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Merge branch 'master' into doc-styles-check

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Axel Kohlmeyer
2020-01-11 21:00:49 -05:00
parent 3b32141330 587fc9d962
commit 675bd26085
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6
doc/src/Errors_warnings.rst
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@ -195,6 +195,12 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
*Fix SRD walls overlap but fix srd overlap not set* *Fix SRD walls overlap but fix srd overlap not set*
You likely want to set this in your input script. You likely want to set this in your input script.
* Fix bond/create is used multiple times or with fix bond/break - may not work as expected*
When using fix bond/create multiple times or in combination with
fix bond/break, the individual fix instances do not share information
about changes they made at the same time step and thus it may result
in unexpected behavior.
*Fix bond/swap will ignore defined angles* *Fix bond/swap will ignore defined angles*
See the doc page for fix bond/swap for more info on this See the doc page for fix bond/swap for more info on this
restriction. restriction.

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doc/src/Examples.rst
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@ -133,6 +133,8 @@ Lowercase directories
+-------------+------------------------------------------------------------------+ +-------------+------------------------------------------------------------------+
| reax | RDX and TATB models using the ReaxFF | | reax | RDX and TATB models using the ReaxFF |
+-------------+------------------------------------------------------------------+ +-------------+------------------------------------------------------------------+
| rerun | use of rerun and read\_dump commands |
+-------------+------------------------------------------------------------------+
| rigid | rigid bodies modeled as independent or coupled | | rigid | rigid bodies modeled as independent or coupled |
+-------------+------------------------------------------------------------------+ +-------------+------------------------------------------------------------------+
| shear | sideways shear applied to 2d solid, with and without a void | | shear | sideways shear applied to 2d solid, with and without a void |

7
doc/txt/Errors_warnings.txt
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@ -239,6 +239,13 @@ will be truncated to attempt to prevent the bond from blowing up. :dd
You likely want to set this in your input script. :dd You likely want to set this in your input script. :dd
{ Fix bond/create is used multiple times or with fix bond/break - may not work as expected} :dt
When using fix bond/create multiple times or in combination with
fix bond/break, the individual fix instances do not share information
about changes they made at the same time step and thus it may result
in unexpected behavior. :dd
{Fix bond/swap will ignore defined angles} :dt {Fix bond/swap will ignore defined angles} :dt
See the doc page for fix bond/swap for more info on this See the doc page for fix bond/swap for more info on this

1
doc/txt/Examples.txt
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@ -94,6 +94,7 @@ python: using embedded Python in a LAMMPS input script
qeq: use of the QEQ package for charge equilibration qeq: use of the QEQ package for charge equilibration
rdf-adf: computing radial and angle distribution functions for water rdf-adf: computing radial and angle distribution functions for water
reax: RDX and TATB models using the ReaxFF reax: RDX and TATB models using the ReaxFF
rerun: use of rerun and read_dump commands
rigid: rigid bodies modeled as independent or coupled rigid: rigid bodies modeled as independent or coupled
shear: sideways shear applied to 2d solid, with and without a void shear: sideways shear applied to 2d solid, with and without a void
snap: NVE dynamics for BCC tantalum crystal using SNAP potential snap: NVE dynamics for BCC tantalum crystal using SNAP potential

1
examples/README
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@ -101,6 +101,7 @@ prd: parallel replica dynamics of vacancy diffusion in bulk Si
python: use of PYTHON package to invoke Python code from input script python: use of PYTHON package to invoke Python code from input script
qeq: use of QEQ package for charge equilibration qeq: use of QEQ package for charge equilibration
reax: RDX and TATB and several other models using ReaxFF reax: RDX and TATB and several other models using ReaxFF
rerun: use of rerun and read_dump commands
rigid: rigid bodies modeled as independent or coupled rigid: rigid bodies modeled as independent or coupled
shear: sideways shear applied to 2d solid, with and without a void shear: sideways shear applied to 2d solid, with and without a void
snap: examples for using several bundled SNAP potentials snap: examples for using several bundled SNAP potentials

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Examples of how to use the rerun and read_dump commands
in.first - run on any number of procs for any size problem
in.rerun - run on same or different proc count for same size problem
in.read_dump - ditto to in.rerun
The thermo output on the same timesteps should be identical
to within round-off errors.
in.rdf.first - produces RDF in rdf.first, 50 bins out to 2.5 sigma
in.rdf.rerun - produces RDF in rdf.rerun, 100 bins out to 5 sigma
In both bases the time averaged RDF is computed 10x times, every 100
steps for 1000 total. In the rerun, the pair style cutoff is changed
so the RDF can be computed to a longer distance without re-running the
simulation. The RDF values in the 2 files should be the same (within
round-off) for the first 50 bins.

