926 -361.60598 18.794545 0.89666113 90 0.035637919 0.012768883 0 0 30 60
- 4000 75.002668 540.46846 -414.8511 14.531966 0.98632724 99 0.025963651 0.0093451705 0 0 33 66
- 5000 79.924788 -2131.1173 -437.21216 15.962121 1.0162159 102 0.019879728 0.0070418993 0 0 34 68
- 6000 95.552773 -3647.0233 -438.24276 19.083253 1.0162159 102 0.015753613 0.0056885133 0 0 34 68
- 7000 79.501736 -2071.5369 -440.77351 15.877631 1.0162159 102 0.01326216 0.0046915318 0 0 34 68
- 8000 62.567091 -3102.9616 -442.21884 12.495541 1.0162159 102 0.011305503 0.0040437885 0 0 34 68
- 9000 68.324047 -3812.7866 -440.46835 13.645287 1.0162159 102 0.0099549538 0.0035157329 0 0 34 68
- 10000 83.857631 -2158.2659 -444.8183 16.747566 1.0162159 102 0.0088200922 0.0031354281 0 0 34 68
- 11000 68.350984 -2084.0789 -440.14081 13.650667 1.0162159 102 0.0081331455 0.0030247424 0 0 34 68
- 12000 76.867315 -1585.6723 -443.36199 15.3515 1.0162159 102 0.0073845932 0.0027532534 0 0 34 68
- 13000 59.74266 -2211.0211 -446.07791 11.931462 1.0162159 102 0.0067756276 0.0025213898 0 0 34 68
- 14000 81.154979 -907.0176 -441.53368 16.207808 1.0162159 102 0.0062527642 0.0023280719 0 0 34 68
- 15000 66.814346 -2804.5134 -455.80704 13.7421 1.0461046 105 0.0059590528 0.0021576214 0 0 35 70
- 16000 71.42983 -3930.4004 -458.43218 14.691394 1.0461046 105 0.0055547473 0.0020163729 0 0 35 70
- 17000 89.624855 -3569.8136 -455.18164 18.433672 1.0461046 105 0.0052173265 0.0018867687 0 0 35 70
- 18000 63.519962 -1882.8157 -456.58939 13.064525 1.0461046 105 0.0049082049 0.0017765986 0 0 35 70
- 19000 71.872698 -2243.5046 -454.93359 14.782481 1.0461046 105 0.0046439115 0.0016748361 0 0 35 70
- 20000 73.660765 -2285.3173 -476.35473 15.589381 1.0759934 108 0.0045124933 0.0015837653 0 0 36 72
- 21000 95.675868 987.92089 -475.46736 20.248603 1.0759934 108 0.004285814 0.0015049513 0 0 36 72
-Loop time of 220.662 on 1 procs for 20000 steps with 108 atoms
-
-Performance: 7.831 ns/day, 3.065 hours/ns, 90.637 timesteps/s
-99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+ 0 326.9865 -4.3508819 -62.258443 14.62027 0.23910963 24 0 0 0 0 8 16
+ 1000 354.423 -3760.1354 -235.34169 51.766914 0.74721761 75 0.046175467 0.011949811 0 0 25 50
+ 2000 335.19661 -3018.659 -270.44089 52.955344 0.80699501 81 0.026473882 0.0068755525 0 0 27 54
+ 3000 333.47175 2657.2052 -336.48359 64.611037 0.98632724 99 0.022634978 0.0060076096 0 0 33 66
+ 4000 321.48504 2055.4786 -345.06113 62.288579 0.98632724 99 0.016897769 0.0045269353 0 0 33 66
+ 5000 333.45735 1918.5375 -368.5463 66.596193 1.0162159 102 0.013784412 0.0036569014 0 0 34 68
+ 6000 301.90666 -698.74074 -371.32122 60.295069 1.0162159 102 0.01160439 0.0030159847 0 0 34 68
+ 7000 336.42505 1537.9483 -378.51731 69.194524 1.0461046 105 0.010174953 0.0025995783 0 0 35 70
+ 8000 338.95331 -1032.1084 -390.7067 69.714524 1.0461046 105 0.0089594585 0.002260114 0 0 35 70
+ 9000 311.44605 -1494.7788 -383.9272 64.056945 1.0461046 105 0.007938083 0.0020156323 0 0 35 70
