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Added Kolmogorov-Crespi potential

This commit is contained in:
Jaap Kroes 2017-02-28 14:59:13 +01:00
parent 49e83b4348
commit a1b40b902d
12 changed files with 1473 additions and 0 deletions
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12
doc/src/Eqs/pair_kolmogorov_crespi_z.tex Normal file
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\documentclass[12pt]{article}
\begin{document}
\begin{eqnarray*}
E & = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
V_{ij} & = & e^{-\lambda(r_{ij} -z_0}) \left[ C + f(\rho_{ij}) + f(\rho_{ji}) - A \left( \frac{r_{ij}}{z_0}\right)^{-6}\right] \\
\rho_{ij}^2 & = & x_{ij}^2 + y_{ij}^2 \\
f(\rho) & = & e^{-(\rho/\delta)^2} \sum_{n=0}^2 C_{2n} { \rho/\delta }^{2n}
\end{eqnarray*}
\end{document}

55
doc/src/pair_kolmogorov_crespi_z.txt Normal file
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@ -0,0 +1,55 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style kolmogorov/crespi/z command :h3
[Syntax:]
pair_style kolmogorov/crespi/z cutoff :pre
[Examples:]
pair_style hybrid/overlay kolmogorov/crespi/z 20.0
pair_coeff * * none
pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C :pre
pair_style hybrid/overlay rebo kolmogorov/crespi/z 14.0
pair_coeff * * rebo CH.airebo C C
pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C :pre
[Description:]
The {kolmogorov/crespi/z} style computes the Kolmogorov-Crespi interaction potential as
described in "(KC)"_#KC. An important simplification is made, which is to
take all normals along the z-axis.
:c,image(Eqs/pair_kolmogorov_crespi_z.jpg)
The parameter file (e.g. CC.KC), is intended for use with metal
"units"_units.html, with energies in meV.
This potential must be used in combination with hybrid/overlay.
Other interactions can be set to zero using pair_style {none}.
[Restrictions:]
This fix is part of the USER-MISC package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
"pair_coeff"_pair_coeff.html
"pair_none"_pair_none.html
[Default:] none
:line
:link(KC)
[(KC)] Kolmogorov, Crespi, Phys. Rev. B 71, 235415 (2005)

1
doc/src/pairs.txt
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@ -39,6 +39,7 @@ Pair Styles :h1
pair_hbond_dreiding
pair_hybrid
pair_kim
pair_kolmogorov_crespi_z
pair_lcbop
pair_line_lj
pair_list

266
examples/USER/misc/kolmogorov-crespi/data.bilayer-graphene Normal file
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info: xyz2data 18:31, Mon 27-02-2017
256 atoms
2 atom types
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0.00000000 19.67609717 ylo yhi
-20.00000000 40.00000000 zlo zhi
Atoms
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139
examples/USER/misc/kolmogorov-crespi/data.graphene-adsorbant Normal file
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@ -0,0 +1,139 @@
info: xyz2data 11:52, Tue 28-02-2017
129 atoms
2 atom types
0.00000000 17.04000000 xlo xhi
0.00000000 19.67609717 ylo yhi
-10.00000000 40.00000000 zlo zhi
Atoms
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3 1 2.13000000 1.22975607 0.00000000
4 1 3.55000000 1.22975607 0.00000000
5 1 0.00000000 2.45951215 0.00000000
6 1 1.42000000 2.45951215 0.00000000
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8 1 3.55000000 3.68926822 0.00000000
9 1 0.00000000 4.91902429 0.00000000
10 1 1.42000000 4.91902429 0.00000000
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13 1 0.00000000 7.37853644 0.00000000
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42 1 5.68000000 4.91902429 0.00000000
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48 1 7.81000000 8.60829251 0.00000000
49 1 4.26000000 9.83804859 0.00000000
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129 2 10.00000000 10.00000000 3.30000000

45
examples/USER/misc/kolmogorov-crespi/in.atom-diffusion Normal file
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@ -0,0 +1,45 @@
# Initialization
units metal
boundary p p p
atom_style atomic
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use 2 atom types so that inter- and intra-layer
# interactions can be specified separately
read_data data.graphene-adsorbant # read lammps data file
mass 1 12.0107 # carbon mass (g/mole) | membrane
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
# Separate atom groups
group membrane type 1
group adsorbant type 2
######################## Potential defition ########################
pair_style hybrid/overlay kolmogorov/crespi/z 14.0
####################################################################
pair_coeff * * none
pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range
####################################################################
#### Simulation settings ####
timestep 0.0001
fix thermostat adsorbant nve
fix rigid_membrane membrane setforce 0 0 0
compute COM1 membrane com
compute COM2 adsorbant com
############################
# Output
#dump 1 all xyz 100 trajec.xyz
#dump_modify 1 format line "%s %12.6f %12.6f %12.6f" element "C" "C"
thermo 100
thermo_style custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu
thermo_modify line one format float %14.8f
###### Run molecular dynamics ######
run 10000

45
examples/USER/misc/kolmogorov-crespi/in.bilayer-graphene Normal file
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# Initialization
units metal
boundary p p p
atom_style atomic
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use 2 atom types so that inter- and intra-layer
# interactions can be specified separately
read_data data.bilayer-graphene # read lammps data file
mass 1 12.0107 # carbon mass (g/mole) | membrane
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
# Separate atom groups
group membrane type 1
group adsorbant type 2
######################## Potential defition ########################
pair_style hybrid/overlay rebo kolmogorov/crespi/z 14.0
####################################################################
pair_coeff * * rebo CH.airebo C C # chemical
pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range
####################################################################
#### Simulation settings ####
timestep 0.0001
velocity all create 300.0 12345
fix thermostat all nve
compute COM1 membrane com
compute COM2 adsorbant com
############################
# Output
#dump 1 all xyz 100 trajec.xyz
#dump_modify 1 format line "%s %12.6f %12.6f %12.6f" element "C" "C"
thermo 10
thermo_style custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu
thermo_modify line one format float %14.8f
###### Run molecular dynamics ######
run 1000

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LAMMPS (17 Nov 2016)
# Initialization
units metal
boundary p p p
atom_style atomic
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use 2 atom types so that inter- and intra-layer
# interactions can be specified separately
read_data data.graphene-adsorbant # read lammps data file
orthogonal box = (0 0 -10) to (17.04 19.6761 40)
1 by 1 by 1 MPI processor grid
reading atoms ...