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examples/rerun/in.first Normal file
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# 3d Lennard-Jones melt
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
units lj
atom_style atomic
lattice fcc 0.8442
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
dump 1 all custom 100 lj.dump id type x y z vx vy vz
thermo 100
run 1000

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# 3d Lennard-Jones melt
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
units lj
atom_style atomic
lattice fcc 0.8442
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
dump 1 all custom 100 lj.dump id type x y z
compute myRDF all rdf 50 cutoff 2.5
fix 2 all ave/time 100 10 1000 c_myRDF[*] file rdf.first mode vector
thermo 100
run 1000

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# 3d Lennard-Jones melt
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
units lj
atom_style atomic
lattice fcc 0.8442
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
mass 1 1.0
pair_style lj/cut 5.0
pair_coeff 1 1 1.0 1.0
neighbor 0.3 bin
compute myRDF all rdf 100 cutoff 5.0
fix 2 all ave/time 100 10 1000 c_myRDF[*] file rdf.rerun mode vector
thermo 100
rerun lj.dump dump x y z

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# 3d Lennard-Jones melt
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
units lj
atom_style atomic
lattice fcc 0.8442
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
thermo 100
read_dump lj.dump 200 x y z vx vy vz
run 0 post no
read_dump lj.dump 800 x y z vx vy vz
run 0 post no
read_dump lj.dump 600 x y z vx vy vz
run 0 post no
read_dump lj.dump 400 x y z vx vy vz
run 0 post no

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# 3d Lennard-Jones melt
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
units lj
atom_style atomic
lattice fcc 0.8442
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
thermo 100
rerun lj.dump first 200 last 800 every 200 &
dump x y z vx vy vz

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LAMMPS (09 Jan 2020)
# 3d Lennard-Jones melt
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable xx equal 20*1
variable yy equal 20*$y
variable yy equal 20*1
variable zz equal 20*$z
variable zz equal 20*1
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 20 0 ${yy} 0 ${zz}
region box block 0 20 0 20 0 ${zz}
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.00173283 secs
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
dump 1 all custom 100 lj.dump id type x y z vx vy vz
thermo 100
run 1000
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 24 24 24
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 7.869 | 7.869 | 7.869 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6134356 -5.0197073
100 0.7574531 -5.7585055 0 -4.6223613 0.20726105
200 0.75953175 -5.7618892 0 -4.6226272 0.20910575
300 0.74624286 -5.741962 0 -4.6226327 0.32016436
400 0.74155675 -5.7343359 0 -4.6220356 0.3777989
500 0.73249345 -5.7206946 0 -4.6219887 0.44253023
600 0.72087255 -5.7029314 0 -4.6216563 0.55730354
700 0.71489947 -5.693532 0 -4.6212164 0.61322381
800 0.70876958 -5.6840594 0 -4.6209382 0.66822293
900 0.70799522 -5.6828388 0 -4.6208791 0.66961272
1000 0.70325878 -5.6750833 0 -4.6202281 0.7112575
Loop time of 6.3349 on 4 procs for 1000 steps with 32000 atoms
Performance: 68193.673 tau/day, 157.856 timesteps/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.3538 | 4.6712 | 5.0021 | 12.8 | 73.74
Neigh | 0.59378 | 0.65229 | 0.75202 | 8.0 | 10.30
Comm | 0.28101 | 0.69839 | 1.0586 | 38.5 | 11.02
Output | 0.21601 | 0.21682 | 0.21718 | 0.1 | 3.42
Modify | 0.074002 | 0.074803 | 0.075779 | 0.2 | 1.18
Other | | 0.0214 | | | 0.34
Nlocal: 8000 ave 8049 max 7942 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Nghost: 8632.5 ave 8685 max 8591 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Neighs: 299934 ave 303105 max 295137 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Total # of neighbors = 1199738
Ave neighs/atom = 37.4918
Neighbor list builds = 50
Dangerous builds not checked
Total wall time: 0:00:06

