diff --git a/examples/gcmc/H2O.txt b/examples/gcmc/H2O.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b56f869693ea2be0da413b2260de353e512c80e7
--- /dev/null
+++ b/examples/gcmc/H2O.txt
@@ -0,0 +1,62 @@
+# CO2 molecule file. TraPPE model.
+
+3 atoms
+2 bonds
+1 angles
+
+Coords
+
+1 1.12456 0.09298 1.27452
+2 1.53683 0.75606 1.89928
+3 0.49482 0.56390 0.65678
+
+Types
+
+1 1
+2 2
+3 2
+
+Charges
+
+1 -0.8472
+2 0.4236
+3 0.4236
+
+Bonds
+
+1 1 1 2
+2 1 1 3
+
+Angles
+
+1 1 2 1 3
+
+Shake Flags
+
+1 1
+2 1
+3 1
+
+Shake Atoms
+
+1 1 2 3
+2 1 2 3
+3 1 2 3
+
+Shake Bond Types
+
+1 1 1 1
+2 1 1 1
+3 1 1 1
+
+Special Bond Counts
+
+1 2 0 0
+2 1 1 0
+3 1 1 0
+
+Special Bonds
+
+1 2 3
+2 1 3
+3 1 2
diff --git a/examples/gcmc/in.gcmc.co2 b/examples/gcmc/in.gcmc.co2
index 0961e2b5568496b6c50e700eb635d83907ebb7d2..d11ef72fddc80a732684b8eba32a14c3356c4f30 100644
--- a/examples/gcmc/in.gcmc.co2
+++ b/examples/gcmc/in.gcmc.co2
@@ -64,7 +64,7 @@ fix_modify myrigidnvt dynamic/dof no
# gcmc
variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
-fix mygcmc all gcmc 100 100 100 0 54341 ${temp} ${mu} ${disp} mol &
+fix mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol &
co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
# output
diff --git a/examples/gcmc/in.gcmc.h2o b/examples/gcmc/in.gcmc.h2o
new file mode 100644
index 0000000000000000000000000000000000000000..7ffaafa9753b22e949efa55ecd482c9ffd2b6fdc
--- /dev/null
+++ b/examples/gcmc/in.gcmc.h2o
@@ -0,0 +1,88 @@
+# 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}
+region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} 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
+
+# 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
+
+# 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
+neighbor 2.0 bin
+neigh_modify every 1 delay 1 check yes
+velocity all create ${temp} 54654
+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
+
+
+
+run 1000
+
+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
+
+# 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
+thermo 1000
+
+# run
+
+run 20000
+
diff --git a/examples/gcmc/log.24Mar17.gcmc.co2.g++.4 b/examples/gcmc/log.24Mar17.gcmc.co2.g++.4
deleted file mode 100644
index 65504b8d465cbbdb05ce8f355d81496ca8d2dd79..0000000000000000000000000000000000000000
--- a/examples/gcmc/log.24Mar17.gcmc.co2.g++.4
+++ /dev/null
@@ -1,179 +0,0 @@
-LAMMPS (17 Mar 2017)
-# 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
-
-# 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 100 100 100 0 54341 ${temp} ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
-fix mygcmc all gcmc 100 100 100 0 54341 338.0 ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
-fix mygcmc all gcmc 100 100 100 0 54341 338.0 -8.1 ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
-fix mygcmc all gcmc 100 100 100 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
-fix mygcmc all gcmc 100 100 100 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert 1.66666666666667 group co2 rigid myrigidnvt
-
-# 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
-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:439)
-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) = 15.4 | 15.4 | 15.4 Mbytes
-Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc
- 0 386.52184 23582.465 -3.2433417 14.209828 0.5846359 24 0 0 0 0
-WARNING: Using kspace solver on system with no charge (../kspace.cpp:289)
- 1000 760.80877 -39.270882 -3.5239626 12.851016 0.29231795 12 0.24161633 0.22984103 0.71087092 0.85283311
- 2000 308.0739 -255.061 -20.411926 14.386853 0.73079488 30 0.26075352 0.24898725 0.73128383 0.88590474
- 3000 432.34358 -1361.3278 -12.644057 15.894387 0.5846359 24 0.21121583 0.21051229 0.70036003 0.86735027
- 4000 631.524 -63.488785 -3.6517158 13.804656 0.36539744 15 0.22486443 0.22886173 0.72358173 0.87172606
- 5000 730.61244 -1029.284 -6.2144028 19.600352 0.43847693 18 0.23017182 0.22740779 0.72281887 0.87820845
