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# Tersoff parameters for various elements and mixtures
# multiple entries can be added to this file, LAMMPS reads the ones it needs
# these entries are in LAMMPS "metal" units:
# A,B = eV; lambda1,lambda2,lambda3 = 1/Angstroms; R,D = Angstroms
# other quantities are unitless
# Aidan Thompson (athomps at sandia.gov) takes full blame for this
# file. It specifies various potentials published by J. Tersoff for
# silicon, carbon and germanium. Since Tersoff published several
# different silicon potentials, I refer to them using atom types
# Si(B), Si(C) and Si(D). The last two are almost almost identical but
# refer to two different publications. These names should be used in
# the LAMMPS command when the file is invoked. For example:
# pair_coeff * * SiCGe.tersoff Si(B). The Si(D), C and Ge potentials
# can be used pure silicon, pure carbon, pure germanium, binary SiC,
# and binary SiGe, but not binary GeC or ternary SiGeC. LAMMPS will
# generate an error if this file is used with any combination
# involving C and Ge, since there are no entries for the GeC
# interactions (Tersoff did not publish parameters for this
# cross-interaction.)
# format of a single entry (one or more lines):
# element 1, element 2, element 3,
# m, gamma, lambda3, c, d, costheta0, n, beta, lambda2, B, R, D, lambda1, A
# The original Tersoff potential for Silicon, Si(B)
# J. Tersoff, PRB, 37, 6991 (1988)
Si(B) Si(B) Si(B) 3.0 1.0 1.3258 4.8381 2.0417 0.0000 22.956
0.33675 1.3258 95.373 3.0 0.2 3.2394 3264.7
# The later Tersoff potential for Silicon, Si(C)
# J. Tersoff, PRB, 38, 9902 (1988)
Si(C) Si(C) Si(C) 3.0 1.0 1.7322 1.0039e5 16.218 -0.59826 0.78734
1.0999e-6 1.7322 471.18 2.85 0.15 2.4799 1830.8
# The later Tersoff potential for Carbon, Silicon, and Germanium
# J. Tersoff, PRB, 39, 5566 (1989) + errata (PRB 41, 3248)
# The Si and C parameters are very close to those in SiC.tersoff
C C C 3.0 1.0 0.0 3.8049e4 4.3484 -0.57058 0.72751 1.5724e-7 2.2119 346.74 1.95 0.15 3.4879 1393.6
Si(D) Si(D) Si(D) 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 1.1000e-6 1.7322 471.18 2.85 0.15 2.4799 1830.8
Ge Ge Ge 3.0 1.0 0.0 1.0643e5 15.652 -0.43884 0.75627 9.0166e-7 1.7047 419.23 2.95 0.15 2.4451 1769.0
C Si(D) Si(D) 3.0 1.0 0.0 3.8049e4 4.3484 -0.57058 0.72751 1.5724e-7 1.97205 395.1451 2.3573 0.1527 2.9839 1597.3111
C Si(D) C 3.0 1.0 0.0 3.8049e4 4.3484 -0.57058 0.72751 0.0 0.0 0.0 1.95 0.15 0.0 0.0
C C Si(D) 3.0 1.0 0.0 3.8049e4 4.3484 -0.57058 0.72751 0.0 0.0 0.0 2.3573 0.1527 0.0 0.0
Si(D) C C 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 1.1000e-6 1.97205 395.1451 2.3573 0.1527 2.9839 1597.3111
Si(D) Si(D) C 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 0.0 0.0 0.0 2.3573 0.1527 0.0 0.0
Si(D) C Si(D) 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 0.0 0.0 0.0 2.85 0.15 0.0 0.0
Si(D) Ge Ge 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 1.1000e-6 1.71845 444.7177 2.8996 0.1500 2.4625 1799.6347
Si(D) Si(D) Ge 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 0.0 0.0 0.0 2.8996 0.1500 0.0 0.0
Si(D) Ge Si(D) 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 0.0 0.0 0.0 2.85 0.15 0.0 0.0
Ge Si(D) Si(D) 3.0 1.0 0.0 1.0643e5 15.652 -0.43884 0.75627 9.0166e-7 1.71845 444.7177 2.8996 0.1500 2.4625 1799.6347
Ge Si(D) Ge 3.0 1.0 0.0 1.0643e5 15.652 -0.43884 0.75627 0.0 0.0 0.0 2.95 0.15 0.0 0.0
Ge Ge Si(D) 3.0 1.0 0.0 1.0643e5 15.652 -0.43884 0.75627 0.0 0.0 0.0 2.8996 0.1500 0.0 0.0
# Optimized Tersoff for Carbon: Lindsay and Broido PRB 81, 205441 (2010)
# element 1, element 2, element 3,
# m, gamma, lambda3, c, d, costheta0, n, beta, lambda2, B, R, D, lambda1, A
C(O) C(O) C(O) 3.0 1.0 0.0 3.8049e4 4.3484 -0.930 0.72751 1.5724e-7 2.2119 430.0 1.95 0.15 3.4879 1393.6

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i-PI path integral interface examples
=====================================
This folder contains a couple of examples to run LAMMPS as a client,
exchanging information on the atomic configurations, energy and forces
with the i-PI Python interface
[http://epfl-cosmo.github.io/gle4md/index.html?page=ipi]. These
examples require a working copy of i-PI and compiling LAMMPS in a UNIX
environment. Note that a copy of i-PI is provided with LAMMPS, in the
tools/i-pi directory.