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LAMMPS (09 Jan 2020)
# 3d Lennard-Jones melt
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable xx equal 20*1
variable yy equal 20*$y
variable yy equal 20*1
variable zz equal 20*$z
variable zz equal 20*1
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 20 0 ${yy} 0 ${zz}
region box block 0 20 0 20 0 ${zz}
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.00100017 secs
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
dump 1 all custom 100 lj.dump id type x y z
compute myRDF all rdf 50 cutoff 2.5
fix 2 all ave/time 100 10 1000 c_myRDF[*] file rdf.first mode vector
thermo 100
run 1000
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 24 24 24
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) compute rdf, occasional
attributes: half, newton on, cut 2.8
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 8.487 | 8.487 | 8.487 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6134356 -5.0197073
100 0.7574531 -5.7585055 0 -4.6223613 0.20726105
200 0.75953175 -5.7618892 0 -4.6226272 0.20910575
300 0.74624286 -5.741962 0 -4.6226327 0.32016436
400 0.74155675 -5.7343359 0 -4.6220356 0.3777989
500 0.73249345 -5.7206946 0 -4.6219887 0.44253023
600 0.72087255 -5.7029314 0 -4.6216563 0.55730354
700 0.71489947 -5.693532 0 -4.6212164 0.61322381
800 0.70876958 -5.6840594 0 -4.6209382 0.66822293
900 0.70799522 -5.6828388 0 -4.6208791 0.66961272
1000 0.70325878 -5.6750833 0 -4.6202281 0.7112575
Loop time of 7.44016 on 4 procs for 1000 steps with 32000 atoms
Performance: 58063.267 tau/day, 134.406 timesteps/s
99.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.3881 | 5.5809 | 5.7111 | 5.4 | 75.01
Neigh | 0.80101 | 0.82776 | 0.85702 | 2.2 | 11.13
Comm | 0.31801 | 0.48426 | 0.72201 | 22.5 | 6.51
Output | 0.17801 | 0.17801 | 0.17801 | 0.0 | 2.39
Modify | 0.31201 | 0.33076 | 0.33701 | 1.9 | 4.45
Other | | 0.0385 | | | 0.52
Nlocal: 8000 ave 8049 max 7942 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Nghost: 8632.5 ave 8685 max 8591 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Neighs: 299934 ave 303105 max 295137 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Total # of neighbors = 1199738
Ave neighs/atom = 37.4918
Neighbor list builds = 50
Dangerous builds not checked
Total wall time: 0:00:07

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LAMMPS (09 Jan 2020)
# 3d Lennard-Jones melt
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable xx equal 20*1
variable yy equal 20*$y
variable yy equal 20*1
variable zz equal 20*$z
variable zz equal 20*1
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 20 0 ${yy} 0 ${zz}
region box block 0 20 0 20 0 ${zz}
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.00183487 secs
mass 1 1.0
pair_style lj/cut 5.0
pair_coeff 1 1 1.0 1.0
neighbor 0.3 bin
compute myRDF all rdf 100 cutoff 5.0
fix 2 all ave/time 100 10 1000 c_myRDF[*] file rdf.rerun mode vector
thermo 100
rerun lj.dump dump x y z
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.3
ghost atom cutoff = 5.3
binsize = 2.65, bins = 13 13 13
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) compute rdf, occasional
attributes: half, newton on, cut 5.3
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 15.19 | 15.19 | 15.19 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -7.1616928 0 -7.1616928 -6.8899898
100 0 -6.1442754 0 -6.1442754 -1.0825318
200 0 -6.1472483 0 -6.1472483 -1.0817213
300 0 -6.1274033 0 -6.1274033 -0.95961014
400 0 -6.1202956 0 -6.1202956 -0.8988851
500 0 -6.1067136 0 -6.1067136 -0.82660368
600 0 -6.0893179 0 -6.0893179 -0.70264528
700 0 -6.0803044 0 -6.0803044 -0.64232743
800 0 -6.0710303 0 -6.0710303 -0.5824798
900 0 -6.0698963 0 -6.0698963 -0.58057929
1000 0 -6.0627642 0 -6.0627642 -0.53599799
Loop time of 3.07661 on 4 procs for 11 steps with 32000 atoms
Performance: 1544.558 tau/day, 3.575 timesteps/s
99.8% 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 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 3.077 | | |100.00
Nlocal: 8000 ave 8049 max 7942 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Nghost: 20028 ave 20060 max 19988 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Neighs: 2.10417e+06 ave 2.12604e+06 max 2.07878e+06 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Total # of neighbors = 8416685
Ave neighs/atom = 263.021
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:03

