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frostedoyster committed Sep 17, 2024
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7 changes: 7 additions & 0 deletions examples/heat-capacity/README.rst
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Running, analizing and visualizing a path integral MD simulation
================================================================

This example shows how to run a path integral molecular dynamics
simulation using ``i-PI``, analyze the output and visualize the
trajectory in ``chemiscope``. It uses `LAMMPS <http://lammps.org>`_
as the driver to simulate the q-TIP4P/f water model.
30 changes: 30 additions & 0 deletions examples/heat-capacity/data/in.lmp
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units electron
atom_style full

pair_style lj/cut/tip4p/long 1 2 1 1 0.278072379 17.007
bond_style class2
angle_style harmonic
kspace_style pppm/tip4p 0.0001

read_data data/water_32_data.lmp
pair_coeff * * 0 0
pair_coeff 1 1 0.000295147 5.96946

neighbor 2.0 bin

timestep 0.00025

#velocity all create 298.0 2345187

#thermo_style multi
#thermo 1

#fix 1 all nvt temp 298.0 298.0 30.0 tchain 1
#fix 1 all nve
fix 1 all ipi h2o-lammps 32342 unix


#dump 1 all xyz 25 dump.xyz

run 100000000

40 changes: 40 additions & 0 deletions examples/heat-capacity/data/input_piglet.xml
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35 changes: 35 additions & 0 deletions examples/heat-capacity/data/input_pimd.xml
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<simulation verbosity='medium' safe_stride='100'>
<output prefix='simulation'>
<properties stride='1' filename='out'> [ step, time{picosecond}, conserved{electronvolt}, temperature{kelvin}, kinetic_cv{electronvolt}, potential{electronvolt}, pressure_cv{megapascal}, kinetic_td{electronvolt} ] </properties>
<trajectory filename='pos' stride='20'> positions </trajectory>
<trajectory filename='kin' stride='20'> kinetic_cv </trajectory>
<trajectory filename='kod' stride='20'> kinetic_od </trajectory>
</output>
<total_steps> 200 </total_steps>
<prng>
<seed> 32342 </seed>
</prng>
<ffsocket name='lmpserial' mode='unix' pbc='false'>
<address>h2o-lammps</address> <latency> 1e-4 </latency>
</ffsocket>
<system>
<initialize nbeads='8'>
<file mode='pdb' units='angstrom'> data/water_32.pdb </file>
<velocities mode='thermal' units='kelvin'> 298 </velocities>
</initialize>
<forces>
<force forcefield='lmpserial'> lmpserial </force>
</forces>
<ensemble>
<temperature units='kelvin'>298</temperature>
</ensemble>
<motion mode='dynamics'>
<dynamics mode='nvt'>
<thermostat mode='pile_g'>
<tau units="femtosecond"> 5.0 </tau>
</thermostat>
<timestep units='femtosecond'> 0.5 </timestep>
</dynamics>
</motion>
</system>
</simulation>
98 changes: 98 additions & 0 deletions examples/heat-capacity/data/water_32.pdb
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CRYST1 10.260 10.260 10.260 90.00 90.00 90.00 P 1
ATOM 1 O 1 1 3.756 4.710 9.494 0.00 0.00 O
ATOM 2 H 1 1 4.604 4.272 9.671 0.00 0.00 H
ATOM 3 H 1 1 3.998 5.320 8.788 0.00 0.00 H
ATOM 4 O 1 1 9.933 8.841 0.366 0.00 0.00 O
ATOM 5 H 1 1 10.132 8.196 1.120 0.00 0.00 H
ATOM 6 H 1 1 9.368 8.449 -0.316 0.00 0.00 H
ATOM 7 O 1 1 0.321 1.492 5.796 0.00 0.00 O
ATOM 8 H 1 1 -0.287 1.993 5.241 0.00 0.00 H
ATOM 9 H 1 1 0.791 2.061 6.364 0.00 0.00 H
ATOM 10 O 1 1 8.035 9.735 4.307 0.00 0.00 O
ATOM 11 H 1 1 7.203 9.789 4.847 0.00 0.00 H
ATOM 12 H 1 1 8.636 9.307 4.920 0.00 0.00 H
ATOM 13 O 1 1 5.663 9.082 0.660 0.00 0.00 O
ATOM 14 H 1 1 6.378 9.721 0.814 0.00 0.00 H
ATOM 15 H 1 1 5.213 8.991 1.552 0.00 0.00 H