+ 10000 330.70877 2082.4597 -366.57249 68.018822 1.0461046 105 0.0071412985 0.0018148454 0 0 35 70
+ 11000 286.34718 2238.3752 -370.91119 60.601806 1.0759934 108 0.0066641451 0.0016519521 0 0 36 72
+ 12000 371.02522 3048.7157 -398.51333 78.522854 1.0759934 108 0.0061145907 0.0015128339 0 0 36 72
+ 13000 392.87611 4486.1134 -387.07077 83.147323 1.0759934 108 0.0056427384 0.0013968431 0 0 36 72
+ 14000 332.80747 3586.2698 -406.12151 70.434545 1.0759934 108 0.0052496417 0.0012945729 0 0 36 72
+ 15000 325.61844 4198.3864 -387.5733 68.913077 1.0759934 108 0.0048934679 0.0012098238 0 0 36 72
+ 16000 254.10285 1560.976 -409.98615 55.292559 1.1058821 111 0.0047204383 0.0011320612 0 0 37 74
+ 17000 367.46414 2750.8283 -412.22037 79.959878 1.1058821 111 0.0044407568 0.0010659592 0 0 37 74
+ 18000 407.74215 2308.5027 -408.73046 88.724338 1.1058821 111 0.0042016342 0.0010049017 0 0 37 74
+ 19000 341.53799 5777.9814 -407.00637 74.31837 1.1058821 111 0.0039877848 0.00095025921 0 0 37 74
+ 20000 395.75303 3159.4677 -403.82798 86.115516 1.1058821 111 0.0037874635 0.00090297077 0 0 37 74
+Loop time of 231.351 on 1 procs for 20000 steps with 111 atoms
+
+Performance: 7.469 ns/day, 3.213 hours/ns, 86.449 timesteps/s
+99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 37.459 | 37.459 | 37.459 | 0.0 | 16.98
-Bond | 0.087067 | 0.087067 | 0.087067 | 0.0 | 0.04
-Kspace | 0.90234 | 0.90234 | 0.90234 | 0.0 | 0.41
-Neigh | 1.2299 | 1.2299 | 1.2299 | 0.0 | 0.56
-Comm | 0.95437 | 0.95437 | 0.95437 | 0.0 | 0.43
-Output | 0.0010636 | 0.0010636 | 0.0010636 | 0.0 | 0.00
-Modify | 179.85 | 179.85 | 179.85 | 0.0 | 81.51
-Other | | 0.1754 | | | 0.08
-
-Nlocal: 108 ave 108 max 108 min
+Pair | 39.09 | 39.09 | 39.09 | 0.0 | 16.90
+Bond | 0.092728 | 0.092728 | 0.092728 | 0.0 | 0.04
+Kspace | 0.87751 | 0.87751 | 0.87751 | 0.0 | 0.38
+Neigh | 3.9658 | 3.9658 | 3.9658 | 0.0 | 1.71
+Comm | 1.0608 | 1.0608 | 1.0608 | 0.0 | 0.46
+Output | 0.00096035 | 0.00096035 | 0.00096035 | 0.0 | 0.00
+Modify | 186.07 | 186.07 | 186.07 | 0.0 | 80.43
+Other | | 0.1892 | | | 0.08
+
+Nlocal: 111 ave 111 max 111 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 7850 ave 7850 max 7850 min
+Nghost: 8070 ave 8070 max 8070 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 99828 ave 99828 max 99828 min
+Neighs: 105469 ave 105469 max 105469 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Total # of neighbors = 99828
-Ave neighs/atom = 924.333
+Total # of neighbors = 105469
+Ave neighs/atom = 950.171
Ave special neighs/atom = 2
-Neighbor list builds = 20439
+Neighbor list builds = 20910
Dangerous builds = 0
-Total wall time: 0:03:40
+Total wall time: 0:03:51
diff --git a/examples/gcmc/log.30Mar18.gcmc.h2o.g++.4 b/examples/gcmc/log.30Mar18.gcmc.h2o.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..c5caf57113594ce82deedc9f24df1e5b94b2fcd6
--- /dev/null
+++ b/examples/gcmc/log.30Mar18.gcmc.h2o.g++.4
@@ -0,0 +1,237 @@
+LAMMPS (30 Mar 2018)
+ using 1 OpenMP thread(s) per MPI task
+# fix gcmc example with fix shake
+