- 6000 752.43412 503.4547 -3.7053679 16.447663 0.36539744 15 0.22943971 0.226183 0.71450085 0.87447436
- 7000 660.68448 828.51735 -10.592278 21.006666 0.51155641 21 0.24702096 0.24218506 0.71815602 0.8740222
- 8000 331.58822 -621.22187 -5.3705759 7.2482776 0.36539744 15 0.23211903 0.22906813 0.70281376 0.86269411
- 9000 413.91538 869.51669 -11.28701 15.216905 0.5846359 24 0.23246466 0.22923961 0.70832684 0.86244176
- 10000 242.20861 -808.23311 -5.4533937 5.2945044 0.36539744 15 0.22024676 0.22031775 0.70785097 0.85712561
- 11000 348.20046 -372.16895 -3.4663358 7.6114092 0.36539744 15 0.2252033 0.22688969 0.71513402 0.86123263
- 12000 251.99682 303.30092 -18.58289 11.768089 0.73079488 30 0.20916844 0.21068047 0.694787 0.84635875
- 13000 306.83592 -1582.0137 -20.810287 14.329041 0.73079488 30 0.19494837 0.196527 0.67554784 0.83056119
- 14000 476.57411 268.94927 -14.185859 19.888076 0.65771539 27 0.19779631 0.20016859 0.67957528 0.83375167
- 15000 267.03534 730.71183 -9.3348616 9.8171066 0.5846359 24 0.19468305 0.19814971 0.68032974 0.83810439
- 16000 639.83235 2190.3244 -9.6666503 26.701062 0.65771539 27 0.19520687 0.19848997 0.68514387 0.84100361
- 17000 2237.1203 -222.59057 -0.18248834 4.4456205 0.073079488 3 0.20412446 0.20757814 0.69175318 0.8434939
- 18000 754.44841 205.54694 -10.501943 27.736031 0.5846359 24 0.2129422 0.21508015 0.69665031 0.84758331
- 19000 1610.1148 1293.6003 -0.20849836 3.1996309 0.073079488 3 0.22061668 0.22356929 0.69949369 0.84851405
- 20000 231.61458 -39.696514 -4.6452226 5.0629266 0.36539744 15 0.21984893 0.22246517 0.69914635 0.85058457
-Loop time of 21.1019 on 4 procs for 20000 steps with 15 atoms
-
-Performance: 81.888 ns/day, 0.293 hours/ns, 947.781 timesteps/s
-98.9% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.31897 | 0.41973 | 0.49748 | 10.1 | 1.99
-Bond | 0.014808 | 0.015063 | 0.015289 | 0.2 | 0.07
-Kspace | 0.3813 | 0.46228 | 0.56585 | 9.8 | 2.19
-Neigh | 0.049173 | 0.050043 | 0.050868 | 0.3 | 0.24
-Comm | 0.9755 | 0.99686 | 1.0205 | 1.9 | 4.72
-Output | 0.0014546 | 0.0015051 | 0.0016098 | 0.2 | 0.01
-Modify | 19.043 | 19.062 | 19.085 | 0.4 | 90.33
-Other | | 0.09438 | | | 0.45
-
-Nlocal: 3.75 ave 6 max 3 min
-Histogram: 3 0 0 0 0 0 0 0 0 1
-Nghost: 876.5 ave 937 max 818 min
-Histogram: 1 1 0 0 0 0 0 0 1 1
-Neighs: 490.5 ave 647 max 363 min
-Histogram: 1 0 1 0 0 1 0 0 0 1
-
-Total # of neighbors = 1962
-Ave neighs/atom = 130.8
-Ave special neighs/atom = 2
-Neighbor list builds = 40070
-Dangerous builds = 115
-
-Total wall time: 0:00:21
diff --git a/examples/gcmc/log.24Mar17.gcmc.co2.g++.1 b/examples/gcmc/log.6Jul17.gcmc.co2.g++.1
similarity index 50%
rename from examples/gcmc/log.24Mar17.gcmc.co2.g++.1
rename to examples/gcmc/log.6Jul17.gcmc.co2.g++.1
index 7562476bf33d4639532dc538e00925adc9844975..f9e494c43fdcd1ccd557a5366c0a6145daf69be1 100644
--- a/examples/gcmc/log.24Mar17.gcmc.co2.g++.1
+++ b/examples/gcmc/log.6Jul17.gcmc.co2.g++.1
@@ -1,4 +1,5 @@
-LAMMPS (17 Mar 2017)
+LAMMPS (6 Jul 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
@@ -80,11 +81,11 @@ fix_modify myrigidnvt dynamic/dof no
# gcmc
variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
-fix mygcmc all gcmc 100 100 100 0 54341 ${temp} ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
-fix mygcmc all gcmc 100 100 100 0 54341 338.0 ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
-fix mygcmc all gcmc 100 100 100 0 54341 338.0 -8.1 ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
-fix mygcmc all gcmc 100 100 100 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
-fix mygcmc all gcmc 100 100 100 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert 1.66666666666667 group co2 rigid myrigidnvt
+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
# output
@@ -106,7 +107,7 @@ WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
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:439)
+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)
@@ -122,56 +123,58 @@ Neighbor list info ...