ATOM 16 O 1 1 8.130 0.215 1.201 0.00 0.00 O
ATOM 17 H 1 1 8.196 -0.065 2.118 0.00 0.00 H
ATOM 18 H 1 1 8.938 -0.161 0.818 0.00 0.00 H
ATOM 19 O 1 1 8.177 4.165 0.716 0.00 0.00 O
ATOM 20 H 1 1 7.895 5.066 0.840 0.00 0.00 H
ATOM 21 H 1 1 7.722 3.562 1.341 0.00 0.00 H
ATOM 22 O 1 1 6.341 3.256 9.678 0.00 0.00 O
ATOM 23 H 1 1 7.133 3.423 10.189 0.00 0.00 H
ATOM 24 H 1 1 6.507 2.398 9.350 0.00 0.00 H
ATOM 25 O 1 1 0.136 7.798 2.738 0.00 0.00 O
ATOM 26 H 1 1 -0.006 8.300 3.584 0.00 0.00 H
ATOM 27 H 1 1 0.314 6.905 2.966 0.00 0.00 H
ATOM 28 O 1 1 5.027 2.563 6.169 0.00 0.00 O
ATOM 29 H 1 1 5.538 3.336 6.262 0.00 0.00 H
ATOM 30 H 1 1 5.313 2.031 6.922 0.00 0.00 H
ATOM 31 O 1 1 7.164 2.542 2.418 0.00 0.00 O
ATOM 32 H 1 1 6.248 2.467 2.667 0.00 0.00 H
ATOM 33 H 1 1 7.384 1.681 2.057 0.00 0.00 H
ATOM 34 O 1 1 3.336 9.051 3.265 0.00 0.00 O
ATOM 35 H 1 1 2.818 8.341 2.787 0.00 0.00 H
ATOM 36 H 1 1 2.733 9.794 3.398 0.00 0.00 H
ATOM 37 O 1 1 1.476 1.420 0.819 0.00 0.00 O
ATOM 38 H 1 1 1.060 0.568 0.631 0.00 0.00 H
ATOM 39 H 1 1 1.582 1.509 1.770 0.00 0.00 H
ATOM 40 O 1 1 1.222 4.946 3.218 0.00 0.00 O
ATOM 41 H 1 1 2.111 4.703 3.522 0.00 0.00 H
ATOM 42 H 1 1 1.342 4.956 2.245 0.00 0.00 H
ATOM 43 O 1 1 6.790 6.491 4.488 0.00 0.00 O
ATOM 44 H 1 1 7.083 5.755 5.074 0.00 0.00 H
ATOM 45 H 1 1 6.747 7.293 4.975 0.00 0.00 H
ATOM 46 O 1 1 9.330 3.465 4.430 0.00 0.00 O
ATOM 47 H 1 1 9.974 3.956 3.918 0.00 0.00 H
ATOM 48 H 1 1 8.583 3.143 3.966 0.00 0.00 H
ATOM 49 O 1 1 7.484 4.543 6.379 0.00 0.00 O
ATOM 50 H 1 1 7.604 4.450 7.328 0.00 0.00 H
ATOM 51 H 1 1 8.241 4.098 5.987 0.00 0.00 H
ATOM 52 O 1 1 0.448 5.701 8.219 0.00 0.00 O
ATOM 53 H 1 1 0.573 4.840 7.871 0.00 0.00 H
ATOM 54 H 1 1 0.720 5.651 9.123 0.00 0.00 H
ATOM 55 O 1 1 0.736 4.082 0.545 0.00 0.00 O
ATOM 56 H 1 1 1.032 3.147 0.501 0.00 0.00 H
ATOM 57 H 1 1 -0.250 3.978 0.476 0.00 0.00 H
ATOM 58 O 1 1 4.229 2.582 3.562 0.00 0.00 O
ATOM 59 H 1 1 4.650 2.364 4.424 0.00 0.00 H
ATOM 60 H 1 1 4.306 3.526 3.496 0.00 0.00 H
ATOM 61 O 1 1 3.749 5.318 3.591 0.00 0.00 O
ATOM 62 H 1 1 3.577 5.600 2.690 0.00 0.00 H
ATOM 63 H 1 1 4.519 5.812 3.831 0.00 0.00 H
ATOM 64 O 1 1 0.242 8.540 5.195 0.00 0.00 O
ATOM 65 H 1 1 0.243 9.452 5.454 0.00 0.00 H
ATOM 66 H 1 1 0.725 8.102 5.864 0.00 0.00 H
ATOM 67 O 1 1 6.065 0.243 8.171 0.00 0.00 O
ATOM 68 H 1 1 6.685 -0.360 8.559 0.00 0.00 H
ATOM 69 H 1 1 5.235 -0.020 8.586 0.00 0.00 H
ATOM 70 O 1 1 7.362 8.029 9.049 0.00 0.00 O
ATOM 71 H 1 1 6.719 7.831 8.312 0.00 0.00 H
ATOM 72 H 1 1 6.813 7.839 9.757 0.00 0.00 H
ATOM 73 O 1 1 1.971 1.171 3.631 0.00 0.00 O
ATOM 74 H 1 1 1.520 1.399 4.474 0.00 0.00 H
ATOM 75 H 1 1 2.821 1.577 3.533 0.00 0.00 H
ATOM 76 O 1 1 7.674 6.605 2.134 0.00 0.00 O
ATOM 77 H 1 1 7.143 6.490 2.918 0.00 0.00 H
ATOM 78 H 1 1 8.563 6.681 2.409 0.00 0.00 H
ATOM 79 O 1 1 2.769 7.384 7.275 0.00 0.00 O
ATOM 80 H 1 1 2.353 8.088 7.748 0.00 0.00 H
ATOM 81 H 1 1 2.249 6.554 7.408 0.00 0.00 H
ATOM 82 O 1 1 2.253 2.791 7.349 0.00 0.00 O
ATOM 83 H 1 1 2.718 3.230 8.076 0.00 0.00 H
ATOM 84 H 1 1 2.955 2.671 6.707 0.00 0.00 H
ATOM 85 O 1 1 3.652 9.953 9.290 0.00 0.00 O
ATOM 86 H 1 1 4.114 9.509 9.983 0.00 0.00 H
ATOM 87 H 1 1 3.199 10.639 9.784 0.00 0.00 H
ATOM 88 O 1 1 5.263 6.708 7.589 0.00 0.00 O
ATOM 89 H 1 1 4.318 7.082 7.707 0.00 0.00 H
ATOM 90 H 1 1 5.455 7.057 6.733 0.00 0.00 H
ATOM 91 O 1 1 3.507 6.721 1.020 0.00 0.00 O
ATOM 92 H 1 1 4.097 7.303 0.607 0.00 0.00 H
ATOM 93 H 1 1 3.586 5.984 0.419 0.00 0.00 H
ATOM 94 O 1 1 5.455 9.196 5.888 0.00 0.00 O
ATOM 95 H 1 1 5.473 9.602 6.758 0.00 0.00 H
ATOM 96 H 1 1 4.549 9.238 5.484 0.00 0.00 H
END
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