+# 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 h2omol H2O.txt
+Read molecule h2omol:
+ 3 atoms with max type 2
+ 2 bonds with max type 1
+ 1 angles with max type 1
+ 0 dihedrals with max type 0
+ 0 impropers with max type 0
+create_atoms 0 box mol h2omol 464563 units box
+Created 24 atoms
+ Time spent = 0.00285625 secs
+
+# rigid SPC/E water model
+
+pair_coeff 1 1 0.15535 3.166
+pair_coeff * 2 0.0000 0.0000
+
+bond_coeff 1 1000 1.0
+angle_coeff 1 100 109.47
+
+# masses
+
+mass 1 15.9994
+mass 2 1.0
+
+# MD settings
+
+group h2o type 1 2
+24 atoms in group h2o
+neighbor 2.0 bin
+neigh_modify every 1 delay 1 check yes
+velocity all create ${temp} 54654
+velocity all create 338.0 54654
+timestep 1.0
+
+minimize 0.0 0.0 100 1000
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168)
+Ewald initialization ...
+ using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+ G vector (1/distance) = 0.170448
+ 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
+Neighbor list info ...
+ update every 1 steps, delay 0 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) = 11.85 | 11.85 | 11.85 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 338 -4.9610706 9.2628112e-06 18.211756 730.90791
+ 100 338 -15.742442 0.14954269 7.579918 -637.49568
+Loop time of 0.0695416 on 4 procs for 100 steps with 24 atoms
+
+94.4% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+Minimization stats:
+ Stopping criterion = max iterations
+ Energy initial, next-to-last, final =
+ -4.96106135393 -15.5388622715 -15.592899346
+ Force two-norm initial, final = 15.474 18.1478
+ Force max component initial, final = 5.80042 7.56514
+ Final line search alpha, max atom move = 0.00151131 0.0114333
+ Iterations, force evaluations = 100 328
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0093951 | 0.017625 | 0.028943 | 5.3 | 25.34
+Bond | 0.00035357 | 0.00042325 | 0.00055075 | 0.0 | 0.61
+Kspace | 0.00664 | 0.019695 | 0.029924 | 6.1 | 28.32
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.022505 | 0.02509 | 0.027851 | 1.3 | 36.08
+Output | 3.3855e-05 | 3.5942e-05 | 4.1485e-05 | 0.0 | 0.05
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 0.006672 | | | 9.59
+
+Nlocal: 6 ave 8 max 3 min
+Histogram: 1 0 0 0 1 0 0 0 0 2
+Nghost: 1722 ave 1725 max 1720 min
+Histogram: 2 0 0 0 0 0 1 0 0 1
+Neighs: 1256.75 ave 2101 max 667 min
+Histogram: 1 0 1 0 1 0 0 0 0 1
+
+Total # of neighbors = 5027
+Ave neighs/atom = 209.458
+Ave special neighs/atom = 2
+Neighbor list builds = 0
+Dangerous builds = 0
+reset_timestep 0
+
+# rigid constraints with thermostat
+
+fix mynvt h2o nvt temp ${temp} ${temp} 100
+fix mynvt h2o nvt temp 338.0 ${temp} 100
+fix mynvt h2o nvt temp 338.0 338.0 100
+fix wshake h2o shake 0.0001 50 0 b 1 a 1 mol h2omol
+ 0 = # of size 2 clusters
+ 0 = # of size 3 clusters
+ 0 = # of size 4 clusters
+ 8 = # of frozen angles
+
+# important to make temperature dofs dynamic
+
+compute_modify thermo_temp dynamic/dof yes
+compute_modify mynvt_temp dynamic/dof yes
+
+run 1000
+Ewald initialization ...