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
-Per MPI rank memory allocation (min/avg/max) = 15.61 | 15.61 | 15.61 Mbytes
+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
0 364.27579 4238.8631 -9.6809388 13.391989 0.5846359 24 0 0 0 0
- 1000 311.39835 -327.93481 -8.6795381 9.9010062 0.51155641 21 0.13302848 0.12331626 0.6894397 0.90997852
WARNING: Using kspace solver on system with no charge (../kspace.cpp:289)
- 2000 905.66812 319.43347 -0.50350961 6.2991241 0.14615898 6 0.20952183 0.20430213 0.71797992 0.92626683
- 3000 275.57393 -719.89718 -26.534978 14.238181 0.80387436 33 0.21291069 0.20460696 0.72899202 0.9133259
- 4000 254.70771 -245.01902 -20.981537 13.160079 0.80387436 33 0.17245726 0.16974613 0.70145764 0.90542759
- 5000 96.073601 -517.98124 -34.019065 5.441166 0.87695385 36 0.14174575 0.13607057 0.6776754 0.90155771
- 6000 397.57265 148.92645 -7.2012893 10.665797 0.43847693 18 0.12299956 0.1202471 0.66165464 0.90274793
- 7000 455.4271 -347.44181 -5.9244703 12.217875 0.43847693 18 0.15182038 0.14791307 0.67904236 0.90560829
- 8000 301.03124 -627.45324 -13.251012 11.066909 0.5846359 24 0.16687346 0.16315516 0.6936719 0.91129375
- 9000 256.5747 -565.67983 -17.814128 11.981874 0.73079488 30 0.15458482 0.15131825 0.68966283 0.90993975
- 10000 443.60076 89.586912 -6.077863 11.900606 0.43847693 18 0.16092552 0.16020353 0.69882461 0.91422145
- 11000 436.43777 64.412921 -6.7128469 11.708443 0.43847693 18 0.17453966 0.17480683 0.70679243 0.91369445
- 12000 594.42207 849.07743 -3.3708621 10.040536 0.29231795 12 0.17461606 0.17568622 0.71175869 0.91333367
- 13000 426.85849 -1093.1334 -17.524618 17.813377 0.65771539 27 0.17742896 0.17792831 0.71363306 0.91450124
- 14000 317.75995 336.31107 -10.46774 11.681912 0.5846359 24 0.18331181 0.18427921 0.71715557 0.91652256
- 15000 272.65129 317.50536 -26.428336 14.087176 0.80387436 33 0.17449167 0.175957 0.71122398 0.91528038
- 16000 344.28567 -577.91079 -18.177927 16.077919 0.73079488 30 0.1661682 0.16781514 0.70485136 0.91508882
- 17000 134.55928 -193.5668 -30.297136 7.6208177 0.87695385 36 0.15965609 0.1605036 0.69658104 0.9140445
- 18000 231.87302 -446.07671 -14.875027 9.6763722 0.65771539 27 0.15270985 0.15351831 0.69002918 0.91372795
- 19000 328.6835 -280.22365 -20.001303 16.982214 0.80387436 33 0.15201017 0.15272181 0.69023195 0.91272534
- 20000 0 -20.39554 -0.14872889 -0 0 0 0.15600204 0.15750795 0.69503275 0.9138765
-Loop time of 30.9008 on 1 procs for 20000 steps with 0 atoms
-
-Performance: 55.921 ns/day, 0.429 hours/ns, 647.233 timesteps/s
-99.8% CPU use with 1 MPI tasks x no OpenMP threads
+ 1000 420.43475 1722.4052 -9.6956123 15.456579 0.5846359 24 0.20879341 0.20713005 0 0
+ 2000 302.29516 -547.83641 -22.017674 14.11699 0.73079488 30 0.1742478 0.1678018 0 0
+ 3000 316.6934 -1080.2672 -8.2218891 10.069364 0.51155641 21 0.13544917 0.13720634 0 0
+ 4000 246.81618 -679.83642 -14.577244 10.29997 0.65771539 27 0.1568939 0.15860229 0 0
+ 5000 260.22849 -896.29914 -16.097593 10.859684 0.65771539 27 0.13138744 0.13547049 0 0
+ 6000 291.70796 -1521.99 -22.303136 13.622574 0.73079488 30 0.12615476 0.12717694 0 0
+ 7000 236.02638 -599.92186 -27.580831 13.367447 0.87695385 36 0.119703 0.12145398 0 0
+ 8000 321.45341 688.10577 -10.09204 11.817696 0.5846359 24 0.10917411 0.11032646 0 0
+ 9000 502.85382 -302.31056 -0.22330142 0.99927447 0.073079488 3 0.1254105 0.12905828 0 0
+ 10000 249.98239 -510.0091 -32.815145 15.399767 0.95003334 39 0.1274504 0.12875623 0 0
+ 11000 247.59424 -1129.0274 -25.320205 12.792544 0.80387436 33 0.11739076 0.11916784 0 0
+ 12000 0 -20.39554 -0.14872889 -0 0 0 0.1254933 0.12920375 0 0
+ 13000 1272.2738 -474.79484 -0.29450485 8.8489483 0.14615898 6 0.13767133 0.14112496 0 0
+ 14000 516.54246 -36.296516 -5.0012009 11.291243 0.36539744 15 0.15632744 0.15955377 0 0
+ 15000 307.09233 1951.9301 -14.820362 12.815375 0.65771539 27 0.15393544 0.15716192 0 0
+ 16000 198.31989 -559.48443 -30.459487 11.231925 0.87695385 36 0.1482565 0.15025652 0 0