129 atoms
mass 1 12.0107 # carbon mass (g/mole) | membrane
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
# Separate atom groups
group membrane type 1
128 atoms in group membrane
group adsorbant type 2
1 atoms in group adsorbant
######################## Potential defition ########################
pair_style hybrid/overlay kolmogorov/crespi/z 14.0
####################################################################
pair_coeff * * none
pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range
####################################################################
#### Simulation settings ####
timestep 0.0001
fix thermostat adsorbant nve
fix rigid_membrane membrane setforce 0 0 0
compute COM1 membrane com
compute COM2 adsorbant com
############################
# Output
#dump 1 all xyz 100 trajec.xyz
#dump_modify 1 format line "%s %12.6f %12.6f %12.6f" element "C" "C"
thermo 100
thermo_style custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu
thermo_modify line one format float %14.8f
###### Run molecular dynamics ######
run 10000
Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 16
ghost atom cutoff = 16
binsize = 8 -> bins = 3 3 7
Memory usage per processor = 2.48399 Mbytes
Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3]
0 0.00000000 -0.02562011 -0.02562011 0.00000000 0.00000000 3.30000000
100 0.01000000 -0.02562011 -0.02584808 0.01377831 0.00000000 3.30302413
200 0.02000000 -0.02562011 -0.02650010 0.05318658 0.00000000 3.31198892
300 0.03000000 -0.02562011 -0.02748822 0.11290898 0.00000000 3.32658305
400 0.04000000 -0.02562011 -0.02868854 0.18545625 0.00000000 3.34632324
500 0.05000000 -0.02562011 -0.02996656 0.26269978 0.00000000 3.37059992
600 0.06000000 -0.02562011 -0.03120006 0.33725276 0.00000000 3.39872815
700 0.07000000 -0.02562011 -0.03229421 0.40338328 0.00000000 3.42999603
800 0.08000000 -0.02562011 -0.03318758 0.45737874 0.00000000 3.46370507
900 0.09000000 -0.02562011 -0.03385069 0.49745690 0.00000000 3.49919977
1000 0.10000000 -0.02562011 -0.03428002 0.52340564 0.00000000 3.53588638
1100 0.11000000 -0.02562011 -0.03449041 0.53612164 0.00000000 3.57324216
1200 0.12000000 -0.02562011 -0.03450775 0.53717016 0.00000000 3.61081749
1300 0.13000000 -0.02562011 -0.03436312 0.52842859 0.00000000 3.64823296
1400 0.14000000 -0.02562011 -0.03408851 0.51183115 0.00000000 3.68517357
1500 0.15000000 -0.02562011 -0.03371417 0.48920613 0.00000000 3.72138134
1600 0.16000000 -0.02562011 -0.03326714 0.46218758 0.00000000 3.75664759
1700 0.17000000 -0.02562011 -0.03277063 0.43217815 0.00000000 3.79080541
1800 0.18000000 -0.02562011 -0.03224395 0.40034589 0.00000000 3.82372274
1900 0.19000000 -0.02562011 -0.03170282 0.36763982 0.00000000 3.85529629
2000 0.20000000 -0.02562011 -0.03115972 0.33481494 0.00000000 3.88544626
2100 0.21000000 -0.02562011 -0.03062440 0.30246010 0.00000000 3.91411185
2200 0.22000000 -0.02562011 -0.03010433 0.27102702 0.00000000 3.94124749
2300 0.23000000 -0.02562011 -0.02960514 0.24085558 0.00000000 3.96681976
2400 0.24000000 -0.02562011 -0.02913096 0.21219623 0.00000000 3.99080483
2500 0.25000000 -0.02562011 -0.02868478 0.18522907 0.00000000 4.01318637
2600 0.26000000 -0.02562011 -0.02826867 0.16007955 0.00000000 4.03395384
2700 0.27000000 -0.02562011 -0.02788403 0.13683143 0.00000000 4.05310113
2800 0.28000000 -0.02562011 -0.02753171 0.11553708 0.00000000 4.07062542
2900 0.29000000 -0.02562011 -0.02721220 0.09622581 0.00000000 4.08652629
3000 0.30000000 -0.02562011 -0.02692571 0.07891041 0.00000000 4.10080498
3100 0.31000000 -0.02562011 -0.02667226 0.06359229 0.00000000 4.11346382
3200 0.32000000 -0.02562011 -0.02645177 0.05026555 0.00000000 4.12450573
3300 0.33000000 -0.02562011 -0.02626406 0.03892009 0.00000000 4.13393390
3400 0.34000000 -0.02562011 -0.02610893 0.02954399 0.00000000 4.14175142
3500 0.35000000 -0.02562011 -0.02598618 0.02212545 0.00000000 4.14796110
3600 0.36000000 -0.02562011 -0.02589566 0.01665409 0.00000000 4.15256529
3700 0.37000000 -0.02562011 -0.02583722 0.01312208 0.00000000 4.15556569
3800 0.38000000 -0.02562011 -0.02581079 0.01152492 0.00000000 4.15696329
3900 0.39000000 -0.02562011 -0.02581636 0.01186148 0.00000000 4.15675830
4000 0.40000000 -0.02562011 -0.02585398 0.01413478 0.00000000 4.15495012
4100 0.41000000 -0.02562011 -0.02592375 0.01835185 0.00000000 4.15153731
4200 0.42000000 -0.02562011 -0.02602587 0.02452390 0.00000000 4.14651764