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LAMMPS (09 Jan 2020)
# 3d Lennard-Jones melt
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable xx equal 20*1
variable yy equal 20*$y
variable yy equal 20*1
variable zz equal 20*$z
variable zz equal 20*1
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 20 0 ${yy} 0 ${zz}
region box block 0 20 0 20 0 ${zz}
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.001724 secs
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
thermo 100
read_dump lj.dump 200 x y z vx vy vz
orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
32000 atoms before read
32000 atoms in snapshot
0 atoms purged
32000 atoms replaced
0 atoms trimmed
0 atoms added
32000 atoms after read
run 0 post no
WARNING: No fixes defined, atoms won't move (../verlet.cpp:52)
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 24 24 24
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.841 | 6.843 | 6.846 Mbytes
Step Temp E_pair E_mol TotEng Press
200 0.75953173 -5.7618854 0 -4.6226234 0.20912952
Loop time of 2.26498e-06 on 4 procs for 0 steps with 32000 atoms
read_dump lj.dump 800 x y z vx vy vz
orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
32000 atoms before read
32000 atoms in snapshot
0 atoms purged
32000 atoms replaced
0 atoms trimmed
0 atoms added
32000 atoms after read
run 0 post no
WARNING: No fixes defined, atoms won't move (../verlet.cpp:52)
Per MPI rank memory allocation (min/avg/max) = 6.841 | 6.843 | 6.846 Mbytes
Step Temp E_pair E_mol TotEng Press
800 0.70876957 -5.6840545 0 -4.6209334 0.66823926
Loop time of 5.36442e-07 on 4 procs for 0 steps with 32000 atoms
read_dump lj.dump 600 x y z vx vy vz
orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
32000 atoms before read
32000 atoms in snapshot
0 atoms purged
32000 atoms replaced
0 atoms trimmed
0 atoms added
32000 atoms after read
run 0 post no
WARNING: No fixes defined, atoms won't move (../verlet.cpp:52)
Per MPI rank memory allocation (min/avg/max) = 6.841 | 6.843 | 6.846 Mbytes
Step Temp E_pair E_mol TotEng Press
600 0.72087256 -5.7029306 0 -4.6216556 0.55729873
Loop time of 7.7486e-07 on 4 procs for 0 steps with 32000 atoms
read_dump lj.dump 400 x y z vx vy vz
orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
32000 atoms before read
32000 atoms in snapshot
0 atoms purged
32000 atoms replaced
0 atoms trimmed
0 atoms added
32000 atoms after read
run 0 post no
WARNING: No fixes defined, atoms won't move (../verlet.cpp:52)
Per MPI rank memory allocation (min/avg/max) = 6.841 | 6.843 | 6.846 Mbytes
Step Temp E_pair E_mol TotEng Press
400 0.74155677 -5.7343336 0 -4.6220332 0.37780193
Loop time of 5.36442e-07 on 4 procs for 0 steps with 32000 atoms
Total wall time: 0:00:00

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LAMMPS (09 Jan 2020)
# 3d Lennard-Jones melt
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable xx equal 20*1
variable yy equal 20*$y
variable yy equal 20*1
variable zz equal 20*$z
variable zz equal 20*1
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 20 0 ${yy} 0 ${zz}
region box block 0 20 0 20 0 ${zz}
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.00100017 secs
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
thermo 100
rerun lj.dump first 200 last 800 every 200 dump x y z vx vy vz
WARNING: No fixes defined, atoms won't move (../verlet.cpp:52)
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 24 24 24
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.716 | 6.718 | 6.721 Mbytes
Step Temp E_pair E_mol TotEng Press
200 0.75953173 -5.7618854 0 -4.6226234 0.20912952
400 0.74155677 -5.7343336 0 -4.6220332 0.37780193
600 0.72087256 -5.7029306 0 -4.6216556 0.55729873
800 0.70876957 -5.6840545 0 -4.6209334 0.66823926
Loop time of 0.375898 on 4 procs for 4 steps with 32000 atoms
Performance: 4596.990 tau/day, 10.641 timesteps/s
98.0% 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 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.3759 | | |100.00
Nlocal: 8000 ave 8073 max 7933 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Nghost: 8693.25 ave 8731 max 8658 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs: 299786 ave 302947 max 293888 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Total # of neighbors = 1199142
Ave neighs/atom = 37.4732
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