+ using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+ G vector (1/distance) = 0.170448
+ 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
+Per MPI rank memory allocation (min/avg/max) = 11.6 | 11.6 | 11.6 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 518.26667 -15.742442 0 7.4303753 -613.0781
+ 1000 369.81793 -54.202682 0 -37.667327 294.98832
+Loop time of 0.191619 on 4 procs for 1000 steps with 24 atoms
+
+Performance: 450.894 ns/day, 0.053 hours/ns, 5218.680 timesteps/s
+96.4% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.015873 | 0.028989 | 0.040172 | 5.3 | 15.13
+Bond | 0.00024271 | 0.00027657 | 0.00034404 | 0.0 | 0.14
+Kspace | 0.022896 | 0.034492 | 0.047924 | 5.1 | 18.00
+Neigh | 0.0025764 | 0.0025961 | 0.0026152 | 0.0 | 1.35
+Comm | 0.068467 | 0.070095 | 0.071535 | 0.4 | 36.58
+Output | 4.8161e-05 | 5.0783e-05 | 5.7936e-05 | 0.0 | 0.03
+Modify | 0.049141 | 0.049894 | 0.05072 | 0.3 | 26.04
+Other | | 0.005226 | | | 2.73
+
+Nlocal: 6 ave 8 max 3 min
+Histogram: 1 0 0 0 0 0 1 0 1 1
+Nghost: 1331.5 ave 1369 max 1290 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Neighs: 1259.75 ave 1642 max 428 min
+Histogram: 1 0 0 0 0 0 0 1 0 2
+
+Total # of neighbors = 5039
+Ave neighs/atom = 209.958
+Ave special neighs/atom = 2
+Neighbor list builds = 27
+Dangerous builds = 0
+reset_timestep 0
+
+# gcmc
+
+variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
+fix mygcmc h2o gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
+fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
+fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake
+fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert ${tfac} group h2o shake wshake
+fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert 1.66666666666667 group h2o shake wshake
+
+# atom counts
+
+variable oxygen atom "type==1"
+variable hydrogen atom "type==2"
+group oxygen dynamic all var oxygen
+dynamic group oxygen defined
+group hydrogen dynamic all var hydrogen
+dynamic group hydrogen defined
+variable nO equal count(oxygen)
+variable nH equal count(hydrogen)
+
+# 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)
+thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH
+thermo 1000
+
+# run
+
+run 20000
+Ewald initialization ...
+ using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+ G vector (1/distance) = 0.170448
+ 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:485)
+0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc
+0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
+ERROR: fix gcmc does currently not support full_energy option with molecules on more than 1 MPI process. (../fix_gcmc.cpp:721)
+Last command: run 20000
diff --git a/examples/gcmc/log.23Oct17.gcmc.lj.g++.1 b/examples/gcmc/log.30Mar18.gcmc.lj.g++.1
similarity index 52%
rename from examples/gcmc/log.23Oct17.gcmc.lj.g++.1
rename to examples/gcmc/log.30Mar18.gcmc.lj.g++.1
index a38dfeee77897b740bfecfaedd046676a6ad56b3..20a25c0f954627cd3445b1fbb6406f5610fb8cd0 100644
--- a/examples/gcmc/log.23Oct17.gcmc.lj.g++.1
+++ b/examples/gcmc/log.30Mar18.gcmc.lj.g++.1
@@ -1,4 +1,4 @@
-LAMMPS (23 Oct 2017)
+LAMMPS (30 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# GCMC for LJ simple fluid, no dynamics
# T = 2.0
@@ -36,17 +36,22 @@ Created orthogonal box = (0 0 0) to (5 5 5)
pair_coeff * * 1.0 1.0
mass * 1.0
+# we recommend setting up a dedicated group for gcmc
+
+group gcmcgroup type 1
+0 atoms in group gcmcgroup
+
# gcmc
-fix mygcmc all gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp}
-fix mygcmc all gcmc 1 100 100 1 29494 2.0 ${mu} ${disp}
-fix mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 ${disp}
-fix mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 1.0
+fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp}
+fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 2.0 ${mu} ${disp}
+fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 2.0 -1.25 ${disp}
+fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 2.0 -1.25 1.0
# atom count
variable type1 atom "type==1"
-group type1 dynamic all var type1
+group type1 dynamic gcmcgroup var type1
dynamic group type1 defined
variable n1 equal count(type1)
@@ -97,40 +102,40 @@ Neighbor list info ...
