diff --git a/doc/src/fix_bond_react.txt b/doc/src/fix_bond_react.txt
index b5f9a730842b73805d146d4dc07b2ee0b2c00062..4a7c2428c16aa050a24f71d685960d9d952b65a4 100644
--- a/doc/src/fix_bond_react.txt
+++ b/doc/src/fix_bond_react.txt
@@ -11,9 +11,9 @@ fix bond/react command :h3
[Syntax:]
fix ID group-ID bond/react common_keyword values ...
- react react-ID react-group-ID Nevery Rmin template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
- react react-ID react-group-ID Nevery Rmin template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
- react react-ID react-group-ID Nevery Rmin template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
+ react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
+ react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
+ react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
... :pre
ID, group-ID are documented in "fix"_fix.html command. Group-ID is ignored. :ulb,l
@@ -24,12 +24,13 @@ common_keyword = {stabilization}
{stabilization} values = group-ID xmax
group-ID = user-assigned ID of an internally-created dynamic group that excludes reacting atoms, and can be used by a subsequent time integration fix such as nvt, npt, or nve (cannot be 'all')
{xmax} value = distance
- distance = xmax value that is used by an internally created "nve/limit"_nve_limit.html integrator
+ distance = xmax value that is used by an internally created "nve/limit"_fix_nve_limit.html integrator
react = mandatory argument indicating new reaction specification
react-ID = user-assigned name for the reaction
react-group-ID = only atoms in this group are available for the reaction
Nevery = attempt reaction every this many steps :l
- Rmin = bonding pair atoms separated by less than Rmin can initiate reaction (distance units) :l
+ Rmin = bonding pair atoms must be separated by more than Rmin to initiate reaction (distance units) :l
+ Rmax = bonding pair atoms must be separated by less than Rmax to initiate reaction (distance units) :l
template-ID(pre-reacted) = ID of a molecule template containing pre-reaction topology :l
template-ID(post-reacted) = ID of a molecule template containing post-reaction topology :l
map_file = name of file specifying corresponding atomIDs in the pre- and post-reacted templates :l
@@ -46,15 +47,15 @@ react = mandatory argument indicating new reaction specification
molecule mol1 pre_reacted_topology.txt
molecule mol2 post_reacted_topology.txt
-fix 5 all bond/react stabilization no react myrxn1 all 1 3.25 mol1 mol2 map_file.txt
+fix 5 all bond/react stabilization no react myrxn1 all 1 0 3.25 mol1 mol2 map_file.txt
molecule mol1 pre_reacted_rxn1.txt
molecule mol2 post_reacted_rxn1.txt
molecule mol3 pre_reacted_rxn2.txt
molecule mol4 post_reacted_rxn2.txt
fix 5 all bond/react stabilization yes nvt_grp .03 &
- react myrxn1 all 1 3.25 mol1 mol2 map_file_rxn1.txt prob 0.50 12345 &
- react myrxn2 all 1 2.75 mol3 mol4 map_file_rxn2.txt prob 0.25 12345
+ react myrxn1 all 1 0 3.25 mol1 mol2 map_file_rxn1.txt prob 0.50 12345 &
+ react myrxn2 all 1 0 2.75 mol3 mol4 map_file_rxn2.txt prob 0.25 12345
fix 6 nvt_grp nvt temp 300 300 100 # system-wide thermostat must be defined after bond/react :pre
[Description:]
@@ -101,9 +102,14 @@ The group-ID set using the {stabilization} keyword should be a
previously unused group-ID. The fix bond/react command creates a
"dynamic group"_group.html of this name that excludes reacting atoms.
This dynamic group-ID should then be used by a subsequent system-wide
-time integrator, as shown in the second example above. It is necessary
-to place the time integration command after the fix bond/react command
-due to the internal dynamic grouping performed by fix bond/react.
+time integrator, as shown in the second example above. It is currently
+necessary to place the time integration command after the fix
+bond/react command due to the internal dynamic grouping performed by
+fix bond/react.
+
+NOTE: The internally created group currently applies to all atoms in
+the system, i.e. you should generally not have a separate thermostat
+which acts on the 'all' group.
The following comments pertain to each 'react' argument:
@@ -118,21 +124,20 @@ modified to match the post-reaction template.
A bonding atom pair will be identified if several conditions are met.
First, a pair of atoms within the specified react-group-ID of type
-typei and typej must be within a distance Rmin of each other. The atom
-types typei and typej are specified in the pre- and post-reaction
-templates. The distance calculation uses the pair neighbor list,
-therefore bonded neighbor exclusions may prevent a reaction between
-1st, 2nd or 3rd bonded neighbor atoms. If multiple bonding atom pairs
-are identified for an atom, the closest bonding atom partner is set as
-its "nearest" bonding partner. Then, if both an atomi and atomj have
-each other as their nearest bonding partners, these two atoms are
-identified as the bonding atom pair of the reaction site. Once this
-unique bonding atom pair is identified for each reaction, there could
-two or more reactions that involve a given atom on the same timestep.
-If this is the case, only one such reaction is permitted to occur.
-This reaction is chosen randomly from all potential reactions. This
-capability allows e.g. for different reaction pathways to proceed from
-identical reaction sites with user-specified probabilities.
+typei and typej must separated by a distance between Rmin and Rmax. It
+is possible that multiple bonding atom pairs are identified: if the
+bonding atoms in the pre-reacted template are not 1-2, 1-3, or 1-4
+neighbors, the closest bonding atom partner is set as its bonding
+partner; otherwise, the farthest potential partner is chosen. Then, if
+both an atomi and atomj have each other as their nearest bonding
+partners, these two atoms are identified as the bonding atom pair of
+the reaction site. Once this unique bonding atom pair is identified
+for each reaction, there could two or more reactions that involve a
+given atom on the same timestep. If this is the case, only one such
+reaction is permitted to occur. This reaction is chosen randomly from
+all potential reactions. This capability allows e.g. for different
+reaction pathways to proceed from identical reaction sites with
+user-specified probabilities.
The pre-reacted molecule template is specified by a molecule command.
This molecule template file contains a sample reaction site and its
@@ -262,9 +267,11 @@ angles, dihedrals or impropers are supported.
A few capabilities to note: 1) You may specify as many 'react'
arguments as desired. For example, you could break down a complicated
reaction mechanism into several reaction steps, each defined by its
-own 'react' argument. 2) While typically a bond is formed between the
-bonding atom pairs specified in the pre-reacted molecule template,
-this is not required.
+own 'react' argument. 2) While typically a bond is formed or removed
+between the bonding atom pairs specified in the pre-reacted molecule
+template, this is not required. 3) By reversing the order of the pre-
+and post- reacted molecule templates in another 'react' argument, you
+can allow for the possibility of one or more reverse reactions.
The optional keywords deal with the probability of a given reaction
occurring as well as the stable equilibration of each reaction site as
@@ -300,14 +307,14 @@ reaction:
fix 1 bond_react_MASTER_group temp/rescale 1 300 300 10 1
NOTE: This command must be added after the fix bond/react command, and
-will apply to all reaction steps.
+will apply to all reactions.
Computationally, each timestep this fix operates, it loops over
-neighbor lists and computes distances between pairs of atoms in the
-list. It also communicates between neighboring processors to
-coordinate which bonds are created. All of these operations increase
-the cost of a timestep. Thus you should be cautious about invoking
-this fix too frequently.
+neighbor lists (for bond-forming reactions) and computes distances
+between pairs of atoms in the list. It also communicates between
+neighboring processors to coordinate which bonds are created and/or
+removed. All of these operations increase the cost of a timestep. Thus
+you should be cautious about invoking this fix too frequently.
You can dump out snapshots of the current bond topology via the dump
local command.
diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/in.large_nylon_melt b/examples/USER/misc/bond_react/nylon,6-6_melt/in.large_nylon_melt
index 072a8e3c456af5547403b35d859b08a5c512f941..f2dc506ddef28d978d48eb90569302e0de27124b 100644
--- a/examples/USER/misc/bond_react/nylon,6-6_melt/in.large_nylon_melt
+++ b/examples/USER/misc/bond_react/nylon,6-6_melt/in.large_nylon_melt
@@ -32,8 +32,8 @@ thermo 50
# dump 1 all xyz 100 test_vis.xyz
fix myrxns all bond/react stabilization yes statted_grp .03 &
- react rxn1 all 1 2.9 mol1 mol2 rxn1_stp1_map &
- react rxn2 all 1 5 mol3 mol4 rxn1_stp2_map
+ react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map &
+ react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
# stable at 800K
fix 1 statted_grp nvt temp 800 800 100
diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1 b/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1
index f3b3840a925573ab1b83db1402cd68c5579dab35..653c7582f8d7aba4c8800e5fcfff5ebb22d44a15 100644
--- a/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1
+++ b/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1
@@ -84,7 +84,9 @@ thermo 50
# dump 1 all xyz 100 test_vis.xyz
-fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 5 mol3 mol4 rxn1_stp2_map
+fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
+WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
+WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp defined
dynamic group bond_react_MASTER_group defined
@@ -132,39 +134,42 @@ Per MPI rank memory allocation (min/avg/max) = 209.1 | 209.1 | 209.1 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 800 3666.3948 0.80366765 0 0
50 673.95238 -9670.9169 0.80366765 31 0
- 100 693.69241 -4696.4359 0.80366765 57 22
- 150 715.44689 -14740.892 0.80366765 77 50
- 200 721.16898 -1411.95 0.80366765 84 66
-Loop time of 107.389 on 1 procs for 200 steps with 35200 atoms
+ 100 697.22819 -4624.0512 0.80366765 57 22
+ 150 723.60507 -17175.571 0.80366765 76 48
+ 200 736.71277 -12961.963 0.80366765 84 64
+Loop time of 102.825 on 1 procs for 200 steps with 35200 atoms
-Performance: 0.161 ns/day, 149.151 hours/ns, 1.862 timesteps/s
+Performance: 0.168 ns/day, 142.812 hours/ns, 1.945 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 27.191 | 27.191 | 27.191 | 0.0 | 25.32
-Bond | 11.46 | 11.46 | 11.46 | 0.0 | 10.67
-Kspace | 4.2507 | 4.2507 | 4.2507 | 0.0 | 3.96
-Neigh | 55.544 | 55.544 | 55.544 | 0.0 | 51.72
-Comm | 0.41715 | 0.41715 | 0.41715 | 0.0 | 0.39
-Output | 0.0011044 | 0.0011044 | 0.0011044 | 0.0 | 0.00
-Modify | 8.4756 | 8.4756 | 8.4756 | 0.0 | 7.89
-Other | | 0.04897 | | | 0.05
+Pair | 27.193 | 27.193 | 27.193 | 0.0 | 26.45
+Bond | 11.324 | 11.324 | 11.324 | 0.0 | 11.01
+Kspace | 4.1878 | 4.1878 | 4.1878 | 0.0 | 4.07
+Neigh | 54.724 | 54.724 | 54.724 | 0.0 | 53.22
+Comm | 0.40662 | 0.40662 | 0.40662 | 0.0 | 0.40
+Output | 0.0011101 | 0.0011101 | 0.0011101 | 0.0 | 0.00
+Modify | 4.9422 | 4.9422 | 4.9422 | 0.0 | 4.81
+Other | | 0.04545 | | | 0.04
Nlocal: 35200 ave 35200 max 35200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 38406 ave 38406 max 38406 min
+Nghost: 38403 ave 38403 max 38403 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 6.92787e+06 ave 6.92787e+06 max 6.92787e+06 min
+Neighs: 6.9281e+06 ave 6.9281e+06 max 6.9281e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Total # of neighbors = 6927872
-Ave neighs/atom = 196.815
-Ave special neighs/atom = 9.83489
+Total # of neighbors = 6928101
+Ave neighs/atom = 196.821
+Ave special neighs/atom = 9.83727
Neighbor list builds = 200
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data
-Total wall time: 0:01:48
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:01:43
diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4 b/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4
index 992a97e77ef920433575efd080df965045460154..cc0dda60c7dcec4b775d0d5cd6cdad4f6b751124 100644
--- a/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4
+++ b/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4
@@ -84,7 +84,9 @@ thermo 50
# dump 1 all xyz 100 test_vis.xyz
-fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 5 mol3 mol4 rxn1_stp2_map
+fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
+WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
+WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp defined
dynamic group bond_react_MASTER_group defined
@@ -132,39 +134,42 @@ Per MPI rank memory allocation (min/avg/max) = 81.11 | 81.13 | 81.15 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 800 3666.3948 0.80366765 0 0
50 673.95238 -9670.9169 0.80366765 31 0
- 100 693.69241 -4696.4359 0.80366765 57 22
- 150 715.43654 -14742.205 0.80366765 77 50
- 200 721.1906 -1411.4303 0.80366765 84 66
-Loop time of 56.2311 on 4 procs for 200 steps with 35200 atoms
+ 100 697.22819 -4624.0512 0.80366765 57 22
+ 150 724.40407 -17166.729 0.80366765 76 49
+ 200 737.28582 -12968.224 0.80366765 84 65
+Loop time of 51.171 on 4 procs for 200 steps with 35200 atoms
-Performance: 0.307 ns/day, 78.099 hours/ns, 3.557 timesteps/s
-99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
+Performance: 0.338 ns/day, 71.071 hours/ns, 3.908 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 | 13.86 | 14.034 | 14.406 | 5.8 | 24.96
-Bond | 5.5592 | 5.5952 | 5.6492 | 1.4 | 9.95
-Kspace | 2.3969 | 2.7523 | 2.9203 | 12.5 | 4.89
-Neigh | 27.265 | 27.268 | 27.271 | 0.0 | 48.49
-Comm | 0.75523 | 0.77355 | 0.79381 | 1.7 | 1.38
-Output | 0.00051904 | 0.0007363 | 0.0013669 | 0.0 | 0.00
-Modify | 5.7629 | 5.7634 | 5.7641 | 0.0 | 10.25
-Other | | 0.04441 | | | 0.08
-
-Nlocal: 8800 ave 8912 max 8666 min
-Histogram: 1 0 0 1 0 0 0 0 1 1
-Nghost: 18358.8 ave 18432 max 18189 min
-Histogram: 1 0 0 0 0 0 0 0 1 2
-Neighs: 1.73197e+06 ave 1.77209e+06 max 1.68475e+06 min
+Pair | 12.926 | 13.247 | 13.493 | 6.7 | 25.89
+Bond | 5.2132 | 5.2733 | 5.3367 | 1.9 | 10.31
+Kspace | 2.3601 | 2.6534 | 3.0067 | 16.0 | 5.19
+Neigh | 25.93 | 25.934 | 25.937 | 0.1 | 50.68
+Comm | 0.73273 | 0.75464 | 0.78505 | 2.3 | 1.47
+Output | 0.00045228 | 0.00067407 | 0.0013323 | 0.0 | 0.00
+Modify | 3.2682 | 3.2686 | 3.2692 | 0.0 | 6.39
+Other | | 0.03995 | | | 0.08
+
+Nlocal: 8800 ave 8913 max 8652 min
+Histogram: 1 0 0 0 1 0 0 0 1 1
+Nghost: 18366 ave 18461 max 18190 min
+Histogram: 1 0 0 0 0 0 0 1 1 1
+Neighs: 1.73203e+06 ave 1.77261e+06 max 1.68165e+06 min
Histogram: 1 0 1 0 0 0 0 0 0 2
-Total # of neighbors = 6927873
-Ave neighs/atom = 196.815
-Ave special neighs/atom = 9.83489
+Total # of neighbors = 6928132
+Ave neighs/atom = 196.822
+Ave special neighs/atom = 9.83608
Neighbor list builds = 200
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data
-Total wall time: 0:00:57
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:52
diff --git a/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon b/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon
index 3e21f69331c46b9527f224d58b1d03ca941705a3..1f7e9c42b7b4098fd355dec8afc696e42631321c 100644
--- a/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon
+++ b/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon
@@ -33,8 +33,8 @@ thermo 50
# dump 1 all xyz 1 test_vis.xyz
fix myrxns all bond/react stabilization yes statted_grp .03 &
- react rxn1 all 1 2.9 mol1 mol2 rxn1_stp1_map &
- react rxn2 all 1 5 mol3 mol4 rxn1_stp2_map
+ react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map &
+ react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
fix 1 statted_grp nvt temp 300 300 100
diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.1 b/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.1
index a65a5306f3d8fd89ad5d6b2c4fcb757a6a90a395..344439f94c5906e1fc7417921b89434ae0a7b8b5 100644
--- a/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.1
+++ b/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.1
@@ -85,7 +85,9 @@ thermo 50
# dump 1 all xyz 1 test_vis.xyz
-fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 5 mol3 mol4 rxn1_stp2_map
+fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
+WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
+WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp defined
dynamic group bond_react_MASTER_group defined