+ 17000 246.99311 657.85683 -18.579206 11.53442 0.73079488 30 0.14143958 0.14375423 0 0
+ 18000 467.13468 167.03738 -1.0945268 5.569759 0.21923846 9 0.13847359 0.14098533 0 0
+ 19000 359.54027 -1413.5407 -12.156233 13.217895 0.5846359 24 0.15169146 0.15294205 0 0
+ 20000 227.79597 -1204.5652 -23.24144 10.637925 0.73079488 30 0.14917199 0.15022946 0 0
+Loop time of 20.153 on 1 procs for 20000 steps with 30 atoms
+
+Performance: 85.744 ns/day, 0.280 hours/ns, 992.408 timesteps/s
+99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 2.1985 | 2.1985 | 2.1985 | 0.0 | 7.11
-Bond | 0.029596 | 0.029596 | 0.029596 | 0.0 | 0.10
-Kspace | 0.23123 | 0.23123 | 0.23123 | 0.0 | 0.75
-Neigh | 0.16141 | 0.16141 | 0.16141 | 0.0 | 0.52
-Comm | 0.20628 | 0.20628 | 0.20628 | 0.0 | 0.67
-Output | 0.00068831 | 0.00068831 | 0.00068831 | 0.0 | 0.00
-Modify | 28.022 | 28.022 | 28.022 | 0.0 | 90.69
-Other | | 0.05058 | | | 0.16
-
-Nlocal: 0 ave 0 max 0 min
+Pair | 2.5352 | 2.5352 | 2.5352 | 0.0 | 12.58
+Bond | 0.026112 | 0.026112 | 0.026112 | 0.0 | 0.13
+Kspace | 0.25 | 0.25 | 0.25 | 0.0 | 1.24
+Neigh | 0.10364 | 0.10364 | 0.10364 | 0.0 | 0.51
+Comm | 0.22907 | 0.22907 | 0.22907 | 0.0 | 1.14
+Output | 0.0013065 | 0.0013065 | 0.0013065 | 0.0 | 0.01
+Modify | 16.957 | 16.957 | 16.957 | 0.0 | 84.14
+Other | | 0.05061 | | | 0.25
+
+Nlocal: 30 ave 30 max 30 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 0 ave 0 max 0 min
+Nghost: 2310 ave 2310 max 2310 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 0 ave 0 max 0 min
+Neighs: 7736 ave 7736 max 7736 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Total # of neighbors = 0
-Neighbor list builds = 40367
-Dangerous builds = 118
+Total # of neighbors = 7736
+Ave neighs/atom = 257.867
+Ave special neighs/atom = 2
+Neighbor list builds = 20349
+Dangerous builds = 0
-Total wall time: 0:00:30
+Total wall time: 0:00:20
diff --git a/examples/gcmc/log.6Jul17.gcmc.co2.g++.4 b/examples/gcmc/log.6Jul17.gcmc.co2.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..0df25430d26c07b98085c31a2ac162c90f5bd763
--- /dev/null
+++ b/examples/gcmc/log.6Jul17.gcmc.co2.g++.4
@@ -0,0 +1,180 @@
+LAMMPS (6 Jul 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
+
+# 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
+
+# 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
+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
+ 0 386.52184 23582.465 -3.2433417 14.209828 0.5846359 24 0 0 0 0
+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
+ 2000 459.73529 238.91592 -0.42937831 5.4815343 0.21923846 9 0.30392058 0.30105616 0 0
+ 3000 255.47773 -479.67802 -36.850434 15.738299 0.95003334 39 0.22220744 0.2197582 0 0
+ 4000 182.70803 -1059.2262 -43.044833 12.163134 1.0231128 42 0.16781689 0.16716177 0 0
+ 5000 234.00907 -1821.0444 -46.04795 15.578317 1.0231128 42 0.13498091 0.13704201 0 0
+ 6000 163.42759 -774.67294 -49.686261 11.691518 1.0961923 45 0.11401677 0.11296973 0 0
+ 7000 171.64616 -355.23516 -49.323434 12.27947 1.0961923 45 0.098302308 0.098552065 0 0
+ 8000 251.29791 -905.47863 -37.841209 15.480807 0.95003334 39 0.086856972 0.08638658 0 0
+ 9000 143.69498 -849.95393 -49.073188 10.279858 1.0961923 45 0.078261061 0.077955243 0 0
+ 10000 239.35727 -1158.1879 -43.562047 15.934355 1.0231128 42 0.070789792 0.070807529 0 0
+ 11000 169.51213 -1574.7885 -51.125228 12.126803 1.0961923 45 0.065008734 0.06498871 0 0
+ 12000 181.39739 160.11631 -46.850937 12.977068 1.0961923 45 0.059648717 0.059514803 0 0
+ 13000 164.14601 -1107.7629 -50.726722 11.742914 1.0961923 45 0.055207333 0.055097701 0 0
+ 14000 287.26285 418.51463 -41.664766 19.123497 1.0231128 42 0.051346789 0.051222285 0 0
+ 15000 256.94593 -532.36615 -41.651618 17.105257 1.0231128 42 0.047870301 0.047861685 0 0
+ 16000 166.92132 151.15933 -39.957018 11.11219 1.0231128 42 0.045205599 0.045042211 0 0
+ 17000 163.22452 -1299.8119 -42.677558 10.866089 1.0231128 42 0.043122086 0.042993687 0 0
+ 18000 158.01154 475.77329 -48.803162 11.304057 1.0961923 45 0.041016683 0.040647229 0 0