Note that the i-PI examples listed here are designed for the public V1.0
version of i-PI. Refer to the LAMMPS examples distributed with i-PI if you
are using a development version.
Path integral simulation of graphene
------------------------------------
The example in this folder uses the external wrapper i-PI to perform
path integral molecular dynamics simulation of a graphene sheet, using
LAMMPS as the force back-end. The output is generated by i-PI. Please
refer to its documentation for an explanation of the input parameters
and the format of the output.
How to run i-PI
---------------
You should have a relatively recent (>=2.5) version of Python and Numpy,
and the public version of i-PI. You can then run i-PI by executing
```bash
$PATHTOIPI/i-pi i-pi_input.xml
```
In a separate terminal, then, you should run LAMMPS compiled to provide
fix_ipi functionalities.
```bash
$LAMMPS < in.graphene
```
You can run multiple instances of LAMMPS if you want to exploit the
parallelism over the path integral beads.

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<simulation verbosity="medium">
<initialize nbeads='8'>
<file mode='xyz' units="angstrom"> i-pi_positions.xyz </file>
<cell mode='manual' units="angstrom"> [ 51.8,0,0,0, 49.84,0,0,0, 200 ] </cell>
<velocities mode='thermal' units='kelvin'> 300 </velocities>
</initialize>
<output prefix='graphene'>
<properties stride='5' filename='out' flush="10" > [ step, time{picosecond}, conserved{electronvolt}, temperature{kelvin}, kinetic_cv{electronvolt}, potential{electronvolt}, pressure_cv{megapascal}] </properties>
<properties stride='5' filename='iso' flush="10" > [ isotope_tdfep(1.167;C), isotope_scfep(1.167;0) ] </properties>
<trajectory stride='20' filename='pos' flush="100"> positions{angstrom}</trajectory>
<checkpoint stride='2000' />
</output>
<total_steps>1000</total_steps>
<total_time>128000</total_time>
<prng><seed>8417</seed></prng>
<forces>
<socket mode="unix">
<address>graphene</address>
</socket>
</forces>
<ensemble mode='nvt'>
<thermostat mode='gle'>
<A shape='(5,5)'>
[ 1.124524713863e-3, 1.648702679619e-6, 6.970075857471e-5, -2.202066291263e-4, 1.401342873485e-3, -1.681700567912e-6, 5.197673899653e-10, 4.365423872046e-6, -1.200041116490e-6, 2.564577183580e-6, -8.965478630849e-5, -4.365423872046e-6, 8.218704940997e-6, 3.114246791997e-5, -6.044142906315e-5, -6.272281358913e-5, 1.200041116490e-6, -3.114246791997e-5, 1.612301941566e-4, 6.958958085115e-5, 1.318373360752e-3, -2.564577183580e-6, 6.044142906315e-5, -6.958958085115e-5, 1.872119364197e-3]
</A>
</thermostat>
<timestep units="femtosecond">1.0</timestep>
<temperature units='kelvin'>300</temperature>
<fixcom> True </fixcom>
</ensemble>
</simulation>

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960
# CELL(abcABC): 97.88781 94.18395 377.94522 90.00000 90.00000 90.00000 Traj: positions{angstrom} Step: 0 Bead: 1
C 7.15475e-01 1.26524e+00 9.97915e+01
C 2.09985e+00 1.18143e+00 9.97109e+01
C 5.07242e+00 1.23374e+00 9.96719e+01
C 4.29041e+00 4.98626e+01 9.97308e+01
C 6.47807e+00 1.15077e+00 9.95883e+01
C 7.18569e+00 4.97877e+01 9.95694e+01
C 9.35911e+00 1.19990e+00 9.95027e+01
C 8.63601e+00 6.42175e-03 9.94842e+01
C 1.08206e+01 1.21481e+00 9.95814e+01
C 1.15374e+01 -1.68189e-02 9.95679e+01
C 1.37470e+01 1.18985e+00 9.96755e+01
C 1.51563e+01 1.23490e+00 9.95861e+01
C 1.80384e+01 1.25728e+00 9.96417e+01
C 1.72820e+01 4.98419e+01 9.96231e+01
C 1.94063e+01 1.27641e+00 9.96542e+01
C 2.23076e+01 1.32718e+00 9.93593e+01
C 2.37552e+01 1.25278e+00 9.91791e+01
C 2.44592e+01 4.98163e+01 9.91590e+01