@@ -131,235 +133,238 @@ Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.34 | 33.34 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 300 346.78165 0.0034851739 0 0
50 296.70408 -51.30066 0.0034851739 1 0
- 100 275.26011 39.120329 0.0034851739 1 1
- 150 438.68516 35.257539 0.0034851739 1 1
- 200 394.48971 15.444537 0.0034851739 1 1
- 250 356.00369 50.185792 0.0034851739 1 1
- 300 301.25816 -26.891497 0.0034851739 1 1
- 350 279.17264 12.694513 0.0034851739 1 1
- 400 248.71641 10.684558 0.0034851739 1 1
- 450 240.30602 12.963034 0.0034851739 1 1
- 500 252.71279 0.91620356 0.0034851739 1 1
- 550 300.56824 18.541436 0.0034851739 1 1
- 600 306.46441 -1.9736081 0.0034851739 1 1
- 650 336.4537 21.474831 0.0034851739 1 1
- 700 323.46217 8.486376 0.0034851739 1 1
- 750 271.87146 5.9615231 0.0034851739 1 1
- 800 268.43041 36.676068 0.0034851739 1 1
- 850 269.02683 7.6295416 0.0034851739 1 1
- 900 282.03605 -1.4688833 0.0034851739 1 1
- 950 243.69136 -22.771489 0.0034851739 1 1
- 1000 285.01348 17.925748 0.0034851739 1 1
- 1050 383.47985 0.70536985 0.0034851739 1 1
- 1100 368.97167 -4.3046933 0.0034851739 1 1
- 1150 373.64459 6.3491837 0.0034851739 1 1
- 1200 332.90575 -36.501095 0.0034851739 1 1
- 1250 314.04078 -13.382767 0.0034851739 1 1
- 1300 305.84166 4.7713641 0.0034851739 1 1
- 1350 286.22145 37.621803 0.0034851739 1 1
- 1400 265.52855 23.621002 0.0034851739 1 1
- 1450 281.807 -31.266828 0.0034851739 1 1
- 1500 275.33855 33.495565 0.0034851739 1 1
- 1550 273.04973 -22.913871 0.0034851739 1 1
- 1600 308.18478 -17.98151 0.0034851739 1 1
- 1650 333.27664 28.987529 0.0034851739 1 1
- 1700 296.16091 -1.1440455 0.0034851739 1 1
- 1750 365.75611 34.574845 0.0034851739 1 1
- 1800 292.83503 -33.199654 0.0034851739 1 1
- 1850 261.50282 42.608703 0.0034851739 1 1
- 1900 315.14188 -31.058803 0.0034851739 1 1
- 1950 335.12895 12.40597 0.0034851739 1 1
- 2000 278.08586 -5.3178633 0.0034851739 1 1
- 2050 283.23847 -3.3974302 0.0034851739 1 1
- 2100 281.38904 0.70263324 0.0034851739 1 1
- 2150 302.23197 23.372316 0.0034851739 1 1
- 2200 337.49259 -4.8716803 0.0034851739 1 1
- 2250 409.64134 -12.043721 0.0034851739 1 1
- 2300 309.21764 -21.824645 0.0034851739 1 1
- 2350 290.97879 18.690281 0.0034851739 1 1
- 2400 341.816 -16.967741 0.0034851739 1 1
- 2450 310.28034 27.375518 0.0034851739 1 1
- 2500 248.89429 17.061192 0.0034851739 1 1
- 2550 273.10927 0.10481657 0.0034851739 1 1
- 2600 289.56101 -9.7239939 0.0034851739 1 1
- 2650 298.99719 -33.140576 0.0034851739 1 1
- 2700 326.05198 -24.509827 0.0034851739 1 1
- 2750 319.20612 24.305526 0.0034851739 1 1
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+Loop time of 1.84987 on 1 procs for 10000 steps with 44 atoms
-Performance: 445.042 ns/day, 0.054 hours/ns, 5150.945 timesteps/s
-99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
+Performance: 467.059 ns/day, 0.051 hours/ns, 5405.774 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 | 0.26479 | 0.26479 | 0.26479 | 0.0 | 13.64
-Bond | 0.76875 | 0.76875 | 0.76875 | 0.0 | 39.60
-Kspace | 0.32111 | 0.32111 | 0.32111 | 0.0 | 16.54
-Neigh | 0.41333 | 0.41333 | 0.41333 | 0.0 | 21.29
-Comm | 0.025956 | 0.025956 | 0.025956 | 0.0 | 1.34
-Output | 0.0043445 | 0.0043445 | 0.0043445 | 0.0 | 0.22
-Modify | 0.12526 | 0.12526 | 0.12526 | 0.0 | 6.45
-Other | | 0.01786 | | | 0.92
+Pair | 0.26152 | 0.26152 | 0.26152 | 0.0 | 14.14
+Bond | 0.74069 | 0.74069 | 0.74069 | 0.0 | 40.04
+Kspace | 0.30505 | 0.30505 | 0.30505 | 0.0 | 16.49
+Neigh | 0.39991 | 0.39991 | 0.39991 | 0.0 | 21.62
+Comm | 0.02261 | 0.02261 | 0.02261 | 0.0 | 1.22
+Output | 0.0034585 | 0.0034585 | 0.0034585 | 0.0 | 0.19
+Modify | 0.099979 | 0.099979 | 0.099979 | 0.0 | 5.40
+Other | | 0.01666 | | | 0.90
Nlocal: 44 ave 44 max 44 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 62 ave 62 max 62 min
+Nghost: 44 ave 44 max 44 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 812 ave 812 max 812 min
+Neighs: 823 ave 823 max 823 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Total # of neighbors = 812
-Ave neighs/atom = 18.4545
+Total # of neighbors = 823
+Ave neighs/atom = 18.7045
Ave special neighs/atom = 9.77273
Neighbor list builds = 10000
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data
+
+Please see the log.cite file for references relevant to this simulation
+
Total wall time: 0:00:01
diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.4 b/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.4
index dddc9f2801e6c62482640b4bed730d57e324854b..377781f48f7091dbc910d9ce1ab0f98723abb7bb 100644
--- a/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.4
+++ b/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.4
@@ -85,7 +85,9 @@ thermo 50
# dump 1 all xyz 1 test_vis.xyz
-fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 5 mol3 mol4 rxn1_stp2_map
+fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
+WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
+WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp defined
dynamic group bond_react_MASTER_group defined
@@ -131,235 +133,238 @@ Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.69 | 34.37 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 300 346.78165 0.0034851739 0 0
50 296.70408 -51.30066 0.0034851739 1 0
- 100 275.26011 39.120329 0.0034851739 1 1
- 150 438.68516 35.257539 0.0034851739 1 1
- 200 394.48971 15.444537 0.0034851739 1 1
- 250 356.00369 50.185792 0.0034851739 1 1
- 300 301.25816 -26.891497 0.0034851739 1 1
- 350 279.17264 12.694513 0.0034851739 1 1
- 400 248.71641 10.684558 0.0034851739 1 1
- 450 240.30602 12.963034 0.0034851739 1 1
- 500 252.71279 0.91620356 0.0034851739 1 1
- 550 300.56824 18.541436 0.0034851739 1 1
- 600 306.46441 -1.9736081 0.0034851739 1 1
- 650 336.4537 21.474831 0.0034851739 1 1
- 700 323.46217 8.486376 0.0034851739 1 1
- 750 271.87146 5.9615231 0.0034851739 1 1
- 800 268.43041 36.676068 0.0034851739 1 1
- 850 269.02683 7.6295416 0.0034851739 1 1
- 900 282.03605 -1.4688833 0.0034851739 1 1
- 950 243.69136 -22.771489 0.0034851739 1 1
- 1000 285.01348 17.925748 0.0034851739 1 1
- 1050 383.47985 0.70536985 0.0034851739 1 1
- 1100 368.97167 -4.3046933 0.0034851739 1 1
- 1150 373.64459 6.3491837 0.0034851739 1 1
- 1200 332.90575 -36.501095 0.0034851739 1 1
- 1250 314.04078 -13.382767 0.0034851739 1 1
- 1300 305.84166 4.7713641 0.0034851739 1 1
- 1350 286.22145 37.621803 0.0034851739 1 1
- 1400 265.52855 23.621002 0.0034851739 1 1
- 1450 281.807 -31.266828 0.0034851739 1 1
- 1500 275.33855 33.495565 0.0034851739 1 1
- 1550 273.04973 -22.913871 0.0034851739 1 1
- 1600 308.18478 -17.98151 0.0034851739 1 1
- 1650 333.27664 28.987529 0.0034851739 1 1
- 1700 296.16091 -1.1440455 0.0034851739 1 1
- 1750 365.75611 34.574845 0.0034851739 1 1
- 1800 292.83503 -33.199654 0.0034851739 1 1
- 1850 261.50282 42.608703 0.0034851739 1 1
- 1900 315.14188 -31.058803 0.0034851739 1 1
- 1950 335.12895 12.40597 0.0034851739 1 1
- 2000 278.08586 -5.3178633 0.0034851739 1 1
- 2050 283.23847 -3.3974302 0.0034851739 1 1
- 2100 281.38904 0.70263324 0.0034851739 1 1
- 2150 302.23197 23.372316 0.0034851739 1 1
- 2200 337.49259 -4.8716803 0.0034851739 1 1
- 2250 409.64134 -12.043721 0.0034851739 1 1
- 2300 309.21764 -21.824645 0.0034851739 1 1
- 2350 290.97879 18.690281 0.0034851739 1 1
- 2400 341.816 -16.967741 0.0034851739 1 1
- 2450 310.28034 27.375518 0.0034851739 1 1
- 2500 248.89429 17.061192 0.0034851739 1 1
- 2550 273.10927 0.1048166 0.0034851739 1 1
- 2600 289.56101 -9.7239939 0.0034851739 1 1
- 2650 298.99719 -33.140576 0.0034851739 1 1
- 2700 326.05198 -24.509827 0.0034851739 1 1
- 2750 319.20612 24.305526 0.0034851739 1 1
- 2800 304.8715 -15.076941 0.0034851739 1 1
- 2850 374.38923 2.0874883 0.0034851739 1 1
- 2900 354.01554 -20.595102 0.0034851739 1 1
- 2950 289.89296 48.39731 0.0034851739 1 1
- 3000 312.10013 -8.5105996 0.0034851739 1 1
- 3050 296.97004 -31.008446 0.0034851739 1 1
- 3100 251.72228 35.710197 0.0034851739 1 1
- 3150 315.35895 -43.331536 0.0034851739 1 1
- 3200 334.67773 13.331058 0.0034851739 1 1
- 3250 308.1669 37.236121 0.0034851739 1 1
- 3300 329.47601 30.798598 0.0034851739 1 1
- 3350 299.40055 2.0785585 0.0034851739 1 1
- 3400 272.41031 32.744921 0.0034851739 1 1
- 3450 279.34594 -26.181793 0.0034851739 1 1