+ 19000 138.49297 -1585.1508 -47.517099 9.9077098 1.0961923 45 0.038929287 0.038436764 0 0
+ 20000 173.84439 -1362.6301 -53.002743 12.436731 1.0961923 45 0.036973919 0.036523816 0 0
+Loop time of 31.8386 on 4 procs for 20000 steps with 45 atoms
+
+Performance: 54.274 ns/day, 0.442 hours/ns, 628.168 timesteps/s
+98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 1.1546 | 1.6687 | 2.1338 | 29.5 | 5.24
+Bond | 0.019769 | 0.020369 | 0.02132 | 0.4 | 0.06
+Kspace | 0.53392 | 0.99911 | 1.5116 | 37.8 | 3.14
+Neigh | 0.06737 | 0.067842 | 0.068412 | 0.2 | 0.21
+Comm | 1.9408 | 1.9582 | 1.9733 | 1.1 | 6.15
+Output | 0.0019503 | 0.0020472 | 0.0022476 | 0.3 | 0.01
+Modify | 26.974 | 26.99 | 27.001 | 0.2 | 84.77
+Other | | 0.1322 | | | 0.42
+
+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: 0:00:31
diff --git a/examples/gcmc/log.6Jul17.gcmc.h2o.g++.1 b/examples/gcmc/log.6Jul17.gcmc.h2o.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..3b1606e65d6979747e5f22a920e516f691e052c2
--- /dev/null
+++ b/examples/gcmc/log.6Jul17.gcmc.h2o.g++.1
@@ -0,0 +1,281 @@
+LAMMPS (6 Jul 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 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
+create_atoms 0 box mol h2omol 464563 units box
+Created 24 atoms
+
+# 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) = 11.88 | 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 0.0525794 on 1 procs for 100 steps with 24 atoms
+
+99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+Minimization stats:
+ Stopping criterion = max iterations
+ Energy initial, next-to-last, final =
+ -4.18904713252 -28.9258064504 -29.3268133965
+ Force two-norm initial, final = 18.0027 42.4511
+ Force max component initial, final = 5.8993 16.0523
+ Final line search alpha, max atom move = 0.00353207 0.056698
+ Iterations, force evaluations = 100 238
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.044199 | 0.044199 | 0.044199 | 0.0 | 84.06
+Bond | 0.00049019 | 0.00049019 | 0.00049019 | 0.0 | 0.93
+Kspace | 0.0031631 | 0.0031631 | 0.0031631 | 0.0 | 6.02
+Neigh | 0.00046444 | 0.00046444 | 0.00046444 | 0.0 | 0.88
+Comm | 0.0034101 | 0.0034101 | 0.0034101 | 0.0 | 6.49
+Output | 1.9073e-05 | 1.9073e-05 | 1.9073e-05 | 0.0 | 0.04
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 0.0008333 | | | 1.58
+
+Nlocal: 24 ave 24 max 24 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 2047 ave 2047 max 2047 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 4936 ave 4936 max 4936 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 4936
+Ave neighs/atom = 205.667
+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
+ 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) = 11.63 | 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 0.14263 on 1 procs for 1000 steps with 24 atoms
+
+Performance: 605.764 ns/day, 0.040 hours/ns, 7011.155 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 | 0.10849 | 0.10849 | 0.10849 | 0.0 | 76.07
+Bond | 0.00015426 | 0.00015426 | 0.00015426 | 0.0 | 0.11
+Kspace | 0.01205 | 0.01205 | 0.01205 | 0.0 | 8.45
+Neigh | 0.0046577 | 0.0046577 | 0.0046577 | 0.0 | 3.27
+Comm | 0.011531 | 0.011531 | 0.011531 | 0.0 | 8.08
+Output | 1.6212e-05 | 1.6212e-05 | 1.6212e-05 | 0.0 | 0.01
+Modify | 0.0037699 | 0.0037699 | 0.0037699 | 0.0 | 2.64
+Other | | 0.001957 | | | 1.37
+
+Nlocal: 24 ave 24 max 24 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1660 ave 1660 max 1660 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 5112 ave 5112 max 5112 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 5112
+Ave neighs/atom = 213
+Ave special neighs/atom = 2
+Neighbor list builds = 25
+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
+
+# 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
+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) = 11.63 | 11.63 | 11.63 Mbytes
+Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc
+ 1000 326.9865 -4.3509713 -62.258445 14.62027 0.23910963 24 0 0 0 0