4300 0.43000000 -0.02562011 -0.02616057 0.03266513 0.00000000 4.13988811
4400 0.44000000 -0.02562011 -0.02632813 0.04279292 0.00000000 4.13164506
4500 0.45000000 -0.02562011 -0.02652889 0.05492664 0.00000000 4.12178432
4600 0.46000000 -0.02562011 -0.02676317 0.06908643 0.00000000 4.11030130
4700 0.47000000 -0.02562011 -0.02703129 0.08529164 0.00000000 4.09719124
4800 0.48000000 -0.02562011 -0.02733352 0.10355859 0.00000000 4.08244950
4900 0.49000000 -0.02562011 -0.02767004 0.12389788 0.00000000 4.06607186
5000 0.50000000 -0.02562011 -0.02804086 0.14631034 0.00000000 4.04805502
5100 0.51000000 -0.02562011 -0.02844575 0.17078211 0.00000000 4.02839708
5200 0.52000000 -0.02562011 -0.02888415 0.19727899 0.00000000 4.00709829
5300 0.53000000 -0.02562011 -0.02935502 0.22573844 0.00000000 3.98416189
5400 0.54000000 -0.02562011 -0.02985670 0.25605986 0.00000000 3.95959511
5500 0.55000000 -0.02562011 -0.03038669 0.28809268 0.00000000 3.93341053
5600 0.56000000 -0.02562011 -0.03094143 0.32162137 0.00000000 3.90562766
5700 0.57000000 -0.02562011 -0.03151597 0.35634628 0.00000000 3.87627492
5800 0.58000000 -0.02562011 -0.03210361 0.39186361 0.00000000 3.84539210
5900 0.59000000 -0.02562011 -0.03269556 0.42764084 0.00000000 3.81303330
6000 0.60000000 -0.02562011 -0.03328042 0.46299030 0.00000000 3.77927044
6100 0.61000000 -0.02562011 -0.03384380 0.49704060 0.00000000 3.74419758
6200 0.62000000 -0.02562011 -0.03436783 0.52871353 0.00000000 3.70793588
6300 0.63000000 -0.02562011 -0.03483104 0.55670974 0.00000000 3.67063945
6400 0.64000000 -0.02562011 -0.03520832 0.57951248 0.00000000 3.63250187
6500 0.65000000 -0.02562011 -0.03547159 0.59542438 0.00000000 3.59376331
6600 0.66000000 -0.02562011 -0.03559125 0.60265655 0.00000000 3.55471782
6700 0.67000000 -0.02562011 -0.03553879 0.59948637 0.00000000 3.51572023
6800 0.68000000 -0.02562011 -0.03529110 0.58451568 0.00000000 3.47719153
6900 0.69000000 -0.02562011 -0.03483635 0.55703035 0.00000000 3.43962129
7000 0.70000000 -0.02562011 -0.03418150 0.51745146 0.00000000 3.40356509
7100 0.71000000 -0.02562011 -0.03336032 0.46781889 0.00000000 3.36963482
7200 0.72000000 -0.02562011 -0.03243997 0.41219328 0.00000000 3.33847933
7300 0.73000000 -0.02562011 -0.03152342 0.35679665 0.00000000 3.31075400
7400 0.74000000 -0.02562011 -0.03074422 0.30970201 0.00000000 3.28707906
7500 0.75000000 -0.02562011 -0.03025182 0.27994115 0.00000000 3.26798907
7600 0.76000000 -0.02562011 -0.03018799 0.27608346 0.00000000 3.25387900
7700 0.77000000 -0.02562011 -0.03065928 0.30456818 0.00000000 3.24495492
7800 0.78000000 -0.02562011 -0.03171321 0.36826788 0.00000000 3.24119821
7900 0.79000000 -0.02562011 -0.03332635 0.46576624 0.00000000 3.24235091
8000 0.80000000 -0.02562011 -0.03540847 0.59160963 0.00000000 3.24792582
8100 0.81000000 -0.02562011 -0.03782107 0.73742737 0.00000000 3.25723999
8200 0.82000000 -0.02562011 -0.04040358 0.89351498 0.00000000 3.26946524
8300 0.83000000 -0.02562011 -0.04299943 1.05040805 0.00000000 3.28368734
8400 0.84000000 -0.02562011 -0.04547588 1.20008497 0.00000000 3.29896495
8500 0.85000000 -0.02562011 -0.04773539 1.33664998 0.00000000 3.31438148
8600 0.86000000 -0.02562011 -0.04971913 1.45654768 0.00000000 3.32908572
8700 0.87000000 -0.02562011 -0.05140498 1.55844058 0.00000000 3.34231951
8800 0.88000000 -0.02562011 -0.05280154 1.64284923 0.00000000 3.35343297
8900 0.89000000 -0.02562011 -0.05394019 1.71166905 0.00000000 3.36188901
9000 0.90000000 -0.02562011 -0.05486563 1.76760281 0.00000000 3.36725955
9100 0.91000000 -0.02562011 -0.05562624 1.81357448 0.00000000 3.36921674
9200 0.92000000 -0.02562011 -0.05626439 1.85214388 0.00000000 3.36752214
9300 0.93000000 -0.02562011 -0.05680723 1.88495335 0.00000000 3.36201704
9400 0.94000000 -0.02562011 -0.05725852 1.91222952 0.00000000 3.35261669
9500 0.95000000 -0.02562011 -0.05759110 1.93233038 0.00000000 3.33931122
9600 0.96000000 -0.02562011 -0.05774152 1.94142215 0.00000000 3.32217490
9700 0.97000000 -0.02562011 -0.05760814 1.93336063 0.00000000 3.30138553
9800 0.98000000 -0.02562012 -0.05705439 1.89989139 0.00000000 3.27725394
9900 0.99000000 -0.02562012 -0.05592079 1.83137685 0.00000000 3.25026233
10000 1.00000000 -0.02562012 -0.05404919 1.71825669 0.00000000 3.22110695
Loop time of 0.381846 on 1 procs for 10000 steps with 129 atoms
Performance: 226.269 ns/day, 0.106 hours/ns, 26188.568 timesteps/s