Per MPI rank memory allocation (min/avg/max) = 0.433 | 0.433 | 0.433 Mbytes
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av
0 0 0 0 -0 0 0 0 0 0 0 0 0 0
- 1000 2.4038954 2.1735585 -2.7041368 3.5476844 0.496 62 0.064790036 0.06313096 0.1081294 0.54304 1.4513524 -0.025479219 64.98
- 2000 2.0461168 1.1913842 -2.9880181 3.0212194 0.512 64 0.067416408 0.066335853 0.11306166 0.52736 1.3274665 0.034690004 62.97
- 3000 1.7930436 1.3788681 -3.2212667 2.6505861 0.552 69 0.067733191 0.066877836 0.1133516 0.5344 1.3834744 0.0070582537 63.5
- 4000 1.981449 1.2541054 -2.8222868 2.9217977 0.472 59 0.068546991 0.067856412 0.11442807 0.52504 1.3815629 0.043309657 62.17
- 5000 2.0946818 1.0701629 -3.5213291 3.0977688 0.568 71 0.06813743 0.067567891 0.11342906 0.53824 1.4049567 -0.0054539777 64.15
- 6000 1.9793484 0.68224187 -3.410211 2.9247088 0.536 67 0.067797628 0.067420108 0.11295333 0.5384 1.401683 -0.0066894359 64.37
- 7000 2.1885798 1.6745012 -3.185499 3.2345922 0.544 68 0.068630201 0.068261832 0.11403705 0.5244 1.449239 0.045987399 62.33
- 8000 2.2175324 1.5897263 -3.078898 3.2759002 0.528 66 0.068180395 0.067899629 0.11332691 0.53928 1.5488388 -0.01075766 64.29
- 9000 1.8610779 1.0396231 -2.923262 2.7465908 0.496 62 0.068346453 0.068028117 0.1134132 0.52912 1.4352871 0.027082544 62.87
- 10000 2.1079271 1.1746643 -2.9112062 3.1091925 0.48 60 0.068352878 0.068054948 0.11335434 0.5316 1.4462327 0.018503094 63.2
-Loop time of 20.4081 on 1 procs for 10000 steps with 60 atoms
-
-Performance: 211680.375 tau/day, 490.001 timesteps/s
-98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
+ 1000 2.0603874 2.9024736 -3.2576986 3.0482443 0.584 73 0.069266074 0.066959582 0.11158434 0.53624 1.3978532 0.0014407586 64.19
+ 2000 2.1586837 1.5581387 -2.8420766 3.1857993 0.496 62 0.068487803 0.067570935 0.1126652 0.53128 1.3713694 0.020274019 63.41
+ 3000 2.4664064 0.65471138 -3.3428236 3.6435549 0.528 66 0.068182273 0.067547792 0.11226502 0.53472 1.3892234 0.0070204504 63.68
+ 4000 1.8880496 1.4802782 -2.7846019 2.785647 0.488 61 0.068250075 0.067843541 0.11299989 0.52744 1.299496 0.033918563 63.1
+ 5000 2.0578649 1.3204331 -3.5571862 3.0433213 0.568 71 0.067858571 0.067732262 0.11271981 0.5364 1.4237505 0.00065741209 64
+ 6000 2.3627973 0.97064566 -3.1107668 3.4879388 0.504 63 0.067846204 0.06757018 0.11272207 0.5332 1.3945131 0.014216594 63.7
+ 7000 1.6629817 0.98138972 -2.7780297 2.4514644 0.464 58 0.067451389 0.067269791 0.11263692 0.53688 1.4207486 -0.0012887793 63.82
+ 8000 2.2135488 2.0878792 -3.0471089 3.2707661 0.536 67 0.067926473 0.067738312 0.1135594 0.52736 1.4348314 0.034380623 62.43
+ 9000 1.8904287 0.52639383 -3.3548657 2.7920177 0.52 65 0.06818197 0.068003094 0.11356319 0.53072 1.4528143 0.021683615 63.23
+ 10000 2.2353281 0.73275312 -3.2197702 3.3006016 0.512 64 0.068465059 0.068208485 0.11414748 0.52712 1.4143492 0.03497858 62.44