+ 2000 116.99793 -5344.1527 -286.61595 17.088682 0.74721761 75 0.048183096 0.013941446 0 0
+ 3000 106.86746 -3920.4926 -361.60598 18.794545 0.89666113 90 0.035637919 0.012768883 0 0
+ 4000 75.002668 540.46846 -414.8511 14.531966 0.98632724 99 0.025963651 0.0093451705 0 0
+ 5000 79.924788 -2131.1173 -437.21216 15.962121 1.0162159 102 0.019879728 0.0070418993 0 0
+ 6000 95.552773 -3647.0233 -438.24276 19.083253 1.0162159 102 0.015753613 0.0056885133 0 0
+ 7000 79.501736 -2071.5369 -440.77351 15.877631 1.0162159 102 0.01326216 0.0046915318 0 0
+ 8000 62.567091 -3102.9616 -442.21884 12.495541 1.0162159 102 0.011305503 0.0040437885 0 0
+ 9000 68.324047 -3812.7866 -440.46835 13.645287 1.0162159 102 0.0099549538 0.0035157329 0 0
+ 10000 83.857631 -2158.2659 -444.8183 16.747566 1.0162159 102 0.0088200922 0.0031354281 0 0
+ 11000 68.350984 -2084.0789 -440.14081 13.650667 1.0162159 102 0.0081331455 0.0030247424 0 0
+ 12000 76.867315 -1585.6723 -443.36199 15.3515 1.0162159 102 0.0073845932 0.0027532534 0 0
+ 13000 59.74266 -2211.0211 -446.07791 11.931462 1.0162159 102 0.0067756276 0.0025213898 0 0
+ 14000 81.154979 -907.0176 -441.53368 16.207808 1.0162159 102 0.0062527642 0.0023280719 0 0
+ 15000 66.814346 -2804.5134 -455.80704 13.7421 1.0461046 105 0.0059590528 0.0021576214 0 0
+ 16000 71.42983 -3930.4004 -458.43218 14.691394 1.0461046 105 0.0055547473 0.0020163729 0 0
+ 17000 89.624855 -3569.8136 -455.18164 18.433672 1.0461046 105 0.0052173265 0.0018867687 0 0
+ 18000 63.519962 -1882.8157 -456.58939 13.064525 1.0461046 105 0.0049082049 0.0017765986 0 0
+ 19000 71.872698 -2243.5046 -454.93359 14.782481 1.0461046 105 0.0046439115 0.0016748361 0 0
+ 20000 73.660765 -2285.3173 -476.35473 15.589381 1.0759934 108 0.0045124933 0.0015837653 0 0
+ 21000 95.675868 987.92089 -475.46736 20.248603 1.0759934 108 0.004285814 0.0015049513 0 0
+Loop time of 226.155 on 1 procs for 20000 steps with 108 atoms
+
+Performance: 7.641 ns/day, 3.141 hours/ns, 88.435 timesteps/s
+99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 38.053 | 38.053 | 38.053 | 0.0 | 16.83
+Bond | 0.089673 | 0.089673 | 0.089673 | 0.0 | 0.04
+Kspace | 0.92778 | 0.92778 | 0.92778 | 0.0 | 0.41
+Neigh | 1.2619 | 1.2619 | 1.2619 | 0.0 | 0.56
+Comm | 0.97483 | 0.97483 | 0.97483 | 0.0 | 0.43
+Output | 0.0013306 | 0.0013306 | 0.0013306 | 0.0 | 0.00
+Modify | 184.68 | 184.68 | 184.68 | 0.0 | 81.66
+Other | | 0.171 | | | 0.08
+
+Nlocal: 108 ave 108 max 108 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 7850 ave 7850 max 7850 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 99828 ave 99828 max 99828 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 99828
+Ave neighs/atom = 924.333
+Ave special neighs/atom = 2
+Neighbor list builds = 20439
+Dangerous builds = 0
+
+Total wall time: 0:03:46
diff --git a/examples/gcmc/log.6Jul17.gcmc.h2o.g++.4 b/examples/gcmc/log.6Jul17.gcmc.h2o.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..c04b25f45eaf88e4a82ca9edd8b79a0ec9ac934c
--- /dev/null
+++ b/examples/gcmc/log.6Jul17.gcmc.h2o.g++.4
@@ -0,0 +1,281 @@
+LAMMPS (6 Jul 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
+
+# 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 0.0828406 on 4 procs for 100 steps with 24 atoms
+
+98.7% 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 | 0.012844 | 0.025471 | 0.047008 | 8.1 | 30.75
+Bond | 0.00038934 | 0.00046468 | 0.00054336 | 0.0 | 0.56
+Kspace | 0.0061138 | 0.027556 | 0.04014 | 7.8 | 33.26
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.023276 | 0.023636 | 0.023804 | 0.1 | 28.53
+Output | 3.171e-05 | 3.3557e-05 | 3.8147e-05 | 0.0 | 0.04
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 0.00568 | | | 6.86
+
+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 0.199641 on 4 procs for 1000 steps with 24 atoms
+
+Performance: 432.777 ns/day, 0.055 hours/ns, 5008.996 timesteps/s
+98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.017161 | 0.034988 | 0.05833 | 8.0 | 17.53
+Bond | 0.00017357 | 0.00021374 | 0.00027347 | 0.0 | 0.11
+Kspace | 0.018025 | 0.044624 | 0.065613 | 8.4 | 22.35