- 3500 288.89969 8.935052 0.0034851739 1 1
- 3550 253.4967 9.724471 0.0034851739 1 1
- 3600 294.83266 19.33305 0.0034851739 1 1
- 3650 290.23794 -5.493907 0.0034851739 1 1
- 3700 332.5222 -29.83423 0.0034851739 1 1
- 3750 364.63024 20.706191 0.0034851739 1 1
- 3800 295.3842 -6.9434003 0.0034851739 1 1
- 3850 346.84424 37.796066 0.0034851739 1 1
- 3900 265.67286 -0.3162804 0.0034851739 1 1
- 3950 260.455 -2.2571901 0.0034851739 1 1
- 4000 259.82636 -2.2286207 0.0034851739 1 1
- 4050 257.79848 24.520293 0.0034851739 1 1
- 4100 295.58626 -0.42318895 0.0034851739 1 1
- 4150 265.81352 -49.092436 0.0034851739 1 1
- 4200 302.10333 51.715258 0.0034851739 1 1
- 4250 258.98448 -4.8516657 0.0034851739 1 1
- 4300 327.83401 33.717283 0.0034851739 1 1
- 4350 311.59571 23.580382 0.0034851739 1 1
- 4400 300.64237 -31.866661 0.0034851739 1 1
- 4450 294.15642 -0.11927262 0.0034851739 1 1
- 4500 299.83605 -17.560872 0.0034851739 1 1
- 4550 326.83265 32.818481 0.0034851739 1 1
- 4600 260.39068 -8.0567907 0.0034851739 1 1
- 4650 247.93553 19.462991 0.0034851739 1 1
- 4700 214.22252 -34.118304 0.0034851739 1 1
- 4750 203.15329 27.356204 0.0034851739 1 1
- 4800 257.761 -10.407986 0.0034851739 1 1
- 4850 307.1923 11.711008 0.0034851739 1 1
- 4900 319.00942 4.7808342 0.0034851739 1 1
- 4950 282.2399 24.996151 0.0034851739 1 1
- 5000 311.53284 -3.0012669 0.0034851739 1 1
- 5050 317.58213 32.56782 0.0034851739 1 1
- 5100 267.51502 -47.695103 0.0034851739 1 1
- 5150 260.19047 29.046394 0.0034851739 1 1
- 5200 239.8355 -5.4890372 0.0034851739 1 1
- 5250 234.88522 -18.172649 0.0034851739 1 1
- 5300 236.43278 -39.062111 0.0034851739 1 1
- 5350 280.90083 -2.6932604 0.0034851739 1 1
- 5400 316.65269 23.071363 0.0034851739 1 1
- 5450 345.6322 19.573305 0.0034851739 1 1
- 5500 384.57334 41.50729 0.0034851739 1 1
- 5550 317.14286 9.6992981 0.0034851739 1 1
- 5600 279.93246 -12.076859 0.0034851739 1 1
- 5650 268.06471 1.6196502 0.0034851739 1 1
- 5700 271.85714 -40.378489 0.0034851739 1 1
- 5750 313.88361 10.722652 0.0034851739 1 1
- 5800 281.54499 31.914883 0.0034851739 1 1
- 5850 293.34819 -8.3155887 0.0034851739 1 1
- 5900 249.25215 -17.307228 0.0034851739 1 1
- 5950 268.18645 -4.7223601 0.0034851739 1 1
- 6000 302.99402 -52.615432 0.0034851739 1 1
- 6050 314.57946 34.513152 0.0034851739 1 1
- 6100 345.70342 30.33474 0.0034851739 1 1
- 6150 316.59329 31.862566 0.0034851739 1 1
- 6200 317.85341 -32.23511 0.0034851739 1 1
- 6250 282.97674 0.29367434 0.0034851739 1 1
- 6300 267.91823 19.265617 0.0034851739 1 1
- 6350 226.2098 -13.093573 0.0034851739 1 1
- 6400 307.73307 17.439662 0.0034851739 1 1
- 6450 292.16311 -23.275251 0.0034851739 1 1
- 6500 335.05972 26.936588 0.0034851739 1 1
- 6550 380.7351 19.532324 0.0034851739 1 1
- 6600 373.01041 30.879146 0.0034851739 1 1
- 6650 335.37897 -2.1766711 0.0034851739 1 1
- 6700 298.94275 -10.578361 0.0034851739 1 1
- 6750 255.11449 -50.575851 0.0034851739 1 1
- 6800 222.87598 3.0488985 0.0034851739 1 1
- 6850 268.57268 -43.676136 0.0034851739 1 1
- 6900 260.30442 4.7484508 0.0034851739 1 1
- 6950 289.15739 31.622589 0.0034851739 1 1
- 7000 289.11733 21.636361 0.0034851739 1 1
- 7050 361.08905 22.442487 0.0034851739 1 1
- 7100 368.95006 4.8393179 0.0034851739 1 1
- 7150 331.47878 -36.202032 0.0034851739 1 1
- 7200 304.72518 13.982604 0.0034851739 1 1
- 7250 284.0996 0.53900966 0.0034851739 1 1
- 7300 269.17156 -41.572215 0.0034851739 1 1
- 7350 222.06563 25.56579 0.0034851739 1 1
- 7400 304.09479 15.48238 0.0034851739 1 1
- 7450 298.79046 -7.4369454 0.0034851739 1 1
- 7500 328.78217 14.672853 0.0034851739 1 1
- 7550 347.06589 -37.168123 0.0034851739 1 1
- 7600 362.84157 20.514912 0.0034851739 1 1
- 7650 347.15916 2.3477485 0.0034851739 1 1
- 7700 262.09822 33.901831 0.0034851739 1 1
- 7750 275.85921 -33.536059 0.0034851739 1 1
- 7800 281.16159 -18.288414 0.0034851739 1 1
- 7850 264.83553 -30.566284 0.0034851739 1 1
- 7900 257.35224 -35.087067 0.0034851739 1 1
- 7950 286.30756 26.586163 0.0034851739 1 1
- 8000 248.38175 15.601961 0.0034851739 1 1
- 8050 292.59171 28.784541 0.0034851739 1 1
- 8100 312.52852 0.87995053 0.0034851739 1 1
- 8150 285.62346 -15.337252 0.0034851739 1 1
- 8200 292.24175 -38.192576 0.0034851739 1 1
- 8250 321.61618 -19.030398 0.0034851739 1 1
- 8300 319.42189 55.078305 0.0034851739 1 1
- 8350 308.00357 32.050518 0.0034851739 1 1
- 8400 345.68186 8.7983733 0.0034851739 1 1
- 8450 358.00849 12.434592 0.0034851739 1 1
- 8500 370.14359 4.2184721 0.0034851739 1 1
- 8550 360.6511 12.580836 0.0034851739 1 1
- 8600 290.04938 -4.8422589 0.0034851739 1 1
- 8650 297.95745 -5.3185591 0.0034851739 1 1
- 8700 286.54284 -31.490479 0.0034851739 1 1
- 8750 308.08791 19.24417 0.0034851739 1 1
- 8800 231.72534 12.262217 0.0034851739 1 1
- 8850 329.2349 -8.9133933 0.0034851739 1 1
- 8900 287.64023 10.525164 0.0034851739 1 1
- 8950 341.08296 2.80127 0.0034851739 1 1
- 9000 403.71266 17.88418 0.0034851739 1 1
- 9050 348.95132 -4.5813611 0.0034851739 1 1
- 9100 307.98322 16.707575 0.0034851739 1 1
- 9150 276.75719 -35.563923 0.0034851739 1 1
- 9200 230.15547 3.8091656 0.0034851739 1 1
- 9250 264.64479 -20.97438 0.0034851739 1 1
- 9300 285.70467 13.881735 0.0034851739 1 1
- 9350 297.515 13.599319 0.0034851739 1 1
- 9400 341.45203 -28.494544 0.0034851739 1 1
- 9450 319.29703 -27.907344 0.0034851739 1 1
- 9500 332.50473 4.9891138 0.0034851739 1 1
- 9550 293.10499 -8.3244772 0.0034851739 1 1
- 9600 255.31174 2.2568315 0.0034851739 1 1
- 9650 250.01932 5.7005159 0.0034851739 1 1
- 9700 278.37409 -8.5970424 0.0034851739 1 1
- 9750 294.86737 17.686447 0.0034851739 1 1
- 9800 277.07345 -2.0856886 0.0034851739 1 1
- 9850 295.54707 2.8365471 0.0034851739 1 1
- 9900 311.51074 29.885116 0.0034851739 1 1
- 9950 296.01363 12.206068 0.0034851739 1 1
- 10000 341.35187 -3.0045464 0.0034851739 1 1
-Loop time of 3.64332 on 4 procs for 10000 steps with 44 atoms
+ 100 274.25324 46.715512 0.0034851739 1 1
+ 150 471.61579 31.321598 0.0034851739 1 1
+ 200 362.87766 42.061118 0.0034851739 1 1
+ 250 367.58058 65.303109 0.0034851739 1 1
+ 300 372.38236 -52.421725 0.0034851739 1 1
+ 350 297.69957 17.869945 0.0034851739 1 1
+ 400 258.30433 49.19156 0.0034851739 1 1
+ 450 253.34384 -5.8162637 0.0034851739 1 1
+ 500 269.96465 -43.337517 0.0034851739 1 1
+ 550 303.23718 10.180246 0.0034851739 1 1
+ 600 329.59579 -48.97461 0.0034851739 1 1
+ 650 350.42568 50.983183 0.0034851739 1 1
+ 700 342.03272 35.43465 0.0034851739 1 1
+ 750 269.23405 -41.873166 0.0034851739 1 1
+ 800 245.15025 13.953092 0.0034851739 1 1
+ 850 257.85421 -3.1492141 0.0034851739 1 1
+ 900 316.15644 7.7798301 0.0034851739 1 1
+ 950 299.9124 -15.77014 0.0034851739 1 1
+ 1000 302.89968 -17.049693 0.0034851739 1 1
+ 1050 308.91651 71.84632 0.0034851739 1 1
+ 1100 348.43932 -18.742012 0.0034851739 1 1
+ 1150 309.03036 50.536311 0.0034851739 1 1
+ 1200 318.9761 -16.905746 0.0034851739 1 1
+ 1250 320.42806 -0.057975092 0.0034851739 1 1
+ 1300 289.7824 18.200772 0.0034851739 1 1
+ 1350 284.79836 -9.1978427 0.0034851739 1 1
+ 1400 325.43292 42.082833 0.0034851739 1 1
+ 1450 261.5041 -37.823325 0.0034851739 1 1
+ 1500 298.88723 -5.1647385 0.0034851739 1 1
+ 1550 291.37403 -7.7764201 0.0034851739 1 1
+ 1600 293.83475 22.2458 0.0034851739 1 1
+ 1650 293.80611 24.202512 0.0034851739 1 1
+ 1700 291.70205 -23.397884 0.0034851739 1 1
+ 1750 292.32437 -10.671214 0.0034851739 1 1
+ 1800 302.01367 -11.671025 0.0034851739 1 1
+ 1850 322.1651 24.438331 0.0034851739 1 1
+ 1900 310.45076 45.343592 0.0034851739 1 1
+ 1950 325.91745 -19.847809 0.0034851739 1 1
+ 2000 276.89662 63.387098 0.0034851739 1 1
+ 2050 311.33783 -24.683247 0.0034851739 1 1
+ 2100 346.2336 -27.526891 0.0034851739 1 1
+ 2150 345.30604 -15.722411 0.0034851739 1 1
+ 2200 346.7718 -17.857633 0.0034851739 1 1
+ 2250 304.28676 -1.9965581 0.0034851739 1 1
+ 2300 322.56372 -31.786868 0.0034851739 1 1
+ 2350 282.64326 6.1982735 0.0034851739 1 1
+ 2400 286.65759 -63.207781 0.0034851739 1 1
+ 2450 257.05528 32.931491 0.0034851739 1 1
+ 2500 283.64386 26.912373 0.0034851739 1 1
+ 2550 299.54005 27.277039 0.0034851739 1 1
+ 2600 283.92503 14.660972 0.0034851739 1 1
+ 2650 321.93453 -18.977358 0.0034851739 1 1
+ 2700 376.7189 31.826935 0.0034851739 1 1