C 2.66342e+01 1.27670e+00 9.90688e+01
C 2.80589e+01 1.22070e+00 9.90885e+01
C 3.10029e+01 1.21580e+00 9.90967e+01
C 3.23935e+01 1.21806e+00 9.91951e+01
C 3.52403e+01 1.24742e+00 9.93940e+01
C 3.66656e+01 1.16527e+00 9.95791e+01
C 3.96153e+01 1.16044e+00 9.96550e+01
C 4.09651e+01 1.23964e+00 9.98787e+01
C 4.31792e+01 -5.88367e-03 1.00166e+02
C 4.38776e+01 1.28179e+00 1.00075e+02
C 4.53623e+01 1.24893e+00 1.00040e+02
C 4.81683e+01 1.27366e+00 9.99208e+01
C 4.96696e+01 1.27345e+00 1.00001e+02
C 5.03959e+01 1.09601e-02 1.00104e+02
C 7.56174e-01 3.76124e+00 9.98238e+01
C 2.18247e+00 3.76133e+00 9.97643e+01
C 2.82638e+00 2.50778e+00 9.96712e+01
C 4.35925e+00 2.44300e+00 9.97631e+01
C 5.00628e+00 3.74090e+00 9.97389e+01
C 6.45458e+00 3.72771e+00 9.97150e+01
C 7.20557e+00 2.50215e+00 9.96567e+01
C 8.59516e+00 2.53369e+00 9.97364e+01
C 9.32931e+00 3.78970e+00 9.97350e+01
C 1.08086e+01 3.76443e+00 9.97171e+01
C 1.15551e+01 2.48504e+00 9.96546e+01
C 1.29523e+01 2.51175e+00 9.97536e+01
C 1.37177e+01 3.73244e+00 9.98278e+01
C 1.51433e+01 3.78951e+00 9.96946e+01
C 1.59105e+01 2.48807e+00 9.97076e+01
C 1.73245e+01 2.51722e+00 9.96218e+01
C 1.80234e+01 3.86573e+00 9.96142e+01
C 1.95028e+01 3.76523e+00 9.96809e+01
C 2.01963e+01 2.49746e+00 9.95706e+01
C 2.15903e+01 2.52594e+00 9.95049e+01
C 2.22727e+01 3.74215e+00 9.95433e+01
C 2.36941e+01 3.76361e+00 9.94564e+01
C 2.44605e+01 2.48306e+00 9.92345e+01
C 2.58672e+01 2.51328e+00 9.92446e+01
C 2.65575e+01 3.78264e+00 9.91708e+01
C 2.79403e+01 3.73756e+00 9.91542e+01
C 2.87630e+01 2.49138e+00 9.90104e+01
C 3.02406e+01 2.43653e+00 9.91853e+01
C 3.09422e+01 3.67794e+00 9.93689e+01
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C 3.30942e+01 2.49803e+00 9.94022e+01
C 3.45240e+01 2.54321e+00 9.94370e+01
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C 3.67153e+01 3.73090e+00 9.96235e+01
C 3.74957e+01 2.46816e+00 9.96741e+01
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C 3.95925e+01 3.72094e+00 9.96670e+01
C 4.09643e+01 3.81100e+00 9.98867e+01
C 4.16092e+01 2.50240e+00 9.99189e+01
C 4.31139e+01 2.49241e+00 9.99606e+01
C 4.38609e+01 3.70909e+00 9.99792e+01
C 4.53171e+01 3.81696e+00 9.99525e+01
C 4.61016e+01 2.51291e+00 9.97815e+01
C 4.74989e+01 2.53256e+00 9.98790e+01
C 4.82378e+01 3.78328e+00 9.98946e+01
C 4.96791e+01 3.78153e+00 9.99441e+01
C -3.61630e-04 2.52922e+00 9.98560e+01
C 5.03215e+01 2.52163e+00 9.99528e+01
C 7.33542e-02 4.99492e+00 9.97883e+01
C 2.90472e+00 4.92130e+00 9.97997e+01
C 4.35362e+00 4.94272e+00 9.98204e+01
C 5.07614e+00 6.28027e+00 9.98669e+01
C 7.20903e+00 4.94745e+00 9.97378e+01
C 8.63029e+00 5.00854e+00 9.99069e+01
C 9.33132e+00 6.26477e+00 9.99490e+01
C 1.15603e+01 5.00468e+00 9.98542e+01
C 1.07707e+01 6.22893e+00 9.99342e+01
C 1.30079e+01 4.96013e+00 9.99010e+01
C 1.37542e+01 6.15440e+00 1.00085e+02
C 1.59647e+01 4.97450e+00 9.98998e+01
C 1.52572e+01 6.27153e+00 1.00092e+02
C 1.73532e+01 5.01418e+00 9.98302e+01
C 2.01912e+01 5.01593e+00 9.99073e+01
C 1.94926e+01 6.25424e+00 9.99078e+01
C 2.15799e+01 5.01634e+00 9.97224e+01
C 2.44379e+01 5.02681e+00 9.93652e+01
C 2.58272e+01 5.06410e+00 9.92275e+01
C 2.87350e+01 4.96504e+00 9.92876e+01
C 3.01232e+01 4.90495e+00 9.93011e+01
C 3.08408e+01 6.18012e+00 9.93137e+01
C 3.30954e+01 4.95601e+00 9.94533e+01
C 3.24056e+01 6.20124e+00 9.93675e+01
C 3.44671e+01 4.96070e+00 9.94296e+01
C 3.66464e+01 6.19117e+00 9.94884e+01
C 3.52131e+01 6.21219e+00 9.94760e+01
C 3.74510e+01 4.99791e+00 9.96568e+01
C 3.88754e+01 5.02180e+00 9.96026e+01
C 3.95390e+01 6.27138e+00 9.97042e+01