131.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.30936 | 0.30936 | 0.30936 | 0.0 | 81.02
Neigh | 0.000139 | 0.000139 | 0.000139 | 0.0 | 0.04
Comm | 0.051287 | 0.051287 | 0.051287 | 0.0 | 13.43
Output | 0.00181 | 0.00181 | 0.00181 | 0.0 | 0.47
Modify | 0.005645 | 0.005645 | 0.005645 | 0.0 | 1.48
Other | | 0.01361 | | | 3.56
Nlocal: 129 ave 129 max 129 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1867 ave 1867 max 1867 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 290 ave 290 max 290 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 290
Ave neighs/atom = 2.24806
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (17 Nov 2016)
# Initialization
units metal
boundary p p p
atom_style atomic
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use 2 atom types so that inter- and intra-layer
# interactions can be specified separately
read_data data.bilayer-graphene # read lammps data file
orthogonal box = (0 0 -20) to (17.04 19.6761 40)
2 by 2 by 1 MPI processor grid
reading atoms ...
256 atoms
mass 1 12.0107 # carbon mass (g/mole) | membrane
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
# Separate atom groups
group membrane type 1
128 atoms in group membrane
group adsorbant type 2
128 atoms in group adsorbant
######################## Potential defition ########################
pair_style hybrid/overlay rebo kolmogorov/crespi/z 14.0
####################################################################
pair_coeff * * rebo CH.airebo C C # chemical
Reading potential file CH.airebo with DATE: 2011-10-25
pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range
####################################################################
#### Simulation settings ####
timestep 0.0001
velocity all create 300.0 12345
fix thermostat all nve
compute COM1 membrane com
compute COM2 adsorbant com
############################
# Output
#dump 1 all xyz 100 trajec.xyz
#dump_modify 1 format line "%s %12.6f %12.6f %12.6f" element "C" "C"
thermo 10
thermo_style custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu
thermo_modify line one format float %14.8f
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
3 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 16
ghost atom cutoff = 16
binsize = 8 -> bins = 3 3 8
Memory usage per processor = 3.22197 Mbytes
Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3]
0 0.00000000 -1888.67041214 -1898.55881323 300.00000000 0.00000000 3.30000000
10 0.00100000 -1888.67037221 -1898.21029897 289.42778520 -0.00020126 3.30020126
20 0.00200000 -1888.67021541 -1897.22943612 259.67456089 -0.00041357 3.30041357
30 0.00300000 -1888.66999308 -1895.86681311 218.34126559 -0.00063673 3.30063673
40 0.00400000 -1888.66978354 -1894.47163830 176.02000692 -0.00087055 3.30087055
50 0.00500000 -1888.66966068 -1893.37123377 142.63902862 -0.00111486 3.30111486
60 0.00600000 -1888.66966132 -1892.75822749 124.04127205 -0.00136952 3.30136952
70 0.00700000 -1888.66976974 -1892.63445751 120.28297808 -0.00163441 3.30163441
80 0.00800000 -1888.66992867 -1892.83467462 126.35245792 -0.00190946 3.30190946
90 0.00900000 -1888.67006868 -1893.11387069 134.81862145 -0.00219458 3.30219458
100 0.01000000 -1888.67013621 -1893.25481851 139.09272853 -0.00248973 3.30248973
110 0.01100000 -1888.67011201 -1893.15155790 135.96068294 -0.00279489 3.30279489
120 0.01200000 -1888.67001496 -1892.84002960 126.51230266 -0.00311004 3.30311004
130 0.01300000 -1888.66988997 -1892.47004238 115.29120968 -0.00343519 3.30343519
140 0.01400000 -1888.66979230 -1892.23503116 108.16426723 -0.00377038 3.30377038
150 0.01500000 -1888.66976478 -1892.28630583 109.72070257 -0.00411562 3.30411562
160 0.01600000 -1888.66982054 -1892.66640611 121.25071190 -0.00447099 3.30447099
170 0.01700000 -1888.66993790 -1893.28862637 140.12442721 -0.00483654 3.30483654
180 0.01800000 -1888.67007017 -1893.97029258 160.80119589 -0.00521235 3.30521235
190 0.01900000 -1888.67016712 -1894.50458787 177.00801243 -0.00559851 3.30559851
200 0.02000000 -1888.67019459 -1894.73890106 184.11590729 -0.00599512 3.30599512
210 0.02100000 -1888.67014420 -1894.62906014 180.78501932 -0.00640230 3.30640230
220 0.02200000 -1888.67003680 -1894.25249103 169.36370738 -0.00682016 3.30682016
230 0.02300000 -1888.66991386 -1893.77601613 154.91186767 -0.00724883 3.30724883
240 0.02400000 -1888.66982525 -1893.38995084 143.20188490 -0.00768845 3.30768845