+ 2750 372.20075 -32.821697 0.0034851739 1 1
+ 2800 361.40604 83.035183 0.0034851739 1 1
+ 2850 332.27269 -23.927452 0.0034851739 1 1
+ 2900 331.14638 -0.12328446 0.0034851739 1 1
+ 2950 303.67489 -24.078857 0.0034851739 1 1
+ 3000 311.40462 21.563537 0.0034851739 1 1
+ 3050 284.72849 -23.849667 0.0034851739 1 1
+ 3100 303.48477 39.347763 0.0034851739 1 1
+ 3150 264.2739 -0.22299878 0.0034851739 1 1
+ 3200 300.03351 31.545323 0.0034851739 1 1
+ 3250 288.56663 5.7225229 0.0034851739 1 1
+ 3300 200.13238 -31.239655 0.0034851739 1 1
+ 3350 231.32512 16.631728 0.0034851739 1 1
+ 3400 260.57402 2.1717992 0.0034851739 1 1
+ 3450 301.47128 -42.210623 0.0034851739 1 1
+ 3500 321.77414 40.074365 0.0034851739 1 1
+ 3550 353.21858 28.387783 0.0034851739 1 1
+ 3600 331.45989 -57.800858 0.0034851739 1 1
+ 3650 303.88123 44.86596 0.0034851739 1 1
+ 3700 329.73833 -0.8061567 0.0034851739 1 1
+ 3750 297.55588 -0.49626022 0.0034851739 1 1
+ 3800 286.38794 -10.010003 0.0034851739 1 1
+ 3850 290.17417 -43.51187 0.0034851739 1 1
+ 3900 247.88933 51.23735 0.0034851739 1 1
+ 3950 332.31324 -18.194985 0.0034851739 1 1
+ 4000 325.56802 18.402825 0.0034851739 1 1
+ 4050 338.37594 36.430977 0.0034851739 1 1
+ 4100 370.95478 39.290285 0.0034851739 1 1
+ 4150 348.47859 -7.0779683 0.0034851739 1 1
+ 4200 241.30632 -33.371789 0.0034851739 1 1
+ 4250 242.17258 -9.9861962 0.0034851739 1 1
+ 4300 300.85311 -7.924429 0.0034851739 1 1
+ 4350 273.15684 -21.257282 0.0034851739 1 1
+ 4400 305.77464 -5.8720712 0.0034851739 1 1
+ 4450 314.97697 45.037299 0.0034851739 1 1
+ 4500 310.77723 16.958771 0.0034851739 1 1
+ 4550 302.17421 12.156862 0.0034851739 1 1
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+ 4650 270.86805 -13.767907 0.0034851739 1 1
+ 4700 249.81731 -31.197484 0.0034851739 1 1
+ 4750 285.86481 -9.8916332 0.0034851739 1 1
+ 4800 233.98321 7.1338518 0.0034851739 1 1
+ 4850 302.60551 49.262886 0.0034851739 1 1
+ 4900 316.55055 34.663238 0.0034851739 1 1
+ 4950 357.32741 11.583013 0.0034851739 1 1
+ 5000 400.21044 -8.1780861 0.0034851739 1 1
+ 5050 390.01845 -20.490268 0.0034851739 1 1
+ 5100 378.84249 -41.328772 0.0034851739 1 1
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+ 5300 277.84991 40.682283 0.0034851739 1 1
+ 5350 302.92834 9.1989644 0.0034851739 1 1
+ 5400 283.71964 -1.6583895 0.0034851739 1 1
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+ 5550 369.51272 21.691639 0.0034851739 1 1
+ 5600 372.69786 -38.679919 0.0034851739 1 1
+ 5650 327.41256 11.352201 0.0034851739 1 1
+ 5700 278.9861 -23.82728 0.0034851739 1 1
+ 5750 308.30037 -20.756238 0.0034851739 1 1
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+ 5850 322.9786 -10.731862 0.0034851739 1 1
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+ 5950 287.17515 -36.780057 0.0034851739 1 1
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+ 6050 314.25411 15.99272 0.0034851739 1 1
+ 6100 313.86572 3.4344108 0.0034851739 1 1
+ 6150 325.64197 32.39212 0.0034851739 1 1
+ 6200 367.4298 -27.161154 0.0034851739 1 1
+ 6250 369.30937 39.020881 0.0034851739 1 1
+ 6300 328.92245 -23.175612 0.0034851739 1 1
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+ 6450 265.66574 2.4049735 0.0034851739 1 1
+ 6500 249.3592 13.420453 0.0034851739 1 1
+ 6550 294.5367 10.856753 0.0034851739 1 1
+ 6600 308.20246 18.992923 0.0034851739 1 1
+ 6650 305.43756 -49.57151 0.0034851739 1 1
+ 6700 320.27395 11.339101 0.0034851739 1 1
+ 6750 321.7875 -23.463361 0.0034851739 1 1
+ 6800 303.40316 7.6256997 0.0034851739 1 1
+ 6850 297.18652 51.52186 0.0034851739 1 1
+ 6900 284.19084 -8.496294 0.0034851739 1 1
+ 6950 331.04173 13.227745 0.0034851739 1 1
+ 7000 311.38027 -43.26105 0.0034851739 1 1
+ 7050 286.82046 -14.171194 0.0034851739 1 1
+ 7100 302.81691 12.058085 0.0034851739 1 1
+ 7150 297.18018 -43.110658 0.0034851739 1 1
+ 7200 332.46131 26.051496 0.0034851739 1 1
+ 7250 262.72288 41.161451 0.0034851739 1 1
+ 7300 250.62739 -23.440907 0.0034851739 1 1
+ 7350 296.92141 35.869216 0.0034851739 1 1
+ 7400 245.06807 -13.467896 0.0034851739 1 1
+ 7450 272.2659 -23.292836 0.0034851739 1 1
+ 7500 209.05776 13.888665 0.0034851739 1 1
+ 7550 255.03716 4.9662624 0.0034851739 1 1
+ 7600 312.26011 -37.350427 0.0034851739 1 1
+ 7650 305.5823 55.208039 0.0034851739 1 1
+ 7700 325.13382 -18.370791 0.0034851739 1 1
+ 7750 363.24898 -22.473126 0.0034851739 1 1
+ 7800 350.19254 26.792307 0.0034851739 1 1
+ 7850 271.76418 -17.843445 0.0034851739 1 1
+ 7900 272.70301 -11.709349 0.0034851739 1 1
+ 7950 298.5993 -12.736235 0.0034851739 1 1
+ 8000 274.52611 49.657345 0.0034851739 1 1
+ 8050 304.73711 -0.52485689 0.0034851739 1 1
+ 8100 328.29239 -39.901891 0.0034851739 1 1
+ 8150 406.52096 2.8669076 0.0034851739 1 1
+ 8200 332.17309 -51.168754 0.0034851739 1 1
+ 8250 354.68419 53.003157 0.0034851739 1 1
+ 8300 337.28934 20.766408 0.0034851739 1 1
+ 8350 361.81133 -54.159227 0.0034851739 1 1
+ 8400 305.59597 24.011667 0.0034851739 1 1
+ 8450 303.25823 4.423341 0.0034851739 1 1
+ 8500 253.50747 -11.026949 0.0034851739 1 1
+ 8550 277.13504 23.204625 0.0034851739 1 1
+ 8600 291.40211 -22.253861 0.0034851739 1 1
+ 8650 307.93765 32.14162 0.0034851739 1 1
+ 8700 309.1529 0.36279434 0.0034851739 1 1
+ 8750 355.10326 11.677219 0.0034851739 1 1
+ 8800 330.21328 19.235269 0.0034851739 1 1
+ 8850 241.29109 21.707386 0.0034851739 1 1
+ 8900 319.15363 -60.010115 0.0034851739 1 1
+ 8950 308.88552 -57.637014 0.0034851739 1 1
+ 9000 272.22373 51.15837 0.0034851739 1 1
+ 9050 248.84947 7.3390565 0.0034851739 1 1
+ 9100 221.91564 48.387079 0.0034851739 1 1
+ 9150 298.03506 2.9058639 0.0034851739 1 1
+ 9200 274.25114 -24.597819 0.0034851739 1 1
+ 9250 334.08373 5.1079577 0.0034851739 1 1
+ 9300 383.07285 -23.274763 0.0034851739 1 1
+ 9350 335.00581 20.94212 0.0034851739 1 1
+ 9400 309.23862 34.074744 0.0034851739 1 1
+ 9450 312.62262 -28.468057 0.0034851739 1 1
+ 9500 324.54274 2.851136 0.0034851739 1 1
+ 9550 313.32781 22.468182 0.0034851739 1 1
+ 9600 269.04372 4.064934 0.0034851739 1 1
+ 9650 270.98476 -21.520127 0.0034851739 1 1
+ 9700 236.8736 16.250728 0.0034851739 1 1
+ 9750 333.94686 1.6864148 0.0034851739 1 1
+ 9800 330.91875 12.150018 0.0034851739 1 1
+ 9850 343.8603 25.338853 0.0034851739 1 1
+ 9900 330.93364 -28.292992 0.0034851739 1 1
+ 9950 291.25518 25.795948 0.0034851739 1 1
+ 10000 319.25565 25.323846 0.0034851739 1 1
+Loop time of 3.55353 on 4 procs for 10000 steps with 44 atoms
-Performance: 237.146 ns/day, 0.101 hours/ns, 2744.751 timesteps/s
-94.5% CPU use with 4 MPI tasks x 1 OpenMP threads
+Performance: 243.139 ns/day, 0.099 hours/ns, 2814.105 timesteps/s
+93.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.0029962 | 0.10426 | 0.34564 | 43.9 | 2.86
-Bond | 0.005929 | 0.29803 | 0.95305 | 71.2 | 8.18
-Kspace | 0.83969 | 1.5992 | 1.9344 | 35.6 | 43.89
-Neigh | 0.65468 | 0.66443 | 0.67431 | 0.9 | 18.24
-Comm | 0.1727 | 0.23754 | 0.2745 | 8.0 | 6.52
-Output | 0.0048738 | 0.010774 | 0.028434 | 9.8 | 0.30
-Modify | 0.62478 | 0.70376 | 0.779 | 6.5 | 19.32
-Other | | 0.02531 | | | 0.69
+Pair | 0.0030422 | 0.10454 | 0.35211 | 44.8 | 2.94
+Bond | 0.0063896 | 0.29222 | 0.94356 | 71.3 | 8.22
+Kspace | 0.88508 | 1.6486 | 1.979 | 35.1 | 46.39
+Neigh | 0.61154 | 0.62212 | 0.63307 | 1.0 | 17.51
+Comm | 0.18944 | 0.24549 | 0.29196 | 7.9 | 6.91
+Output | 0.0050066 | 0.011804 | 0.032134 | 10.8 | 0.33
+Modify | 0.52282 | 0.60522 | 0.69588 | 7.9 | 17.03
+Other | | 0.02359 | | | 0.66
-Nlocal: 11 ave 40 max 0 min
-Histogram: 2 1 0 0 0 0 0 0 0 1
-Nghost: 36 ave 47 max 7 min
+Nlocal: 11 ave 44 max 0 min
+Histogram: 3 0 0 0 0 0 0 0 0 1
+Nghost: 33 ave 44 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 3
-Neighs: 203 ave 809 max 0 min
+Neighs: 205.75 ave 823 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
-Total # of neighbors = 812
-Ave neighs/atom = 18.4545
+Total # of neighbors = 823
+Ave neighs/atom = 18.7045
Ave special neighs/atom = 9.77273
Neighbor list builds = 10000
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data
+
+Please see the log.cite file for references relevant to this simulation
+
Total wall time: 0:00:03
diff --git a/src/USER-MISC/fix_bond_react.cpp b/src/USER-MISC/fix_bond_react.cpp
index b3c92eed67354745665760ee5b0f8bb29b68b9ef..86da8a0c4fb306297f2cbdac9575e3cd32ec1dc9 100644