C 4.09454e+01 6.28830e+00 9.96758e+01
C 4.16831e+01 4.97917e+00 9.97852e+01
C 4.31755e+01 4.92600e+00 9.98564e+01
C 4.53625e+01 6.25893e+00 1.00014e+02
C 4.61296e+01 4.94611e+00 9.99725e+01
C 4.74903e+01 4.97929e+00 9.99317e+01
C 4.96879e+01 6.25835e+00 9.98914e+01
C 5.04272e+01 4.95142e+00 9.98507e+01
C 7.44202e-01 6.27981e+00 9.97438e+01
C 6.88070e-02 7.54970e+00 9.98751e+01
C 2.24073e+00 6.25390e+00 9.97347e+01
C 2.90977e+00 7.53360e+00 9.98787e+01
C 4.31267e+00 7.48247e+00 9.99233e+01
C 6.53839e+00 6.19644e+00 9.99361e+01
C 7.24392e+00 7.48431e+00 9.98642e+01
C 8.64919e+00 7.52039e+00 1.00035e+02
C 1.14541e+01 7.43854e+00 1.00118e+02
C 1.30609e+01 7.43411e+00 1.00193e+02
C 1.58865e+01 7.46216e+00 1.00204e+02
C 1.80096e+01 6.32129e+00 9.99934e+01
C 1.73317e+01 7.59535e+00 1.00034e+02
C 2.01633e+01 7.53227e+00 1.00093e+02
C 2.22586e+01 6.25485e+00 9.97886e+01
C 2.16252e+01 7.47374e+00 1.00042e+02
C 2.37090e+01 6.24723e+00 9.95215e+01
C 2.44472e+01 7.45956e+00 9.97329e+01
C 2.65938e+01 6.26486e+00 9.94068e+01
C 2.59269e+01 7.56389e+00 9.95782e+01
C 2.79980e+01 6.27947e+00 9.93186e+01
C 2.87899e+01 7.53591e+00 9.93770e+01
C 3.02013e+01 7.45235e+00 9.93433e+01
C 3.31168e+01 7.55447e+00 9.92450e+01
C 3.44790e+01 7.48432e+00 9.93389e+01
C 3.73901e+01 7.46595e+00 9.93949e+01
C 3.88440e+01 7.45565e+00 9.95290e+01
C 4.17744e+01 7.47535e+00 9.97232e+01
C 4.31668e+01 7.50094e+00 9.98098e+01
C 4.38798e+01 6.20881e+00 9.98295e+01
C 4.60553e+01 7.51885e+00 1.00029e+02
C 4.74587e+01 7.48011e+00 1.00034e+02
C 4.82104e+01 6.22294e+00 9.99435e+01
C 5.04203e+01 7.45810e+00 9.99697e+01
C 8.30528e-01 8.77773e+00 9.98631e+01
C 2.21986e+00 8.79661e+00 9.98252e+01
C 2.90210e+00 1.00354e+01 1.00024e+02
C 4.31699e+00 9.96572e+00 1.00059e+02
C 5.05907e+00 8.75036e+00 1.00059e+02
C 6.47025e+00 8.71765e+00 9.99914e+01
C 7.17050e+00 1.00157e+01 1.00136e+02
C 8.62562e+00 1.00171e+01 1.00115e+02
C 9.37673e+00 8.75425e+00 1.00115e+02
C 1.08201e+01 8.75172e+00 1.00165e+02
C 1.15467e+01 9.95158e+00 1.00387e+02
C 1.29745e+01 9.99930e+00 1.00324e+02
C 1.37689e+01 8.71940e+00 1.00242e+02
C 1.51824e+01 8.67230e+00 1.00214e+02
C 1.58286e+01 9.98723e+00 1.00262e+02
C 1.72465e+01 1.00565e+01 1.00342e+02
C 1.80152e+01 8.83510e+00 1.00111e+02
C 1.95189e+01 8.72224e+00 1.00148e+02
C 2.01578e+01 9.95870e+00 1.00311e+02
C 2.15983e+01 9.96392e+00 1.00153e+02
C 2.23249e+01 8.73572e+00 9.99998e+01
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C 2.80544e+01 8.75455e+00 9.94332e+01
C 2.87933e+01 1.00174e+01 9.93819e+01
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C 3.23652e+01 8.75732e+00 9.92849e+01
C 3.31202e+01 1.00008e+01 9.92750e+01
C 3.45341e+01 9.99506e+00 9.92639e+01
C 3.52413e+01 8.70544e+00 9.92539e+01
C 3.66712e+01 8.74182e+00 9.93861e+01
C 3.73720e+01 9.99555e+00 9.94924e+01
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C 4.39089e+01 8.71878e+00 1.00086e+02
C 4.53361e+01 8.78477e+00 1.00116e+02
C 4.60229e+01 9.98575e+00 1.00214e+02
C 4.74987e+01 9.97083e+00 1.00183e+02
C 4.81831e+01 8.76035e+00 1.00024e+02
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C 4.75037e+01 4.49211e+01 1.00529e+02
C 5.17696e+01 4.48270e+01 1.00021e+02
C 5.04292e+01 4.49001e+01 1.00252e+02
C 7.30105e-01 4.60826e+01 1.00009e+02
C 2.08918e+00 4.60817e+01 9.98491e+01
C 2.92463e+00 4.73456e+01 9.97780e+01
C 4.28775e+00 4.73762e+01 9.97162e+01
C 5.04080e+00 4.60969e+01 9.97694e+01
C 6.49382e+00 4.60473e+01 9.97890e+01
C 7.18528e+00 4.73546e+01 9.97215e+01
C 8.68969e+00 4.73310e+01 9.95536e+01
C 9.32820e+00 4.60222e+01 9.96547e+01
C 1.08237e+01 4.61129e+01 9.95817e+01