250 0.02500000 -1888.66980630 -1893.23138936 138.39193056 -0.00813913 3.30813913
260 0.02600000 -1888.66986130 -1893.32993923 141.38012476 -0.00860097 3.30860097
270 0.02700000 -1888.66996305 -1893.60070606 149.59171763 -0.00907408 3.30907408
280 0.02800000 -1888.67006686 -1893.88587226 158.24010433 -0.00955849 3.30955849
290 0.02900000 -1888.67012981 -1894.02402669 162.42960292 -0.01005424 3.31005424
300 0.03000000 -1888.67012722 -1893.91715234 159.18726627 -0.01056129 3.31056129
310 0.03100000 -1888.67005731 -1893.57037242 148.66857852 -0.01107957 3.31107957
320 0.03200000 -1888.66994573 -1893.09358619 134.20694883 -0.01160898 3.31160898
330 0.03300000 -1888.66983589 -1892.66132663 121.09614207 -0.01214935 3.31214935
340 0.03400000 -1888.66977410 -1892.44446345 114.51869676 -0.01270046 3.31270046
350 0.03500000 -1888.66978826 -1892.53901235 117.38674604 -0.01326207 3.31326207
360 0.03600000 -1888.66987439 -1892.92337288 129.04508371 -0.01383390 3.31383390
370 0.03700000 -1888.66999800 -1893.46445570 145.45701555 -0.01441561 3.31441561
380 0.03800000 -1888.67010960 -1893.97065516 160.81100020 -0.01500688 3.31500688
390 0.03900000 -1888.67016540 -1894.26835818 169.84119247 -0.01560734 3.31560734
400 0.04000000 -1888.67014667 -1894.26967975 169.88185546 -0.01621664 3.31621664
410 0.04100000 -1888.67006166 -1894.00321069 161.80014280 -0.01683442 3.31683442
420 0.04200000 -1888.66994367 -1893.60086324 149.59707418 -0.01746033 3.31746033
430 0.04300000 -1888.66984058 -1893.24559841 138.82197275 -0.01809405 3.31809405
440 0.04400000 -1888.66979399 -1893.09727874 134.32357877 -0.01873527 3.31873527
450 0.04500000 -1888.66982139 -1893.22837442 138.30000378 -0.01938373 3.31938373
460 0.04600000 -1888.66990972 -1893.59670383 149.47191354 -0.02003918 3.32003918
470 0.04700000 -1888.67002173 -1894.06542598 163.68887743 -0.02070143 3.32070143
480 0.04800000 -1888.67011389 -1894.46010842 175.66018439 -0.02137030 3.32137030
490 0.04900000 -1888.67015175 -1894.63688098 181.02206322 -0.02204565 3.32204565
500 0.05000000 -1888.67012158 -1894.53632221 177.97216882 -0.02272740 3.32272740
510 0.05100000 -1888.67003762 -1894.20444731 167.90610436 -0.02341547 3.32341547
520 0.05200000 -1888.66993151 -1893.77231066 154.79891353 -0.02410981 3.32410981
530 0.05300000 -1888.66984505 -1893.40525927 143.66572038 -0.02481040 3.32481040
540 0.05400000 -1888.66981408 -1893.23762083 138.58074854 -0.02551724 3.32551724
550 0.05500000 -1888.66985005 -1893.31793594 141.01630317 -0.02623032 3.32623032
560 0.05600000 -1888.66993737 -1893.59069013 149.28862751 -0.02694963 3.32694963
570 0.05700000 -1888.67003852 -1893.92089571 159.30352588 -0.02767517 3.32767517
580 0.05800000 -1888.67011322 -1894.15124753 166.28980524 -0.02840691 3.32840691
590 0.05900000 -1888.67013192 -1894.16548041 166.72104345 -0.02914478 3.32914478
600 0.06000000 -1888.67008713 -1893.93443318 159.71275856 -0.02988871 3.32988871
610 0.06100000 -1888.66999438 -1893.52841656 147.39760646 -0.03063856 3.33063856
620 0.06200000 -1888.66988809 -1893.09235021 134.17119963 -0.03139416 3.33139416
630 0.06300000 -1888.66980996 -1892.79172016 125.05288240 -0.03215531 3.33215531
640 0.06400000 -1888.66979261 -1892.74755390 123.71346730 -0.03292176 3.33292176
650 0.06500000 -1888.66984332 -1892.98665459 130.96590324 -0.03369323 3.33369323
660 0.06600000 -1888.66994245 -1893.42999868 144.41332389 -0.03446937 3.33446937
670 0.06700000 -1888.67005233 -1893.92310681 159.37018806 -0.03524986 3.33524986
680 0.06800000 -1888.67013309 -1894.29451581 170.63575808 -0.03603430 3.33603430
690 0.06900000 -1888.67015452 -1894.41878117 174.40514192 -0.03682229 3.33682229
700 0.07000000 -1888.67010897 -1894.26288036 169.67671530 -0.03761343 3.33761343
710 0.07100000 -1888.67001367 -1893.89812904 158.61357114 -0.03840729 3.33840729
720 0.07200000 -1888.66990378 -1893.47348746 145.73388454 -0.03920344 3.33920344
730 0.07300000 -1888.66982212 -1893.15984839 136.22099960 -0.04000148 3.34000148
740 0.07400000 -1888.66980109 -1893.08373746 133.91254029 -0.04080098 3.34080098
750 0.07500000 -1888.66984794 -1893.27755511 139.79127024 -0.04160156 3.34160156
760 0.07600000 -1888.66994215 -1893.66837365 151.64528967 -0.04240282 3.34240282
770 0.07700000 -1888.67004554 -1894.10941206 165.02263027 -0.04320441 3.34320441
780 0.07800000 -1888.67011702 -1894.43947545 175.03411436 -0.04400599 3.34400599