--- a/src/USER-MISC/fix_bond_react.cpp
+++ b/src/USER-MISC/fix_bond_react.cpp
@@ -43,6 +43,17 @@ Contributing Author: Jacob Gissinger (jacob.gissinger@colorado.edu)
using namespace LAMMPS_NS;
using namespace FixConst;
+static const char cite_fix_bond_react[] =
+ "fix bond/react:\n\n"
+ "@Article{Gissinger17,\n"
+ " author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},\n"
+ " title = {Modeling chemical reactions in classical molecular dynamics simulations},\n"
+ " journal = {Polymer},\n"
+ " year = 2017,\n"
+ " volume = 128,\n"
+ " pages = {211--217}\n"
+ "}\n\n";
+
#define BIG 1.0e20
#define DELTA 16
#define MAXLINE 256
@@ -62,6 +73,8 @@ enum{ACCEPT,REJECT,PROCEED,CONTINUE,GUESSFAIL,RESTORE};
FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
+ if (lmp->citeme) lmp->citeme->add(cite_fix_bond_react);
+
fix1 = NULL;
fix2 = NULL;
@@ -71,7 +84,6 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
MPI_Comm_size(world,&nprocs);
attempted_rxn = 0;
- ghostcheck_flag = 0;
force_reneighbor = 1;
next_reneighbor = -1;
vector_flag = 1;
@@ -127,7 +139,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
// this looks excessive
// the price of vectorization (all reactions in one command)?
memory->create(nevery,nreacts,"bond/react:nevery");
- memory->create(cutsq,nreacts,"bond/react:cutsq");
+ memory->create(cutsq,nreacts,2,"bond/react:cutsq");
memory->create(unreacted_mol,nreacts,"bond/react:unreacted_mol");
memory->create(reacted_mol,nreacts,"bond/react:reacted_mol");
memory->create(fraction,nreacts,"bond/react:fraction");
@@ -138,6 +150,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
memory->create(jatomtype,nreacts,"bond/react:jatomtype");
memory->create(ibonding,nreacts,"bond/react:ibonding");
memory->create(jbonding,nreacts,"bond/react:jbonding");
+ memory->create(closeneigh,nreacts,"bond/react:closeneigh");
memory->create(groupbits,nreacts,"bond/react:groupbits");
memory->create(reaction_count,nreacts,"bond/react:reaction_count");
memory->create(local_rxn_count,nreacts,"bond/react:local_rxn_count");
@@ -176,7 +189,11 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
double cutoff = force->numeric(FLERR,arg[iarg++]);
if (cutoff < 0.0) error->all(FLERR,"Illegal fix bond/react command 0.5");
- cutsq[rxn] = cutoff*cutoff;
+ cutsq[rxn][0] = cutoff*cutoff;
+
+ cutoff = force->numeric(FLERR,arg[iarg++]);
+ if (cutoff < 0.0) error->all(FLERR,"Illegal fix bond/react command 0.55");
+ cutsq[rxn][1] = cutoff*cutoff;
unreacted_mol[rxn] = atom->find_molecule(arg[iarg++]);
if (unreacted_mol[rxn] == -1) error->all(FLERR,"Unreacted molecule template ID for "
@@ -241,6 +258,23 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
if (atom->molecular != 1)
error->all(FLERR,"Cannot use fix bond/react with non-molecular systems");
+ // check if bonding atoms are 1-2, 1-3, or 1-4 bonded neighbors
+ // if so, we don't need non-bonded neighbor list
+ for (int myrxn = 0; myrxn < nreacts; myrxn++) {
+ closeneigh[myrxn] = -1; // indicates will search non-bonded neighbors
+ onemol = atom->molecules[unreacted_mol[myrxn]];
+ for (int k = 0; k < onemol->nspecial[ibonding[myrxn]-1][2]; k++) {
+ if (onemol->special[ibonding[myrxn]-1][k] == jbonding[myrxn]) {
+ closeneigh[myrxn] = 2; // index for 1-4 neighbor
+ if (k < onemol->nspecial[ibonding[myrxn]-1][1])
+ closeneigh[myrxn] = 1; // index for 1-3 neighbor
+ if (k < onemol->nspecial[ibonding[myrxn]-1][0])
+ closeneigh[myrxn] = 0; // index for 1-2 neighbor
+ break;
+ }
+ }
+ }
+
// initialize Marsaglia RNG with processor-unique seed
random = new class RanMars*[nreacts];
@@ -259,6 +293,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
nmax = 0;
partner = finalpartner = NULL;
distsq = NULL;
+ probability = NULL;
maxcreate = 0;
created = NULL;
local_ncreate = NULL;
@@ -302,6 +337,7 @@ FixBondReact::~FixBondReact()
memory->destroy(local_ncreate);
memory->destroy(ncreate);
memory->destroy(distsq);
+ memory->destroy(probability);
memory->destroy(created);
memory->destroy(edge);
memory->destroy(equivalences);
@@ -320,6 +356,7 @@ FixBondReact::~FixBondReact()
memory->destroy(jatomtype);
memory->destroy(ibonding);
memory->destroy(jbonding);
+ memory->destroy(closeneigh);
memory->destroy(groupbits);
memory->destroy(reaction_count);
memory->destroy(local_rxn_count);
@@ -372,7 +409,7 @@ it will have the name 'i_limit_tags' and will be intitialized to 0 (not in group
void FixBondReact::post_constructor()
{
- //let's add the limit_tags per-atom property fix
+ // let's add the limit_tags per-atom property fix
int len = strlen("per_atom_props") + 1;
id_fix2 = new char[len];
strcpy(id_fix2,"per_atom_props");
@@ -521,7 +558,7 @@ void FixBondReact::init()
// check cutoff for iatomtype,jatomtype
for (int i = 0; i < nreacts; i++) {
- if (force->pair == NULL || cutsq[i] > force->pair->cutsq[iatomtype[i]][jatomtype[i]])
+ if (force->pair == NULL || cutsq[i][1] > force->pair->cutsq[iatomtype[i]][jatomtype[i]])
error->all(FLERR,"Fix bond/react cutoff is longer than pairwise cutoff");
}
@@ -548,10 +585,6 @@ void FixBondReact::init_list(int id, NeighList *ptr)
void FixBondReact::post_integrate()
{
- int inum,jnum,itype,jtype,possible;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *ilist,*jlist,*numneigh,**firstneigh;
-
// check if any reactions could occur on this timestep
int nevery_check = 1;
for (int i = 0; i < nreacts; i++) {
@@ -578,7 +611,6 @@ void FixBondReact::post_integrate()
comm->forward_comm();
// resize bond partner list and initialize it
- // probability array overlays distsq array
// needs to be atom->nmax in length
if (atom->nmax > nmax) {
@@ -587,13 +619,14 @@ void FixBondReact::post_integrate()
memory->destroy(distsq);
memory->destroy(local_ncreate);
memory->destroy(ncreate);
+ memory->destroy(probability);
nmax = atom->nmax;
memory->create(partner,nmax,"bond/react:partner");
memory->create(finalpartner,nmax,"bond/react:finalpartner");
- memory->create(distsq,nmax,"bond/react:distsq");
+ memory->create(distsq,nmax,2,"bond/react:distsq");
memory->create(local_ncreate,nreacts,"bond/react:local_ncreate");
memory->create(ncreate,nreacts,"bond/react:ncreate");
- probability = distsq;
+ memory->create(probability,nmax,"bond/react:probability");
}
// reset create counts
@@ -605,129 +638,28 @@ void FixBondReact::post_integrate()
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
- // NOTE: this might be faster if we remembered neighbor distances from
- // previous timestep and used those --JG
-
// loop over neighbors of my atoms
// each atom sets one closest eligible partner atom ID to bond with
- double **x = atom->x;
tagint *tag = atom->tag;
- int **nspecial = atom->nspecial;
- tagint **special = atom->special;
- int *mask = atom->mask;
int *type = atom->type;
neighbor->build_one(list,1);
- inum = list->inum;
- ilist = list->ilist;
- numneigh = list->numneigh;
- firstneigh = list->firstneigh;
- // per-atom property indicating if in bond/react master group
- int flag;
- int index1 = atom->find_custom("limit_tags",flag);
- int *i_limit_tags = atom->ivector[index1];
-
- int i,j;
+ int j;
- for (int myrxn = 0; myrxn < nreacts; myrxn++) {
+ for (rxnID = 0; rxnID < nreacts; rxnID++) {
for (int ii = 0; ii < nall; ii++) {
partner[ii] = 0;
finalpartner[ii] = 0;
- distsq[ii] = BIG;
+ distsq[ii][0] = 0.0;
+ distsq[ii][1] = BIG;
}
- for (int ii = 0; ii < inum; ii++) { // inum vs nlocal
- i = ilist[ii];
- if (!(mask[i] & groupbits[myrxn])) continue;
- if (i_limit_tags[i] != 0) continue;
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
- jlist = firstneigh[i];
- jnum = numneigh[i];
-
- for (int jj = 0; jj < jnum; jj++) {
- j = jlist[jj];
- j &= NEIGHMASK;
-
- if (!(mask[j] & groupbits[myrxn])) {
- continue;
- }
-
- if (i_limit_tags[j] != 0) {
- continue;
- }
-
- jtype = type[j];
- possible = 0;
-
- if (itype == iatomtype[myrxn] && jtype == jatomtype[myrxn]) {
- possible = 1;
- } else if (itype == jatomtype[myrxn] && jtype == iatomtype[myrxn]) {
- possible = 1;
- }
-
- if (possible == 0) continue;
-
- for (int k = 0; k < nspecial[i][0]; k++)
- if (special[i][k] == tag[j]) possible = 0;
- if (!possible) continue;
-
- // NOTE(for below): certain neighbor list settings prevent 3-cycles anyway!