+Loop time of 21.2409 on 1 procs for 10000 steps with 64 atoms
+
+Performance: 203381.368 tau/day, 470.790 timesteps/s
+99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.46484 | 0.46484 | 0.46484 | 0.0 | 2.28
-Neigh | 1.1447 | 1.1447 | 1.1447 | 0.0 | 5.61
-Comm | 0.1696 | 0.1696 | 0.1696 | 0.0 | 0.83
-Output | 0.000319 | 0.000319 | 0.000319 | 0.0 | 0.00
-Modify | 18.607 | 18.607 | 18.607 | 0.0 | 91.17
-Other | | 0.02194 | | | 0.11
-
-Nlocal: 60 ave 60 max 60 min
+Pair | 0.45931 | 0.45931 | 0.45931 | 0.0 | 2.16
+Neigh | 1.1637 | 1.1637 | 1.1637 | 0.0 | 5.48
+Comm | 0.17294 | 0.17294 | 0.17294 | 0.0 | 0.81
+Output | 0.00027394 | 0.00027394 | 0.00027394 | 0.0 | 0.00
+Modify | 19.416 | 19.416 | 19.416 | 0.0 | 91.41
+Other | | 0.02919 | | | 0.14
+
+Nlocal: 64 ave 64 max 64 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 663 ave 663 max 663 min
+Nghost: 714 ave 714 max 714 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 2133 ave 2133 max 2133 min
+Neighs: 2423 ave 2423 max 2423 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Total # of neighbors = 2133
-Ave neighs/atom = 35.55
+Total # of neighbors = 2423
+Ave neighs/atom = 37.8594
Neighbor list builds = 10000
Dangerous builds = 0
-Total wall time: 0:00:20
+Total wall time: 0:00:21
diff --git a/examples/gcmc/log.23Oct17.gcmc.lj.g++.4 b/examples/gcmc/log.30Mar18.gcmc.lj.g++.4
similarity index 50%
rename from examples/gcmc/log.23Oct17.gcmc.lj.g++.4
rename to examples/gcmc/log.30Mar18.gcmc.lj.g++.4
index ea7dc8116febce3c356ca8782599656cf6250986..819d0ed0869038a7b0bd61a2a7fab6038eff996c 100644
--- a/examples/gcmc/log.23Oct17.gcmc.lj.g++.4
+++ b/examples/gcmc/log.30Mar18.gcmc.lj.g++.4
@@ -1,4 +1,4 @@
-LAMMPS (23 Oct 2017)
+LAMMPS (30 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# GCMC for LJ simple fluid, no dynamics
# T = 2.0
@@ -36,17 +36,22 @@ Created orthogonal box = (0 0 0) to (5 5 5)
pair_coeff * * 1.0 1.0
mass * 1.0
+# we recommend setting up a dedicated group for gcmc
+
+group gcmcgroup type 1
+0 atoms in group gcmcgroup
+
# gcmc
-fix mygcmc all gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp}
-fix mygcmc all gcmc 1 100 100 1 29494 2.0 ${mu} ${disp}
-fix mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 ${disp}
-fix mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 1.0
+fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp}
+fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 2.0 ${mu} ${disp}
+fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 2.0 -1.25 ${disp}
+fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 2.0 -1.25 1.0
# atom count
variable type1 atom "type==1"
-group type1 dynamic all var type1
+group type1 dynamic gcmcgroup var type1
dynamic group type1 defined
variable n1 equal count(type1)
@@ -97,40 +102,40 @@ Neighbor list info ...