C 1.15369e+01 4.73466e+01 9.95860e+01
C 1.29582e+01 4.72784e+01 9.96125e+01
C 1.37271e+01 4.60435e+01 9.96472e+01
C 1.50930e+01 4.61127e+01 9.95635e+01
C 1.58583e+01 4.73785e+01 9.97294e+01
C 1.72789e+01 4.73985e+01 9.96116e+01
C 1.79452e+01 4.60826e+01 9.94249e+01
C 1.94495e+01 4.60899e+01 9.93605e+01
C 2.00219e+01 4.73702e+01 9.94206e+01
C 2.15163e+01 4.73723e+01 9.94195e+01
C 2.22941e+01 4.61857e+01 9.95134e+01
C 2.36798e+01 4.61348e+01 9.94003e+01
C 2.44442e+01 4.73563e+01 9.92012e+01
C 2.65347e+01 4.60797e+01 9.91600e+01
C 2.58708e+01 4.73401e+01 9.91361e+01
C 2.80090e+01 4.61094e+01 9.91644e+01
C 2.87534e+01 4.73349e+01 9.91692e+01
C 3.02010e+01 4.73369e+01 9.91122e+01
C 3.09012e+01 4.60925e+01 9.92039e+01
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C 3.30667e+01 4.73930e+01 9.93392e+01
C 3.45512e+01 4.73178e+01 9.92867e+01
C 3.52214e+01 4.60968e+01 9.94436e+01
C 3.66899e+01 4.60523e+01 9.97064e+01
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C 3.96298e+01 4.61753e+01 9.99690e+01
C 4.10200e+01 4.60835e+01 1.00007e+02
C 4.17696e+01 4.73499e+01 1.00060e+02
C 4.31829e+01 4.73608e+01 1.00283e+02
C 4.39062e+01 4.61143e+01 1.00432e+02
C 4.53055e+01 4.61839e+01 1.00458e+02
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C 4.59829e+01 4.74762e+01 1.00376e+02
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C 6.81507e-01 4.85878e+01 9.99582e+01
C 4.37303e-03 4.98759e+01 9.99471e+01
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C 2.15520e+00 4.85223e+01 9.97402e+01
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C 6.50937e+00 4.85414e+01 9.97322e+01
C 9.41428e+00 4.85563e+01 9.94827e+01
C 1.07786e+01 4.85995e+01 9.95884e+01
C 1.29660e+01 -9.91329e-02 9.95033e+01
C 1.37226e+01 4.85302e+01 9.95657e+01
C 1.58649e+01 4.98478e+01 9.97203e+01
C 1.51609e+01 4.85787e+01 9.97912e+01
C 1.80296e+01 4.85679e+01 9.96091e+01
C 2.01699e+01 4.98653e+01 9.94258e+01
C 1.93953e+01 4.85791e+01 9.95091e+01
C 2.16234e+01 -6.48672e-02 9.93489e+01
C 2.23267e+01 4.86178e+01 9.92783e+01
C 2.37363e+01 4.85910e+01 9.91655e+01
C 2.58865e+01 4.98270e+01 9.91340e+01
C 2.65823e+01 4.85404e+01 9.91717e+01
C 2.87934e+01 6.22910e-02 9.92381e+01
C 2.80452e+01 4.85819e+01 9.92228e+01
C 3.01937e+01 4.98619e+01 9.91516e+01
C 3.08984e+01 4.86035e+01 9.92160e+01
C 3.30668e+01 4.98114e+01 9.91901e+01
C 3.23786e+01 4.85873e+01 9.91677e+01
C 3.45543e+01 4.97795e+01 9.92186e+01
C 3.52966e+01 4.86056e+01 9.92842e+01
C 3.66455e+01 4.85545e+01 9.95527e+01
C 3.73839e+01 4.97791e+01 9.96518e+01
C 3.88479e+01 -2.24395e-02 9.96412e+01
C 3.95669e+01 4.85632e+01 9.97475e+01
C 4.10650e+01 4.86010e+01 9.99904e+01
C 4.17487e+01 -2.43921e-02 9.99918e+01
C 4.52721e+01 4.86448e+01 1.00355e+02
C 4.38467e+01 4.86655e+01 1.00316e+02
C 4.60415e+01 4.98546e+01 1.00235e+02
C 4.75522e+01 1.58747e-02 1.00160e+02
C 4.82431e+01 4.86403e+01 1.00341e+02
C 4.96356e+01 4.86155e+01 1.00246e+02

34
examples/USER/misc/i-pi/in.graphene Normal file
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@ -0,0 +1,34 @@
atom_style atomic
units metal
dimension 3
boundary p p p
read_data ./data.graphene
mass 1 12.01 ##Carbon
### Optimized Tersoff for Carbon: Lindsay and Broido PRB 81, 205441 (2010)
pair_style tersoff
pair_coeff * * C.opt.tersoff C(O)
variable T equal 300
variable V equal vol
variable Lx equal xhi-xlo
variable Ly equal yhi-ylo
print "Lx = ${Lx} A"
print "Ly = ${Ly} A"
print "Volume simulation box = $V A^(3)"
variable Volume equal v_Lx*v_Ly*3.35
print "Volume = Lx*Ly*3.35A = ${Volume} A^(3)"
