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Quantum water heat capacity recipe (#76)
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* Copy path-integrals
* Clean up from PIGLET
* Add heat capacity example to docs index
* Better comments for the heat capacity recipe
* Set manually the fd_delta value for the sc estimator
* Tweaked parameters to get better finite-difference accuracy

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Co-authored-by: Davide Tisi <[email protected]>
Co-authored-by: Michele Ceriotti <[email protected]>
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@frostedoyster @DavideTisi @ceriottm
3 people authored Sep 21, 2024
1 parent a9d1699 commit 947234c
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1 change: 1 addition & 0 deletions docs/src/sampling.rst
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Expand Up @@ -12,3 +12,4 @@ set of configurations of an atomistic system.
examples/path-integrals/path-integrals
examples/pi-metad/pi-metad
examples/batch-cp2k/reference-trajectory
examples/heat-capacity/heat-capacity
7 changes: 7 additions & 0 deletions examples/heat-capacity/README.rst
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Heat capacity of water from path integral molecular dynamics
============================================================

This example shows how to calculate the constant-volume heat
capacity from a path integral molecular dynamics simulation
using ``i-PI``. `LAMMPS <http://lammps.org>`_ is used
as the driver for the evaluation of the q-TIP4P/f water model.
34 changes: 34 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 17.001
# high-pppm precision and shift to get meaningful fd estimates
kspace_style pppm/tip4p 1e-5
pair_modify shift yes
bond_style class2
angle_style harmonic


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

35 changes: 35 additions & 0 deletions examples/heat-capacity/data/input.xml
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<simulation verbosity='medium' safe_stride='100'>
<output prefix='water-cv'>
<properties filename='out' stride='4'>
[ step, time{picosecond}, conserved, potential, kinetic_cv,
scaledcoords(fd_delta=5e-3) ]
</properties>
</output>
<total_steps> 2000 </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
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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
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ATOM 37 O 1 1 1.476 1.420 0.819 0.00 0.00 O
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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
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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
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ATOM 46 O 1 1 9.330 3.465 4.430 0.00 0.00 O
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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
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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
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ATOM 70 O 1 1 7.362 8.029 9.049 0.00 0.00 O
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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
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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
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ATOM 88 O 1 1 5.263 6.708 7.589 0.00 0.00 O
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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
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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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