+Neigh | 0.0029755 | 0.0033154 | 0.0036366 | 0.6 | 1.66
+Comm | 0.059933 | 0.06537 | 0.070709 | 1.5 | 32.74
+Output | 3.4571e-05 | 3.6657e-05 | 4.22e-05 | 0.0 | 0.02
+Modify | 0.043458 | 0.045628 | 0.04767 | 0.9 | 22.86
+Other | | 0.005465 | | | 2.74
+
+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
+
+# 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
+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
+ 1000 369.81793 295.32434 -54.202686 16.535355 0.23910963 24 0 0 0 0
+ 2000 84.544466 -2810.9047 -344.81664 14.364627 0.86677242 87 0.052198354 0.0099581757 0 0
+ 3000 75.188527 -3688.256 -425.02228 14.567977 0.98632724 99 0.030546787 0.0049111089 0 0
+ 4000 75.019396 -5669.3063 -427.69454 14.535207 0.98632724 99 0.019972039 0.0033375609 0 0
+ 5000 90.415371 -2141.7596 -434.65925 17.518218 0.98632724 99 0.014909796 0.002514964 0 0
+ 6000 78.212628 -943.75125 -428.80584 15.153904 0.98632724 99 0.01181521 0.0020316119 0 0
+ 7000 71.754139 -2028.5122 -435.2139 13.902555 0.98632724 99 0.0099466198 0.0016755471 0 0
+ 8000 84.446231 -1969.1657 -428.27313 16.361681 0.98632724 99 0.0084791272 0.0014442102 0 0
+ 9000 70.952348 -2476.9812 -446.33824 14.170197 1.0162159 102 0.0077150892 0.0012556189 0 0
+ 10000 71.418543 -1875.7083 -443.7214 14.263302 1.0162159 102 0.0068355714 0.0011197957 0 0
+ 11000 86.094994 -4508.7581 -444.82687 17.194399 1.0162159 102 0.0061494515 0.0010082475 0 0
+ 12000 81.906091 -1547.8105 -442.36719 16.357815 1.0162159 102 0.0055834729 0.00091775114 0 0
+ 13000 57.221548 -4607.6222 -448.30939 11.42796 1.0162159 102 0.0051230355 0.00084046326 0 0
+ 14000 61.288344 -2518.1779 -445.70636 12.240157 1.0162159 102 0.0047276997 0.00077602396 0 0
+ 15000 85.787669 -2407.7111 -443.3834 17.133022 1.0162159 102 0.0043983485 0.00071920715 0 0
+ 16000 74.845939 -3288.3403 -445.8247 14.947802 1.0162159 102 0.0042321884 0.00080654918 0 0
+ 17000 73.835431 -1926.9566 -445.67476 14.745989 1.0162159 102 0.0039751059 0.00075470749 0 0
+ 18000 72.634985 -3997.552 -447.2351 14.506243 1.0162159 102 0.0037395847 0.00071063946 0 0
+ 19000 96.776472 -714.44132 -453.65552 19.904587 1.0461046 105 0.0036487876 0.00066993446 0 0
+ 20000 75.470786 183.16972 -464.04688 15.522521 1.0461046 105 0.0034630763 0.00063350614 0 0
+ 21000 65.658309 -773.41266 -466.27068 13.504331 1.0461046 105 0.003289113 0.00060198052 0 0
+Loop time of 93.8859 on 4 procs for 20000 steps with 105 atoms
+
+Performance: 18.405 ns/day, 1.304 hours/ns, 213.024 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 | 6.7882 | 10.264 | 14.758 | 93.2 | 10.93
+Bond | 0.028286 | 0.034218 | 0.039038 | 2.5 | 0.04
+Kspace | 0.57255 | 5.2227 | 8.8493 | 133.8 | 5.56
+Neigh | 0.3635 | 0.36915 | 0.37473 | 0.9 | 0.39
+Comm | 2.9961 | 3.2542 | 3.509 | 11.4 | 3.47
+Output | 0.0011675 | 0.0012342 | 0.001375 | 0.2 | 0.00
+Modify | 74.428 | 74.499 | 74.571 | 0.7 | 79.35
+Other | | 0.2411 | | | 0.26
+
+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: 0:01:34
diff --git a/examples/gcmc/log.24Mar17.gcmc.lj.g++.1 b/examples/gcmc/log.6Jul17.gcmc.lj.g++.1
similarity index 88%
rename from examples/gcmc/log.24Mar17.gcmc.lj.g++.1
rename to examples/gcmc/log.6Jul17.gcmc.lj.g++.1
index 36a9fe885d82cea983da3026bc098eb2725dc4ac..69fc2ede1cd28681f7b139e8bb2b1a4976d6df89 100644
--- a/examples/gcmc/log.24Mar17.gcmc.lj.g++.1
+++ b/examples/gcmc/log.6Jul17.gcmc.lj.g++.1
@@ -1,5 +1,4 @@
-LAMMPS (17 Mar 2017)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+LAMMPS (6 Jul 2017)
using 1 OpenMP thread(s) per MPI task
# GCMC for LJ simple fluid, no dynamics
# T = 2.0
@@ -100,20 +99,20 @@ Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v
8000 2.2175324 1.5897263 -3.078898 3.2759002 0.528 66 0.068180395 0.067899629 0.11332691 0.53928 1.5488388 -0.01075766
9000 1.8610779 1.0396231 -2.923262 2.7465908 0.496 62 0.068346453 0.068028117 0.1134132 0.52912 1.4352871 0.027082544
10000 2.1079271 1.1746643 -2.9112062 3.1091925 0.48 60 0.068352878 0.068054948 0.11335434 0.5316 1.4462327 0.018503094