790 0.07900000 -1888.67013297 -1894.54590471 178.26254255 -0.04480726 3.34480726
800 0.08000000 -1888.67008751 -1894.40384142 173.95392406 -0.04560792 3.34560792
810 0.08100000 -1888.66999923 -1894.08389003 164.24973321 -0.04640773 3.34640773
820 0.08200000 -1888.66990447 -1893.72313979 153.30795965 -0.04720647 3.34720647
830 0.08300000 -1888.66984367 -1893.46839190 145.58111626 -0.04800393 3.34800393
840 0.08400000 -1888.66984156 -1893.41412536 143.93481093 -0.04879995 3.34879995
850 0.08500000 -1888.66989670 -1893.56426154 148.48805553 -0.04959439 3.34959439
860 0.08600000 -1888.66998222 -1893.83463719 156.68827294 -0.05038713 3.35038713
870 0.08700000 -1888.67006171 -1894.09325045 164.53181920 -0.05117805 3.35117805
880 0.08800000 -1888.67010273 -1894.21712661 168.28880100 -0.05196706 3.35196706
890 0.08900000 -1888.67008993 -1894.14263950 166.02935656 -0.05275408 3.35275408
900 0.09000000 -1888.67002891 -1893.89014571 158.37090587 -0.05353904 3.35353904
910 0.09100000 -1888.66994326 -1893.55535709 148.21649469 -0.05432186 3.35432186
920 0.09200000 -1888.66986526 -1893.27257949 139.63979178 -0.05510247 3.35510247
930 0.09300000 -1888.66982730 -1893.16330891 136.32582949 -0.05588078 3.35588078
940 0.09400000 -1888.66984631 -1893.28643285 140.06065785 -0.05665670 3.35665670
950 0.09500000 -1888.66991503 -1893.61245342 149.94957268 -0.05743015 3.35743015
960 0.09600000 -1888.67000691 -1894.03423922 162.74316516 -0.05820101 3.35820101
970 0.09700000 -1888.67008649 -1894.40848025 174.09469037 -0.05896915 3.35896915
980 0.09800000 -1888.67012436 -1894.61056767 180.22458605 -0.05973444 3.35973444
990 0.09900000 -1888.67010608 -1894.58107659 179.33042338 -0.06049672 3.36049672
1000 0.10000000 -1888.67003981 -1894.34773305 172.25312330 -0.06125581 3.36125581
Loop time of 2.21183 on 4 procs for 1000 steps with 256 atoms
Performance: 3.906 ns/day, 6.144 hours/ns, 452.115 timesteps/s
120.2% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.9363 | 1.9928 | 2.0303 | 2.5 | 90.10
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.16714 | 0.20465 | 0.26123 | 7.8 | 9.25
Output | 0.002469 | 0.0028505 | 0.003949 | 1.2 | 0.13
Modify | 0.002423 | 0.0026275 | 0.002853 | 0.4 | 0.12
Other | | 0.008904 | | | 0.40
Nlocal: 64 ave 64 max 64 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 1265 ave 1265 max 1265 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 11824 ave 11824 max 11824 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 23648 ave 23648 max 23648 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 94592
Ave neighs/atom = 369.5
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:02

8
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# Kolmogorov-Crespi Potential
#
# Cite as A.N. Kolmogorov & V. H. Crespi,
# Registry-dependent interlayer potential for graphitic systems
# Physical Review B 71, 2354150 (2005)
#
# z0 C0 C2 C4 C delta lambda A S
C C 3.34 15.71 12.29 4.933 3.030 0.578 3.629 10.238 1.0

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Jaap Kroes (Radboud Universiteit)
based on previous versions by Merel van Wijk and by Marco Raguzzoni
This is a simplified version of the potential described in
[Kolmogorov & Crespi, Phys. Rev. B 71, 235415 (2005)]
The simplification is that all normals are taken along the z-direction
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "pair_kolmogorov_crespi_z.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MAXLINE 1024
#define DELTA 4
/* ---------------------------------------------------------------------- */
PairKolmogorovCrespiZ::PairKolmogorovCrespiZ(LAMMPS *lmp) : Pair(lmp)
{
writedata = 1;
// initialize element to parameter maps
nelements = 0;
elements = NULL;
nparams = maxparam = 0;
params = NULL;
elem2param = NULL;
map = NULL;
// always compute energy offset
offset_flag = true;
}
/* ---------------------------------------------------------------------- */
PairKolmogorovCrespiZ::~PairKolmogorovCrespiZ()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(cut);
memory->destroy(offset);
}
if (elements)
for (int i = 0; i < nelements; i++) delete [] elements[i];
delete [] elements;
memory->destroy(params);
memory->destroy(elem2param);
if (allocated) delete [] map;
}
/* ---------------------------------------------------------------------- */