velocity all create $T 345352 mom yes rot yes dist gaussian
timestep 0.001 # 0.001 picosecond = 1 femtosecond
thermo 1000
thermo_style custom step temp pe etotal press pxx pyy pzz
# --------------- i-PI interface -----------------
fix 1 all ipi graphene 31415 unix # UNIX socket
#fix 1 all ipi localhost 31415 # Internet socket
run 5000000

196
examples/USER/misc/pimd/para-h2/H2.data Normal file
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@ -0,0 +1,196 @@
para-Hydrogen density=0.023500
180 atoms
1 atom types
0.000000 19.712190 xlo xhi
0.000000 19.712190 ylo yhi
0.000000 19.712190 zlo zhi
Masses
1 0.5
Atoms
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182
examples/USER/misc/pimd/para-h2/H2.xyz Normal file
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@ -0,0 +1,182 @@
180
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D 7.884876 9.856095 9.856095
D 7.884876 9.856095 13.141460
D 7.884876 9.856095 16.426825
D 7.884876 13.141460 0.000000
D 7.884876 13.141460 3.285365
D 7.884876 13.141460 6.570730
D 7.884876 13.141460 9.856095
D 7.884876 13.141460 13.141460
D 7.884876 13.141460 16.426825
D 7.884876 16.426825 0.000000
D 7.884876 16.426825 3.285365
D 7.884876 16.426825 6.570730
D 7.884876 16.426825 9.856095
D 7.884876 16.426825 13.141460
D 7.884876 16.426825 16.426825
D 11.827314 0.000000 0.000000
D 11.827314 0.000000 3.285365
D 11.827314 0.000000 6.570730
D 11.827314 0.000000 9.856095
D 11.827314 0.000000 13.141460
D 11.827314 0.000000 16.426825
D 11.827314 3.285365 0.000000
D 11.827314 3.285365 3.285365
D 11.827314 3.285365 6.570730
D 11.827314 3.285365 9.856095
D 11.827314 3.285365 13.141460
D 11.827314 3.285365 16.426825
D 11.827314 6.570730 0.000000
D 11.827314 6.570730 3.285365
D 11.827314 6.570730 6.570730
D 11.827314 6.570730 9.856095
D 11.827314 6.570730 13.141460
D 11.827314 6.570730 16.426825
D 11.827314 9.856095 0.000000
D 11.827314 9.856095 3.285365
D 11.827314 9.856095 6.570730
D 11.827314 9.856095 9.856095
D 11.827314 9.856095 13.141460
D 11.827314 9.856095 16.426825
D 11.827314 13.141460 0.000000
D 11.827314 13.141460 3.285365
D 11.827314 13.141460 6.570730
D 11.827314 13.141460 9.856095
D 11.827314 13.141460 13.141460
D 11.827314 13.141460 16.426825
D 11.827314 16.426825 0.000000
D 11.827314 16.426825 3.285365
D 11.827314 16.426825 6.570730
D 11.827314 16.426825 9.856095
D 11.827314 16.426825 13.141460
D 11.827314 16.426825 16.426825
D 15.769752 0.000000 0.000000
D 15.769752 0.000000 3.285365
D 15.769752 0.000000 6.570730
D 15.769752 0.000000 9.856095
D 15.769752 0.000000 13.141460
D 15.769752 0.000000 16.426825
D 15.769752 3.285365 0.000000
D 15.769752 3.285365 3.285365
D 15.769752 3.285365 6.570730
D 15.769752 3.285365 9.856095
D 15.769752 3.285365 13.141460
D 15.769752 3.285365 16.426825
D 15.769752 6.570730 0.000000
D 15.769752 6.570730 3.285365
D 15.769752 6.570730 6.570730
D 15.769752 6.570730 9.856095
D 15.769752 6.570730 13.141460
D 15.769752 6.570730 16.426825
D 15.769752 9.856095 0.000000
D 15.769752 9.856095 3.285365
D 15.769752 9.856095 6.570730
D 15.769752 9.856095 9.856095
D 15.769752 9.856095 13.141460
D 15.769752 9.856095 16.426825
D 15.769752 13.141460 0.000000
D 15.769752 13.141460 3.285365
D 15.769752 13.141460 6.570730
D 15.769752 13.141460 9.856095
D 15.769752 13.141460 13.141460
D 15.769752 13.141460 16.426825
D 15.769752 16.426825 0.000000
D 15.769752 16.426825 3.285365
D 15.769752 16.426825 6.570730
D 15.769752 16.426825 9.856095
D 15.769752 16.426825 13.141460
D 15.769752 16.426825 16.426825

21
examples/USER/misc/pimd/para-h2/NM.info Normal file