- // e.g., in my examples, must use kspace command to include 1-3 neighbors for consideration here
-
- // do not allow a three-membered ring to be created (by the new bond)
- // check 1-3 neighbors of atom I
- for (int k = nspecial[i][0]; k < nspecial[i][1]; k++)
- if (special[i][k] == tag[j]) possible = 0;
- if (possible == 0) {
- continue;
- }
-
- // do not allow a four-membered ring to be created (by the new bond)
- // check 1-4 neighbors of atom I -> probably make an option
-
- /*
- for (k = nspecial[i][1]; k < nspecial[i][2]; k++)
- if (special[i][k] == tag[j]) {
- possible = 0;
- }
- if (possible == 0) continue;
- */
-
- // do not allow 5 membered rings -> probably make this an option
-
- /*
- for (k = nspecial[i][1]; k < nspecial[i][2]; k++) {
- for (m = nspecial[atom->map(special[i][k])][1]; m < nspecial[atom->map(special[i][k])][2]; m++) {
- if (special[atom->map(special[i][k])][m] == tag[j]) possible = 0;
- / }
- }
- if (possible == 0) continue;
- */
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq >= cutsq[myrxn]) {
- continue;
- }
- if (rsq < distsq[i]) {
- partner[i] = tag[j];
- distsq[i] = rsq;
- }
- if (rsq < distsq[j]) {
- partner[j] = tag[i];
- distsq[j] = rsq;
- }
- }
- }
+ // fork between far and close_partner here
+ if (closeneigh[rxnID] < 0) far_partner();
+ else close_partner();
// reverse comm of distsq and partner
// not needed if newton_pair off since I,J pair was seen by both procs
@@ -739,9 +671,9 @@ void FixBondReact::post_integrate()
// for prob check, generate random value for each atom with a bond partner
// forward comm of partner and random value, so ghosts have it
- if (fraction[myrxn] < 1.0) {
+ if (fraction[rxnID] < 1.0) {
for (int i = 0; i < nlocal; i++)
- if (partner[i]) probability[i] = random[myrxn]->uniform();
+ if (partner[i]) probability[i] = random[rxnID]->uniform();
}
commflag = 2;
@@ -764,11 +696,11 @@ void FixBondReact::post_integrate()
// apply probability constraint using RN for atom with smallest ID
- if (fraction[myrxn] < 1.0) {
+ if (fraction[rxnID] < 1.0) {
if (tag[i] < tag[j]) {
- if (probability[i] >= fraction[myrxn]) continue;
+ if (probability[i] >= fraction[rxnID]) continue;
} else {
- if (probability[j] >= fraction[myrxn]) continue;
+ if (probability[j] >= fraction[rxnID]) continue;
}
}
@@ -780,31 +712,17 @@ void FixBondReact::post_integrate()
if (tag[i] < tag[j]) temp_ncreate++;
}
- local_ncreate[myrxn] = temp_ncreate;
+ local_ncreate[rxnID] = temp_ncreate;
// break loop if no even eligible bonding atoms were found (on any proc)
int some_chance;
MPI_Allreduce(&temp_ncreate,&some_chance,1,MPI_INT,MPI_SUM,world);
- if (!some_chance) {
- continue;
- }
+ if (!some_chance) continue;
// communicate final partner
commflag = 3;
comm->forward_comm_fix(this);
-//obsolete comment block
-/*
- // I think this also simplifies for bond/react.
- // but currently unsure how to adapt it - JG
- // create list of created bonds that influence my owned atoms
- // even if between owned-ghost or ghost-ghost atoms
- // finalpartner is now set for owned and ghost atoms so loop over nall
- // OK if duplicates in created list due to ghosts duplicating owned atoms
- // check J < 0 to insure a created bond to unknown atom is included
- // i.e. a bond partner outside of skin length
-*/
-
// add instance to 'created' only if this processor
// owns the atoms with smaller global ID
// NOTE: we no longer care about ghost-ghost instances as bond/create did
@@ -816,21 +734,21 @@ void FixBondReact::post_integrate()
j = atom->map(finalpartner[i]);
// if (j < 0 || tag[i] < tag[j]) {
if (tag[i] < tag[j]) { //atom->map(std::min(tag[i],tag[j])) <= nlocal &&
- if (ncreate[myrxn] == maxcreate) {
+ if (ncreate[rxnID] == maxcreate) {
maxcreate += DELTA;
// third column of 'created': bond/react integer ID
memory->grow(created,maxcreate,2,nreacts,"bond/react:created");
}
// to ensure types remain in same order
// unnecessary now taken from reaction map file
- if (iatomtype[myrxn] == type[i]) {
- created[ncreate[myrxn]][0][myrxn] = tag[i];
- created[ncreate[myrxn]][1][myrxn] = finalpartner[i];
+ if (iatomtype[rxnID] == type[i]) {
+ created[ncreate[rxnID]][0][rxnID] = tag[i];
+ created[ncreate[rxnID]][1][rxnID] = finalpartner[i];
} else {
- created[ncreate[myrxn]][0][myrxn] = finalpartner[i];
- created[ncreate[myrxn]][1][myrxn] = tag[i];
+ created[ncreate[rxnID]][0][rxnID] = finalpartner[i];
+ created[ncreate[rxnID]][1][rxnID] = tag[i];
}
- ncreate[myrxn]++;
+ ncreate[rxnID]++;
}
}
unlimit_bond(); //free atoms that have been relaxed
@@ -854,7 +772,152 @@ void FixBondReact::post_integrate()
superimpose_algorithm();
// free atoms that have been limited after reacting
unlimit_bond();
+}
+
+/* ----------------------------------------------------------------------
+ Search non-bonded neighbor lists if bonding atoms are not in special list
+------------------------------------------------------------------------- */
+
+void FixBondReact::far_partner()
+{
+ int inum,jnum,itype,jtype,possible;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ int *ilist,*jlist,*numneigh,**firstneigh;
+ // loop over neighbors of my atoms
+ // each atom sets one closest eligible partner atom ID to bond with
+
+ double **x = atom->x;
+ tagint *tag = atom->tag;
+ int **nspecial = atom->nspecial;
+ tagint **special = atom->special;
+ int *mask = atom->mask;
+ int *type = atom->type;
+
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
+ // per-atom property indicating if in bond/react master group
+ int flag;
+ int index1 = atom->find_custom("limit_tags",flag);
+ int *i_limit_tags = atom->ivector[index1];
+
+ int i,j;
+
+ for (int ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ if (!(mask[i] & groupbits[rxnID])) continue;
+ if (i_limit_tags[i] != 0) continue;
+ itype = type[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ for (int jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ j &= NEIGHMASK;
+
+ if (!(mask[j] & groupbits[rxnID])) {
+ continue;
+}
+
+ if (i_limit_tags[j] != 0) {
+ continue;
+ }
+
+ jtype = type[j];
+ possible = 0;
+
+ if (itype == iatomtype[rxnID] && jtype == jatomtype[rxnID]) {
+ possible = 1;
+ } else if (itype == jatomtype[rxnID] && jtype == iatomtype[rxnID]) {
+ possible = 1;
+ }
+
+ if (possible == 0) continue;
+
+ // do not allow bonding atoms within special list
+ for (int k = 0; k < nspecial[i][2]; k++)
+ if (special[i][k] == tag[j]) possible = 0;
+ if (!possible) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq >= cutsq[rxnID][1] || rsq <= cutsq[rxnID][0]) {
+ continue;
+ }
+ if (rsq < distsq[i][1]) {
+ partner[i] = tag[j];
+ distsq[i][1] = rsq;
+ }
+ if (rsq < distsq[j][1]) {
+ partner[j] = tag[i];
+ distsq[j][1] = rsq;
+ }
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ Slightly simpler to find bonding partner when a close neighbor
+------------------------------------------------------------------------- */
+
+void FixBondReact::close_partner()
+{
+ int n,i1,i2,itype,jtype;
+ double delx,dely,delz,rsq;
+
+ double **x = atom->x;
+ tagint *tag = atom->tag;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ int **nspecial = atom->nspecial;
+ tagint **special = atom->special;
+
+ // per-atom property indicating if in bond/react master group
+ int flag;
+ int index1 = atom->find_custom("limit_tags",flag);
+ int *i_limit_tags = atom->ivector[index1];
+
+ // loop over special list
+ for (int ii = 0; ii < atom->nlocal; ii++) {
+ itype = type[ii];
+ n = 0;
+ if (closeneigh[rxnID] != 0)
+ n = nspecial[ii][closeneigh[rxnID]-1];
+ for (; n < nspecial[ii][closeneigh[rxnID]]; n++) {
+ i1 = ii;
+ i2 = atom->map(special[ii][n]);
+ jtype = type[i2];
+ if (!(mask[i1] & groupbits[rxnID])) continue;
+ if (!(mask[i2] & groupbits[rxnID])) continue;
+ if (i_limit_tags[i1] != 0) continue;
+ if (i_limit_tags[i2] != 0) continue;
+ if (itype != iatomtype[rxnID] || jtype != jatomtype[rxnID]) continue;
+
+ delx = x[i1][0] - x[i2][0];
+ dely = x[i1][1] - x[i2][1];
+ delz = x[i1][2] - x[i2][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ if (rsq >= cutsq[rxnID][1] || rsq <= cutsq[rxnID][0]) continue;
+
+ if (rsq > distsq[i1][0]) {
+ partner[i1] = tag[i2];
+ distsq[i1][0] = rsq;
+ }
+ if (rsq > distsq[i2][0]) {
+ partner[i2] = tag[i1];
+ distsq[i2][0] = rsq;
+ }
+ }
+ }
}
/* ----------------------------------------------------------------------
@@ -1076,8 +1139,8 @@ void FixBondReact::make_a_guess()
if (assigned_count == nfirst_neighs) status = GUESSFAIL;
// check if all neigh atom types are the same between simulation and unreacted mol
- int mol_ntypes[atom->ntypes];
- int lcl_ntypes[atom->ntypes];
+ int *mol_ntypes = new int[atom->ntypes];
+ int *lcl_ntypes = new int[atom->ntypes];
for (int i = 0; i < atom->ntypes; i++) {
mol_ntypes[i] = 0;
@@ -1096,6 +1159,9 @@ void FixBondReact::make_a_guess()
}
}
+ delete [] mol_ntypes;
+ delete [] lcl_ntypes;
+
// okay everything seems to be in order. let's assign some ID pairs!!!