54
examples/rerun/rdf.09Jan20.first.g++.4 Normal file
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@ -0,0 +1,54 @@
# Time-averaged data for fix 2
# TimeStep Number-of-rows
# Row c_myRDF[1] c_myRDF[2] c_myRDF[3]
1000 50
1 0.025 0 0
2 0.075 0 0
3 0.125 0 0
4 0.175 0 0
5 0.225 0 0
6 0.275 0 0
7 0.325 0 0
8 0.375 0 0
9 0.425 0 0
10 0.475 0 0
11 0.525 0 0
12 0.575 0 0
13 0.625 0 0
14 0.675 0 0
15 0.725 0 0
16 0.775 0 0
17 0.825 0 0
18 0.875 1.53863e-05 6.25e-06
19 0.925 0.0217263 0.00986875
20 0.975 0.506735 0.265431
21 1.025 1.92083 1.33605
22 1.075 2.8749 3.09855
23 1.125 2.7805 4.96541
24 1.175 2.21879 6.59047
25 1.225 1.67622 7.92484
26 1.275 1.25407 9.00629
27 1.325 0.963413 9.90353
28 1.375 0.774441 10.6802
29 1.425 0.656196 11.3871
30 1.475 0.589364 12.0672
31 1.525 0.560681 12.7589
32 1.575 0.560195 13.4961
33 1.625 0.587995 14.3197
34 1.675 0.632155 15.2605
35 1.725 0.706585 16.3758
36 1.775 0.805303 17.7216
37 1.825 0.925415 19.3565
38 1.875 1.05672 21.3271
39 1.925 1.17634 23.6394
40 1.975 1.2557 26.2375
41 2.025 1.30009 29.0653
42 2.075 1.30889 32.0546
43 2.125 1.27704 35.1135
44 2.175 1.21808 38.17
45 2.225 1.13622 41.1536
46 2.275 1.05072 44.0382
47 2.325 0.973786 46.8303
48 2.375 0.910095 49.5533
49 2.425 0.866474 52.256
50 2.475 0.841724 54.991

104
examples/rerun/rdf.09Jan20.rerun.g++.4 Normal file
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@ -0,0 +1,104 @@
# Time-averaged data for fix 2
# TimeStep Number-of-rows
# Row c_myRDF[1] c_myRDF[2] c_myRDF[3]
1000 100
1 0.025 0 0
2 0.075 0 0
3 0.125 0 0
4 0.175 0 0
5 0.225 0 0
6 0.275 0 0
7 0.325 0 0
8 0.375 0 0
9 0.425 0 0
10 0.475 0 0
11 0.525 0 0
12 0.575 0 0
13 0.625 0 0
14 0.675 0 0
15 0.725 0 0
16 0.775 0 0
17 0.825 0 0
18 0.875 1.53863e-05 6.25e-06
19 0.925 0.021685 0.00985
20 0.975 0.506834 0.265463
21 1.025 1.92047 1.33588
22 1.075 2.87514 3.09853
23 1.125 2.78062 4.96547
24 1.175 2.21869 6.59046
25 1.225 1.67626 7.92486
26 1.275 1.25409 9.00633
27 1.325 0.963245 9.90341
28 1.375 0.774535 10.6802
29 1.425 0.65626 11.3871
30 1.475 0.58925 12.0672
31 1.525 0.560782 12.759
32 1.575 0.560133 13.496
33 1.625 0.588008 14.3197
34 1.675 0.632185 15.2605
35 1.725 0.706541 16.3757
36 1.775 0.805341 17.7216
37 1.825 0.925351 19.3565
38 1.875 1.05677 21.3271
39 1.925 1.17639 23.6395
40 1.975 1.25571 26.2376
41 2.025 1.30011 29.0655
42 2.075 1.30883 32.0547
43 2.125 1.27702 35.1134
44 2.175 1.21813 38.17
45 2.225 1.13617 41.1536
46 2.275 1.05073 44.0382
47 2.325 0.97376 46.8302
48 2.375 0.91012 49.5533
49 2.425 0.866556 52.2563
50 2.475 0.841651 54.991
51 2.525 0.839516 57.8301
52 2.575 0.848795 60.8153
53 2.625 0.868861 63.991
54 2.675 0.896335 67.393
55 2.725 0.925794 71.0395
56 2.775 0.961909 74.9685
57 2.825 0.999727 79.2005
58 2.875 1.03745 83.749
59 2.925 1.07355 88.6208
60 2.975 1.10406 93.8039
61 3.025 1.11993 99.2397
62 3.075 1.12062 104.86
63 3.125 1.10531 110.586
64 3.175 1.07711 116.345
65 3.225 1.04268 122.097
66 3.275 1.00838 127.834
67 3.325 0.974855 133.55
68 3.375 0.949817 139.289
69 3.425 0.936519 145.116
70 3.475 0.92942 151.069
71 3.525 0.930926 157.205
72 3.575 0.940561 163.581
73 3.625 0.94956 170.199
74 3.675 0.964202 177.107
75 3.725 0.97905 184.312
76 3.775 0.991906 191.81
77 3.825 1.00093 199.577
78 3.875 1.01248 207.641
79 3.925 1.02301 216.001
80 3.975 1.03474 224.673
81 4.025 1.04171 233.624
82 4.075 1.04725 242.849
83 4.125 1.04997 252.325
84 4.175 1.04758 262.01
85 4.225 1.03985 271.856
86 4.275 1.02755 281.817
87 4.325 1.00883 291.826
88 4.375 0.99045 301.882
89 4.425 0.97287 311.986
90 4.475 0.958469 322.166
91 4.525 0.952552 332.512
92 4.575 0.948064 343.037
93 4.625 0.952592 353.845
94 4.675 0.958837 364.96
95 4.725 0.970831 376.457
96 4.775 0.985248 388.372
97 4.825 0.998873 400.707
98 4.875 1.0119 413.462
99 4.925 1.02446 426.643
100 4.975 1.03613 440.245