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EIGENVALUES
1 0.00000000
2 4.68629150
3 4.68629150
4 16.00000000
5 16.00000000
6 27.31370850
7 27.31370850
8 32.00000000
EIGENVECTORS
0.12500000 0.17677670 -0.00000000 0.17677670 -0.00000000 0.17677670 -0.00000000 0.12500000
0.12500000 0.12500000 -0.12500000 0.00000000 -0.17677670 -0.12500000 -0.12500000 -0.12500000
0.12500000 0.00000000 -0.17677670 -0.17677670 -0.00000000 -0.00000000 0.17677670 0.12500000
0.12500000 -0.12500000 -0.12500000 -0.00000000 0.17677670 0.12500000 -0.12500000 -0.12500000
0.12500000 -0.17677670 -0.00000000 0.17677670 0.00000000 -0.17677670 -0.00000000 0.12500000
0.12500000 -0.12500000 0.12500000 0.00000000 -0.17677670 0.12500000 0.12500000 -0.12500000
0.12500000 -0.00000000 0.17677670 -0.17677670 -0.00000000 0.00000000 -0.17677670 0.12500000
0.12500000 0.12500000 0.12500000 -0.00000000 0.17677670 -0.12500000 0.12500000 -0.12500000

29
examples/USER/misc/pimd/para-h2/in.scp Normal file
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variable ibead uloop 32 pad
variable out_freq string 1
variable job_name string H2
units real
atom_style full
pair_style table linear 10000
neighbor 2.0 bin
neigh_modify every 1 delay 0 check no
read_data H2.data
pair_coeff 1 * pair.table PAIR_H2
timestep 0.001
thermo_style custom step temp pe etotal pzz
thermo ${out_freq}
velocity all create 1.0 1985 rot yes dist gaussian
fix 1 all pimd method nmpimd fmass 1.0 temp 25.0 nhc 4
dump dcd all dcd ${out_freq} dcd/${job_name}_${ibead}.dcd
restart ${out_freq} restart/${job_name}_${ibead}.restart1 restart/${job_name}_${ibead}.restart2
run 100000

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examples/USER/misc/pimd/para-h2/pair.table Normal file
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examples/USER/misc/pimd/para-h2/run.sh Normal file
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mpirun -np 64 lmp_mpi -partition 8x8 -in in.scp -log logfile/log.lammps -screen screen/screen

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examples/USER/misc/pimd/para-h2/vmd.src Normal file
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###################################################################
mol new H2.xyz type xyz first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
animate delete beg 0 end 0 skip 0 0
mol addfile dcd/H2_0.dcd type dcd first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
mol representation CPK
mol color Name
mol material Opaque
mol addrep top
###################################################################
mol new H2.xyz type xyz first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
animate delete beg 0 end 0 skip 0 1
mol addfile dcd/H2_1.dcd type dcd first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
mol representation CPK
mol color Name
mol material Opaque
mol addrep top
###################################################################
mol new H2.xyz type xyz first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
animate delete beg 0 end 0 skip 0 2
mol addfile dcd/H2_2.dcd type dcd first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
mol representation CPK
mol color Name
mol material Opaque
mol addrep top
###################################################################
mol new H2.xyz type xyz first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
animate delete beg 0 end 0 skip 0 3
mol addfile dcd/H2_3.dcd type dcd first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
mol representation CPK
mol color Name
mol material Opaque
mol addrep top