neighbor_loop();
}
@@ -1384,7 +1450,7 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
// if no edge atoms (small reacting molecule), all atoms are landlocked
// we can delete all current topology of landlocked atoms and replace
- // alwasy remove edge atoms from landlocked list
+ // always remove edge atoms from landlocked list
for (int i = 0; i < twomol->natoms; i++) {
if (edge[equivalences[i][1][myrxn]-1][myrxn] == 1) landlocked_atoms[i][myrxn] = 0;
else landlocked_atoms[i][myrxn] = 1;
@@ -1395,7 +1461,6 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
if ((force->dihedral && twomol->dihedralflag) ||
(force->improper && twomol->improperflag)) nspecial_limit = 1;
-
if (nspecial_limit != -1) {
for (int i = 0; i < twomol->natoms; i++) {
for (int j = 0; j < twomol->nspecial[i][nspecial_limit]; j++) {
@@ -1410,11 +1475,21 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
// bad molecule templates check
// if atoms change types, but aren't landlocked, that's bad
-
for (int i = 0; i < twomol->natoms; i++) {
if (twomol->type[i] != onemol->type[equivalences[i][1][myrxn]-1] && landlocked_atoms[i][myrxn] == 0)
error->one(FLERR,"Atom affected by reaction too close to template edge");
}
+
+ // also, if atoms change number of bonds, but aren't landlocked, that could be bad
+ if (me == 0)
+ for (int i = 0; i < twomol->natoms; i++) {
+ if (twomol->nspecial[i][0] != onemol->nspecial[equivalences[i][1][myrxn]-1][0] && landlocked_atoms[i][myrxn] == 0) {
+ char str[128];
+ sprintf(str,"An atom in 'react #%d' changes bond connectivity but not atom type",myrxn+1);
+ error->warning(FLERR,str);
+ break;
+ }
+ }
}
/* ----------------------------------------------------------------------
@@ -1438,7 +1513,8 @@ void FixBondReact::dedup_mega_gloves(int dedup_mode)
dedup_size = global_megasize;
}
- tagint dedup_glove[max_natoms+1][dedup_size];
+ tagint **dedup_glove;
+ memory->create(dedup_glove,max_natoms+1,dedup_size,"bond/react:dedup_glove");
if (dedup_mode == 0) {
for (int i = 0; i < dedup_size; i++) {
@@ -1456,8 +1532,8 @@ void FixBondReact::dedup_mega_gloves(int dedup_mode)
// dedup_mask is size dedup_size and filters reactions that have been deleted
// a value of 1 means this reaction instance has been deleted
- int dedup_mask[dedup_size];
- int dup_list[dedup_size];
+ int *dedup_mask = new int[dedup_size];
+ int *dup_list = new int[dedup_size];
for (int i = 0; i < dedup_size; i++) {
dedup_mask[i] = 0;
@@ -1467,14 +1543,12 @@ void FixBondReact::dedup_mega_gloves(int dedup_mode)
// let's randomly mix up our reaction instances first
// then we can feel okay about ignoring ones we've already deleted (or accepted)
// based off std::shuffle
- // will produce same 'random' sequences on different processors.
- // not really an issue, as reaction lists are independent
+ int *temp_rxn = new int[max_natoms+1];
for (int i = dedup_size-1; i > 0; --i) { //dedup_size
- //choose random entry to swap current one with
- int k = rand() % (i+1);
+ // choose random entry to swap current one with
+ int k = floor(random[0]->uniform()*(i+1));
// swap entries
- int temp_rxn[max_natoms+1];
for (int j = 0; j < max_natoms+1; j++)
temp_rxn[j] = dedup_glove[j][i];
@@ -1483,6 +1557,7 @@ void FixBondReact::dedup_mega_gloves(int dedup_mode)
dedup_glove[j][k] = temp_rxn[j];
}
}
+ delete [] temp_rxn;
for (int i = 0; i < dedup_size; i++) {
if (dedup_mask[i] == 0) {
@@ -1557,6 +1632,10 @@ void FixBondReact::dedup_mega_gloves(int dedup_mode)
}
global_megasize = new_global_megasize;
}
+
+ memory->destroy(dedup_glove);
+ delete [] dedup_mask;
+ delete [] dup_list;
}
/* ----------------------------------------------------------------------
@@ -1743,9 +1822,6 @@ void FixBondReact::ghost_glovecast()
for (int j = 0; j < global_megasize; j++)
global_mega_glove[i][j] = 0;
-
- ghostcheck_flag = 1;
-
if (ghostly_num_mega > 0) {
for (int i = 0; i < max_natoms+1; i++) {
for (int j = 0; j < ghostly_num_mega; j++) {
@@ -1806,7 +1882,8 @@ void FixBondReact::update_everything()
// add check for local atoms as well
int update_num_mega;
- tagint update_mega_glove[max_natoms+1][MAX(local_num_mega,global_megasize)];
+ tagint **update_mega_glove;
+ memory->create(update_mega_glove,max_natoms+1,MAX(local_num_mega,global_megasize),"bond/react:update_mega_glove");
for (int pass = 0; pass < 2; pass++) {
@@ -2217,6 +2294,9 @@ void FixBondReact::update_everything()
}
}
+
+ memory->destroy(update_mega_glove);
+
// something to think about: this could done much more concisely if
// all atom-level info (bond,angles, etc...) were kinda inherited from a common data struct --JG
@@ -2522,7 +2602,10 @@ int FixBondReact::pack_reverse_comm(int n, int first, double *buf)
for (i = first; i < last; i++) {
buf[m++] = ubuf(partner[i]).d;
- buf[m++] = distsq[i];
+ if (closeneigh[rxnID] < 0)
+ buf[m++] = distsq[i][1];
+ else
+ buf[m++] = distsq[i][0];
}
return m;
}
@@ -2538,10 +2621,16 @@ void FixBondReact::unpack_reverse_comm(int n, int *list, double *buf)
if (commflag != 1) {
for (i = 0; i < n; i++) {
j = list[i];
- if (buf[m+1] < distsq[j]) {
+ if (closeneigh[rxnID] < 0)
+ if (buf[m+1] < distsq[j][1]) {
partner[j] = (tagint) ubuf(buf[m++]).i;
- distsq[j] = buf[m++];
+ distsq[j][1] = buf[m++];
} else m += 2;
+ else
+ if (buf[m+1] > distsq[j][0]) {
+ partner[j] = (tagint) ubuf(buf[m++]).i;
+ distsq[j][0] = buf[m++];
+ } else m += 2;
}
}
}
diff --git a/src/USER-MISC/fix_bond_react.h b/src/USER-MISC/fix_bond_react.h
index a0f52c02882353de6c9ddf2794b34e6a58f4b91a..e60fff37fbaa93f6e4e09136a57282cd883d9fe3 100644
--- a/src/USER-MISC/fix_bond_react.h
+++ b/src/USER-MISC/fix_bond_react.h
@@ -53,7 +53,7 @@ class FixBondReact : public Fix {
FILE *fp;
int *iatomtype,*jatomtype;
int *seed;
- double *cutsq,*fraction;
+ double **cutsq,*fraction;
tagint lastcheck;
int stabilization_flag;
int *stabilize_steps_flag;
@@ -66,7 +66,7 @@ class FixBondReact : public Fix {
int nmax; // max num local atoms
int max_natoms; // max natoms in a molecule template
tagint *partner,*finalpartner;
- double *distsq,*probability;
+ double **distsq,*probability;
int *ncreate;
int maxcreate;
int allncreate;
@@ -96,10 +96,9 @@ class FixBondReact : public Fix {
void superimpose_algorithm(); // main function of the superimpose algorithm
int *ibonding,*jbonding;
+ int *closeneigh; // indicates if bonding atoms of a rxn are 1-2, 1-3, or 1-4 neighbors
int nedge,nequivalent; // number of edge, equivalent atoms in mapping file
int attempted_rxn; // there was an attempt!
- int ghostcheck_flag; // idicates whether a reaction instances contains a nonlocal atom
- int this_rxn_count; // num of local reaction occurrences
int *local_rxn_count;
int *ghostly_rxn_count;
int avail_guesses; // num of restore points available
@@ -143,6 +142,8 @@ class FixBondReact : public Fix {
void skip_lines(int, char *);
int parse(char *, char **, int);
+ void far_partner();
+ void close_partner();
void find_landlocked_atoms(int);
void glove_ghostcheck();
void ghost_glovecast();