Per MPI rank memory allocation (min/avg/max) = 0.4477 | 0.4477 | 0.4477 Mbytes
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av
0 0 0 0 -0 0 0 0 0 0 0 0 0 0
- 1000 1.956397 1.7699101 -2.7889468 2.8864874 0.488 61 0.068894746 0.067229075 0.1141726 0.53288 1.3832798 0.013392866 63.44
- 2000 2.040943 0.56060899 -2.8001647 3.0077055 0.456 57 0.069858594 0.068831934 0.11629114 0.5232 1.3587174 0.049995794 62.19
- 3000 2.0004866 1.5736515 -3.3098044 2.9572411 0.552 69 0.069594029 0.068727791 0.11592543 0.53096 1.4129434 0.020022578 63.23
- 4000 2.1127942 2.642809 -2.8865084 3.1211733 0.528 66 0.070268697 0.069533235 0.11693806 0.52424 1.3444615 0.046884078 62.57
- 5000 2.3663648 1.354269 -3.1917346 3.4957662 0.528 66 0.070519633 0.069960064 0.11710321 0.52688 1.3595814 0.036270867 62.56
- 6000 1.9224136 0.82756699 -3.1965 2.839257 0.52 65 0.06985018 0.069474645 0.11628632 0.536 1.47062 0.00141549 63.76
- 7000 2.0266192 1.5593811 -2.9972341 2.9931606 0.52 65 0.070244693 0.069880791 0.11666541 0.52528 1.3246332 0.040754793 62.2
- 8000 1.7790467 1.8680568 -2.8028819 2.6275151 0.52 65 0.070454494 0.070172368 0.11736806 0.524 1.4213649 0.047985191 62.03
- 9000 1.7968847 1.3195587 -3.261001 2.6550983 0.536 67 0.069952011 0.069618327 0.11650087 0.53904 1.4624201 -0.01069837 64.36
- 10000 2.1566109 1.1015729 -3.4999837 3.1880335 0.552 69 0.069603309 0.069284134 0.11625548 0.53128 1.3587249 0.02075238 63.24
-Loop time of 23.8213 on 4 procs for 10000 steps with 69 atoms
-
-Performance: 181350.388 tau/day, 419.793 timesteps/s
-97.6% CPU use with 4 MPI tasks x 1 OpenMP threads
+ 1000 2.4378552 1.9014939 -3.23439 3.6030066 0.544 68 0.073050445 0.070796636 0.11934255 0.52552 1.3006333 0.04152087 62.56
+ 2000 1.9339159 1.0360287 -3.5001391 2.8594327 0.56 70 0.069588893 0.068587488 0.11319584 0.542 1.4012888 -0.020696665 64.56
+ 3000 1.8891807 2.2857708 -3.3755633 2.7954769 0.592 74 0.068329031 0.067640916 0.11187803 0.53536 1.3380926 0.0062359288 64.21
+ 4000 2.0436517 1.7600211 -3.4067452 3.0229014 0.576 72 0.067464211 0.067003868 0.11060324 0.54144 1.4484907 -0.016246603 64.75
+ 5000 2.1512268 1.0811095 -3.2418366 3.1786785 0.536 67 0.066830654 0.066717982 0.1094094 0.54368 1.4962073 -0.025791643 65.04
+ 6000 2.128931 1.5444487 -3.1904474 3.1450116 0.528 66 0.067479197 0.067193531 0.1104464 0.53112 1.4247377 0.019908014 63.01
+ 7000 1.8194311 0.72981963 -3.6601329 2.6912418 0.576 72 0.068131849 0.067910074 0.11182024 0.51968 1.4517098 0.063444774 61.72
+ 8000 1.947817 0.74570466 -3.0935809 2.8753489 0.504 63 0.068034071 0.067855883 0.11217045 0.53304 1.4924302 0.012298733 63.45