void PairKolmogorovCrespiZ::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair, fpair1;
double rsq,r,rhosq,exp1,exp2,r6,r8;
double frho,sumC,sumC2,sumCff,fsum,rdsq;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
jtype = type[j];
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
// rho^2 = r^2 - (n,r) = r^2 - z^2
rhosq = delx*delx + dely*dely;
rsq = rhosq + delz*delz;
if (rsq < cutsq[itype][jtype]) {
int iparam_ij = elem2param[map[itype]][map[jtype]];
Param& p = params[iparam_ij];
r = sqrt(rsq);
r6 = rsq*rsq*rsq;
r8 = r6*rsq;
rdsq = rhosq*p.delta2inv; // (rho/delta)^2
// store exponents
exp1 = exp(-p.lambda*(r-p.z0));
exp2 = exp(-rdsq);
// note that f(rho_ij) equals f(rho_ji) as normals are all along z
sumC = p.C0+p.C2*rdsq+p.C4*rdsq*rdsq;
sumC2 = (2*p.C2+4*p.C4*rdsq)*p.delta2inv;
frho = exp2*sumC;
sumCff = p.C + 2*frho;
// derivatives
fpair = -6.0*p.A*p.z06/r8+p.lambda*exp1/r*sumCff;
fpair1 = exp1*exp2*(4.0*p.delta2inv*sumC-2.0*sumC2);
fsum = fpair + fpair1;
f[i][0] += delx*fsum;
f[i][1] += dely*fsum;
// fi_z does not contain contributions from df/dr
// because rho_ij does not depend on z_i or z_j
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fsum;
f[j][1] -= dely*fsum;
f[j][2] -= delz*fpair;
}
if (eflag) {
evdwl = -p.A*p.z06/r6+ exp1*sumCff+offset[itype][jtype];
}
if (evflag){
ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz);
}
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairKolmogorovCrespiZ::allocate()
{
allocated = 1;
int n = atom->ntypes;
memory->create(setflag,n+1,n+1,"pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
memory->create(cutsq,n+1,n+1,"pair:cutsq");
memory->create(cut,n+1,n+1,"pair:cut");
memory->create(offset,n+1,n+1,"pair:offset");
map = new int[atom->ntypes+1];
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairKolmogorovCrespiZ::settings(int narg, char **arg)
{
if (narg != 1) error->all(FLERR,"Illegal pair_style command");
if (strcmp(force->pair_style)!="hybrid/overlay")
error->all(FLERR,"ERROR: requires hybrid/overlay pair_style");
cut_global = force->numeric(FLERR,arg[0]);
// reset cutoffs that have been explicitly set
if (allocated) {
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
if (setflag[i][j]) cut[i][j] = cut_global;
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairKolmogorovCrespiZ::coeff(int narg, char **arg)
{
int i,j,n;
if (narg != 3 + atom->ntypes)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
int ilo,ihi,jlo,jhi;
force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
// read args that map atom types to elements in potential file
// map[i] = which element the Ith atom type is, -1 if NULL
// nelements = # of unique elements
// elements = list of element names
if (elements) {
for (i = 0; i < nelements; i++) delete [] elements[i];
delete [] elements;
}
elements = new char*[atom->ntypes];
for (i = 0; i < atom->ntypes; i++) elements[i] = NULL;
nelements = 0;
for (i = 3; i < narg; i++) {
if (strcmp(arg[i],"NULL") == 0) {
map[i-2] = -1;
continue;
}
for (j = 0; j < nelements; j++)
if (strcmp(arg[i],elements[j]) == 0) break;
map[i-2] = j;
if (j == nelements) {
n = strlen(arg[i]) + 1;
elements[j] = new char[n];
strcpy(elements[j],arg[i]);
nelements++;
}
}
read_file(arg[2]);
double cut_one = cut_global;
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
cut[i][j] = cut_one;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairKolmogorovCrespiZ::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
if (offset_flag) {
int iparam_ij = elem2param[map[i]][map[j]];
offset[i][j] = params[iparam_ij].A*pow(params[iparam_ij].z0/cut[i][j],6);
} else offset[i][j] = 0.0;
offset[j][i] = offset[i][j];
return cut[i][j];
}
/* ----------------------------------------------------------------------
read Kolmogorov-Crespi potential file
------------------------------------------------------------------------- */
void PairKolmogorovCrespiZ::read_file(char *filename)
{
int params_per_line = 11;
char **words = new char*[params_per_line+1];
memory->sfree(params);
params = NULL;
nparams = maxparam = 0;
// open file on proc 0
FILE *fp;
if (comm->me == 0) {
fp = force->open_potential(filename);
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open KC potential file %s",filename);
error->one(FLERR,str);
}
}
// read each line out of file, skipping blank lines or leading '#'
// store line of params if all 3 element tags are in element list