-Loop time of 13.05 on 1 procs for 10000 steps with 60 atoms
+Loop time of 20.6892 on 1 procs for 10000 steps with 60 atoms
-Performance: 331035.016 tau/day, 766.285 timesteps/s
-100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
+Performance: 208804.611 tau/day, 483.344 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 | 0.37239 | 0.37239 | 0.37239 | 0.0 | 2.85
-Neigh | 0.94764 | 0.94764 | 0.94764 | 0.0 | 7.26
-Comm | 0.092473 | 0.092473 | 0.092473 | 0.0 | 0.71
-Output | 0.00023365 | 0.00023365 | 0.00023365 | 0.0 | 0.00
-Modify | 11.627 | 11.627 | 11.627 | 0.0 | 89.09
-Other | | 0.01054 | | | 0.08
+Pair | 0.47227 | 0.47227 | 0.47227 | 0.0 | 2.28
+Neigh | 1.1729 | 1.1729 | 1.1729 | 0.0 | 5.67
+Comm | 0.17133 | 0.17133 | 0.17133 | 0.0 | 0.83
+Output | 0.00028253 | 0.00028253 | 0.00028253 | 0.0 | 0.00
+Modify | 18.852 | 18.852 | 18.852 | 0.0 | 91.12
+Other | | 0.02063 | | | 0.10
Nlocal: 60 ave 60 max 60 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -126,4 +125,4 @@ Total # of neighbors = 2133
Ave neighs/atom = 35.55
Neighbor list builds = 10000
Dangerous builds = 0
-Total wall time: 0:00:13
+Total wall time: 0:00:20
diff --git a/examples/gcmc/log.24Mar17.gcmc.lj.g++.4 b/examples/gcmc/log.6Jul17.gcmc.lj.g++.4
similarity index 88%
rename from examples/gcmc/log.24Mar17.gcmc.lj.g++.4
rename to examples/gcmc/log.6Jul17.gcmc.lj.g++.4
index 8694d8b95e940268768011a600d6847299a3783b..6bd3b3189cfeda01ff29feefff5d861c8d32b888 100644
--- a/examples/gcmc/log.24Mar17.gcmc.lj.g++.4
+++ b/examples/gcmc/log.6Jul17.gcmc.lj.g++.4
@@ -1,5 +1,4 @@
-LAMMPS (17 Mar 2017)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+LAMMPS (6 Jul 2017)
using 1 OpenMP thread(s) per MPI task
# GCMC for LJ simple fluid, no dynamics
# T = 2.0
@@ -100,20 +99,20 @@ Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v
8000 1.7790467 1.8680568 -2.8028819 2.6275151 0.52 65 0.070454494 0.070172368 0.11736806 0.524 1.4213649 0.047985191
9000 1.7968847 1.3195587 -3.261001 2.6550983 0.536 67 0.069952011 0.069618327 0.11650087 0.53904 1.4624201 -0.01069837
10000 2.1566109 1.1015729 -3.4999837 3.1880335 0.552 69 0.069603309 0.069284134 0.11625548 0.53128 1.3587249 0.02075238
-Loop time of 13.0611 on 4 procs for 10000 steps with 69 atoms
+Loop time of 24.9916 on 4 procs for 10000 steps with 69 atoms
-Performance: 330753.007 tau/day, 765.632 timesteps/s
-99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
+Performance: 172857.936 tau/day, 400.134 timesteps/s
+98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.08888 | 0.09443 | 0.099889 | 1.4 | 0.72
-Neigh | 0.27721 | 0.28532 | 0.29177 | 1.1 | 2.18
-Comm | 0.27648 | 0.28875 | 0.30268 | 1.9 | 2.21
-Output | 0.00029635 | 0.00043058 | 0.00048113 | 0.0 | 0.00
-Modify | 12.384 | 12.384 | 12.384 | 0.0 | 94.82
-Other | | 0.008055 | | | 0.06
+Pair | 0.11696 | 0.12516 | 0.1321 | 1.7 | 0.50
+Neigh | 0.34874 | 0.35644 | 0.36545 | 1.2 | 1.43
+Comm | 0.48531 | 0.51366 | 0.54755 | 3.8 | 2.06
+Output | 0.0005362 | 0.00069767 | 0.00076008 | 0.0 | 0.00
+Modify | 23.956 | 23.972 | 23.988 | 0.3 | 95.92
+Other | | 0.02376 | | | 0.10
Nlocal: 17.25 ave 23 max 10 min
Histogram: 1 0 0 0 0 0 2 0 0 1
@@ -126,4 +125,4 @@ Total # of neighbors = 2823
Ave neighs/atom = 40.913
Neighbor list builds = 10000
Dangerous builds = 0
-Total wall time: 0:00:13
+Total wall time: 0:00:24
diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp
index fbe6b6bb6249c4dcdb6adfd06365b3e90e433908..4405a680f20d09c1c16a0f77d8a880f49128ff82 100644
--- a/src/MC/fix_gcmc.cpp
+++ b/src/MC/fix_gcmc.cpp
@@ -188,6 +188,10 @@ FixGCMC::FixGCMC(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Cannot use fix gcmc shake and not molecule");
if (rigidflag && shakeflag)
error->all(FLERR,"Cannot use fix gcmc rigid and shake");
+ if (rigidflag && (nmcmoves > 0))
+ error->all(FLERR,"Cannot use fix gcmc rigid with MC moves");
+ if (shakeflag && (nmcmoves > 0))
+ error->all(FLERR,"Cannot use fix gcmc shake with MC moves");
// setup of coords and imageflags array