3
src/MC/fix_bond_break.cpp
View File

@ -33,7 +33,8 @@ using namespace FixConst;
FixBondBreak::FixBondBreak(LAMMPS *lmp, int narg, char **arg) : FixBondBreak::FixBondBreak(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), Fix(lmp, narg, arg),
partner(NULL), finalpartner(NULL), distsq(NULL), probability(NULL), broken(NULL), copy(NULL), random(NULL) partner(NULL), finalpartner(NULL), distsq(NULL), probability(NULL),
broken(NULL), copy(NULL), random(NULL)
{ {
if (narg < 6) error->all(FLERR,"Illegal fix bond/break command"); if (narg < 6) error->all(FLERR,"Illegal fix bond/break command");

14
src/MC/fix_bond_create.cpp
View File

@ -18,6 +18,7 @@
#include "respa.h" #include "respa.h"
#include "atom.h" #include "atom.h"
#include "force.h" #include "force.h"
#include "modify.h"
#include "pair.h" #include "pair.h"
#include "comm.h" #include "comm.h"
#include "neighbor.h" #include "neighbor.h"
@ -216,6 +217,19 @@ void FixBondCreate::init()
if (force->pair == NULL || cutsq > force->pair->cutsq[iatomtype][jatomtype]) if (force->pair == NULL || cutsq > force->pair->cutsq[iatomtype][jatomtype])
error->all(FLERR,"Fix bond/create cutoff is longer than pairwise cutoff"); error->all(FLERR,"Fix bond/create cutoff is longer than pairwise cutoff");
// warn if more than one fix bond/create or also a fix bond/break
// because this fix stores per-atom state in bondcount
// if other fixes create/break bonds, this fix will not know about it
int count = 0;
for (int i = 0; i < modify->nfix; i++) {
if (strcmp(modify->fix[i]->style,"bond/create") == 0) count++;
if (strcmp(modify->fix[i]->style,"bond/break") == 0) count++;
}
if (count > 1 && me == 0)
error->warning(FLERR,"Fix bond/create is used multiple times "
" or with fix bond/break - may not work as expected");
// enable angle/dihedral/improper creation if atype/dtype/itype // enable angle/dihedral/improper creation if atype/dtype/itype
// option was used and a force field has been specified // option was used and a force field has been specified

7
src/MC/fix_bond_create.h
View File

@ -170,4 +170,11 @@ See the read_data command for info on setting the "extra special per
atom" header value to allow for additional special values to be atom" header value to allow for additional special values to be
stored. stored.
W: Fix bond/create is used multiple times or with fix bond/break - may not work as expected
When using fix bond/create multiple times or in combination with
fix bond/break, the individual fix instances do not share information
about changes they made at the same time step and thus it may result
in unexpected behavior.
*/ */