+ 9000 1.8942389 1.3367401 -2.8925016 2.7962574 0.504 63 0.068117479 0.067943081 0.11236152 0.536 1.4091106 0.0011494886 63.73
+ 10000 2.2092799 0.95517153 -2.9117781 3.2586879 0.48 60 0.068264792 0.068016591 0.11310789 0.52272 1.4774174 0.051284873 62.04
+Loop time of 29.2417 on 4 procs for 10000 steps with 60 atoms
+
+Performance: 147733.999 tau/day, 341.977 timesteps/s
+96.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.10935 | 0.11844 | 0.12741 | 2.1 | 0.50
-Neigh | 0.33 | 0.33945 | 0.35091 | 1.6 | 1.42
-Comm | 0.49249 | 0.51745 | 0.53856 | 2.7 | 2.17
-Output | 0.00053334 | 0.0007208 | 0.0007906 | 0.0 | 0.00
-Modify | 22.82 | 22.822 | 22.825 | 0.0 | 95.81
-Other | | 0.02289 | | | 0.10
-
-Nlocal: 17.25 ave 23 max 10 min
-Histogram: 1 0 0 0 0 0 2 0 0 1
-Nghost: 506.5 ave 519 max 490 min
-Histogram: 1 0 1 0 0 0 0 0 0 2
-Neighs: 705.75 ave 998 max 369 min
-Histogram: 1 0 0 0 0 1 1 0 0 1
-
-Total # of neighbors = 2823
-Ave neighs/atom = 40.913
+Pair | 0.11648 | 0.1221 | 0.13001 | 1.5 | 0.42
+Neigh | 0.34452 | 0.35618 | 0.36328 | 1.2 | 1.22
+Comm | 0.63561 | 0.65617 | 0.67542 | 1.8 | 2.24
+Output | 0.00056601 | 0.00069755 | 0.00074744 | 0.0 | 0.00
+Modify | 28.069 | 28.076 | 28.082 | 0.1 | 96.01
+Other | | 0.03094 | | | 0.11
+
+Nlocal: 15 ave 16 max 14 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost: 437 ave 446 max 431 min
+Histogram: 2 0 0 0 0 0 1 0 0 1
+Neighs: 529 ave 595 max 437 min
+Histogram: 1 0 0 0 1 0 0 0 0 2
+
+Total # of neighbors = 2116
+Ave neighs/atom = 35.2667
Neighbor list builds = 10000
Dangerous builds = 0
-Total wall time: 0:00:23
+Total wall time: 0:00:29
diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp
index 7ee9cd028ef0f2eb21c2f9f6f8b0acc3af9cf5cc..f2c41c9ccf0559ee3103c99d62994d95e2af907d 100644
--- a/src/MC/fix_gcmc.cpp
+++ b/src/MC/fix_gcmc.cpp
@@ -686,7 +686,7 @@ void FixGCMC::init()
// warning if group id is "all"
- if (groupbit & 1)
+ if ((comm->me == 0) && (groupbit & 1))
error->warning(FLERR, "Fix gcmc is being applied "
"to the default group all");
@@ -1253,6 +1253,10 @@ void FixGCMC::attempt_molecule_deletion()
if (ngas == 0) return;
+ // work-around to avoid n=0 problem with fix rigid/nvt/small
+
+ if (ngas == natoms_per_molecule) return;
+
tagint deletion_molecule = pick_random_gas_molecule();
if (deletion_molecule == -1) return;
@@ -1910,6 +1914,10 @@ void FixGCMC::attempt_molecule_deletion_full()
if (ngas == 0) return;
+ // work-around to avoid n=0 problem with fix rigid/nvt/small
+
+ if (ngas == natoms_per_molecule) return;
+
tagint deletion_molecule = pick_random_gas_molecule();
if (deletion_molecule == -1) return;