###################################################################
mol new H2.xyz type xyz first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
animate delete beg 0 end 0 skip 0 4
mol addfile dcd/H2_4.dcd type dcd first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
mol representation CPK
mol color Name
mol material Opaque
mol addrep top
###################################################################
mol new H2.xyz type xyz first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
animate delete beg 0 end 0 skip 0 5
mol addfile dcd/H2_5.dcd type dcd first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
mol representation CPK
mol color Name
mol material Opaque
mol addrep top
###################################################################
mol new H2.xyz type xyz first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
animate delete beg 0 end 0 skip 0 6
mol addfile dcd/H2_6.dcd type dcd first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
mol representation CPK
mol color Name
mol material Opaque
mol addrep top
###################################################################
mol new H2.xyz type xyz first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
animate delete beg 0 end 0 skip 0 7
mol addfile dcd/H2_7.dcd type dcd first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
mol representation CPK
mol color Name
mol material Opaque
mol addrep top
display projection Orthographic
display depthcue off
rotate x by -90.0

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examples/USER/misc/pimd/prot-hairpin/in.scp Normal file
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variable ibead uloop 8 pad
units real
neigh_modify delay 2 every 1
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long 11 12
pair_modify mix arithmetic
kspace_style pppm 1e-4
read_data system.data
#read_restart restart/system_${ibead}.rest1
special_bonds charmm
fix 1 all pimd method nmpimd fmass 1.0 temp 300.0 nhc 4 sp 2.0
thermo 10
thermo_style custom step temp pe etotal
timestep 0.08
restart 100 restart/system_${ibead}.rest1 restart/system_${ibead}.rest2
group prot id <= 256
dump 1 prot dcd 100 dcd/prot_${ibead}.dcd
run 2000000

1
examples/USER/misc/pimd/prot-hairpin/run.sh Normal file
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mpirun -np 8 lmp_mpi -partition 8x1 -in in.scp -log logfile/log.lammps -screen screen/screen

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examples/USER/misc/pimd/prot-hairpin/system.data Normal file
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examples/USER/misc/srp/data.chain Normal file
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examples/USER/misc/srp/in.srp Normal file
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units lj
atom_style full
boundary p p p
special_bonds lj/coul 1 1 1
newton on on
# save an extra atom type for bond particles
read_data data.chain
neighbor 2.0 bin
neigh_modify every 10 check yes
bond_style harmonic
bond_coeff * 225.0 0.85
comm_modify vel yes
# must use pair hybrid, since srp bond particles
# do not interact with other atoms types
pair_style hybrid dpd 1.0 1.0 373692 srp 0.8 1 mid
pair_coeff 1 1 dpd 60.0 4.5 1.0
pair_coeff 1 2 none
pair_coeff 2 2 srp 100.0
# auto normalization of thermo quantites is turned off by pair srp
# just divide by natoms
variable natoms equal count(all)
variable nPotEng equal c_thermo_pe/v_natoms
thermo 50
thermo_style custom step temp pe v_nPotEng press atoms v_natoms lx ly lz
fix 1 all nve
timestep 0.01
restart 500 mid-run-*.restart
run 1000
write_restart end-run.restart