int i,j,n,m,nwords,ielement,jelement;
char line[MAXLINE],*ptr;
int eof = 0;
while (1) {
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fp);
if (ptr == NULL) {
eof = 1;
fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
if (eof) break;
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
// strip comment, skip line if blank
if ((ptr = strchr(line,'#'))) *ptr = '\0';
nwords = atom->count_words(line);
if (nwords == 0) continue;
// concatenate additional lines until have params_per_line words
while (nwords < params_per_line) {
n = strlen(line);
if (comm->me == 0) {
ptr = fgets(&line[n],MAXLINE-n,fp);
if (ptr == NULL) {
eof = 1;
fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
if (eof) break;
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
if ((ptr = strchr(line,'#'))) *ptr = '\0';
nwords = atom->count_words(line);
}
if (nwords != params_per_line)
error->all(FLERR,"Insufficient format in KC potential file");
// words = ptrs to all words in line
nwords = 0;
words[nwords++] = strtok(line," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f"))) continue;
// ielement,jelement = 1st args
// if these 2 args are in element list, then parse this line
// else skip to next line (continue)
for (ielement = 0; ielement < nelements; ielement++)
if (strcmp(words[0],elements[ielement]) == 0) break;
if (ielement == nelements) continue;
for (jelement = 0; jelement < nelements; jelement++)
if (strcmp(words[1],elements[jelement]) == 0) break;
if (jelement == nelements) continue;
// load up parameter settings and error check their values
if (nparams == maxparam) {
maxparam += DELTA;
params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),
"pair:params");
}
params[nparams].ielement = ielement;
params[nparams].jelement = jelement;
params[nparams].z0 = atof(words[2]);
params[nparams].C0 = atof(words[3]);
params[nparams].C2 = atof(words[4]);
params[nparams].C4 = atof(words[5]);
params[nparams].C = atof(words[6]);
params[nparams].delta = atof(words[7]);
params[nparams].lambda = atof(words[8]);
params[nparams].A = atof(words[9]);
// S provides a convenient scaling of all energies
params[nparams].S = atof(words[10]);
// energies in meV further scaled by S
double meV = 1.0e-3*params[nparams].S;
params[nparams].C *= meV;
params[nparams].A *= meV;
params[nparams].C0 *= meV;
params[nparams].C2 *= meV;
params[nparams].C4 *= meV;
// precompute some quantities
params[nparams].delta2inv = pow(params[nparams].delta,-2);
params[nparams].z06 = pow(params[nparams].z0,6);
nparams++;
if(nparams >= pow(atom->ntypes,3)) break;
}
memory->destroy(elem2param);
memory->create(elem2param,nelements,nelements,"pair:elem2param");
for (i = 0; i < nelements; i++) {
for (j = 0; j < nelements; j++) {
n = -1;
for (m = 0; m < nparams; m++) {
if (i == params[m].ielement && j == params[m].jelement) {
if (n >= 0) error->all(FLERR,"Potential file has duplicate entry");
n = m;
}
}
if (n < 0) error->all(FLERR,"Potential file is missing an entry");
elem2param[i][j] = n;
}
}
delete [] words;
}
/* ---------------------------------------------------------------------- */

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
PairStyle(kolmogorov/crespi/z,PairKolmogorovCrespiZ)
#else
#ifndef LMP_PAIR_KolmogorovCrespiZ_H
#define LMP_PAIR_KolmogorovCrespiZ_H
#include "pair.h"
namespace LAMMPS_NS {
class PairKolmogorovCrespiZ : public Pair {
public:
PairKolmogorovCrespiZ(class LAMMPS *);
virtual ~PairKolmogorovCrespiZ();
virtual void compute(int, int);
void settings(int, char **);
void coeff(int, char **);
double init_one(int, int);
protected:
int me;
struct Param {
double z0,C0,C2,C4,C,delta,lambda,A,S;
double delta2inv,z06;
int ielement,jelement;
};
Param *params; // parameter set for I-J interactions
char **elements; // names of unique elements
int **elem2param; // mapping from element pairs to parameters
int *map; // mapping from atom types to elements
int nelements; // # of unique elements
int nparams; // # of stored parameter sets
int maxparam; // max # of parameter sets
double cut_global;
double **cut;
double **offset;
void read_file( char * );
void allocate();
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Incorrect args for pair coefficients
Self-explanatory. Check the input script or data file.
E: All pair coeffs are not set
All pair coefficients must be set in the data file or by the
pair_coeff command before running a simulation.
*/