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Quantum water heat capacity recipe #76

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merged 28 commits into from
Sep 21, 2024
Merged

Quantum water heat capacity recipe #76

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942f3b8
Copy path-integrals
frostedoyster Sep 17, 2024
27c3724
Clean up from PIGLET
frostedoyster Sep 17, 2024
203f60a
Merge branch 'main' into heat-capacity
DavideTisi Sep 17, 2024
3f191e4
Heat capacity tutorial draft
frostedoyster Sep 18, 2024
74eb0d2
Add heat capacity example to docs index
frostedoyster Sep 18, 2024
c985c0c
Better comments for the heat capacity recipe
frostedoyster Sep 18, 2024
d77fb5c
Fix estimator mess
frostedoyster Sep 18, 2024
669f0e3
Fix linter?
frostedoyster Sep 18, 2024
5d230d7
Small tweaks
frostedoyster Sep 18, 2024
4017a41
Set manually the fd_delta value for the sc estimator
ceriottm Sep 19, 2024
77217ba
Tweaked parameters to get better finite-difference accuracy
ceriottm Sep 20, 2024
683f21c
Error estimates
frostedoyster Sep 21, 2024
2b5db8d
More explanation
frostedoyster Sep 21, 2024
139b730
Updated heat capacity example to my satisfaction
ceriottm Sep 21, 2024
c2a5b3a
Copy path-integrals
frostedoyster Sep 17, 2024
762a2c8
Clean up from PIGLET
frostedoyster Sep 17, 2024
3903624
Heat capacity tutorial draft
frostedoyster Sep 18, 2024
1e879bd
Add heat capacity example to docs index
frostedoyster Sep 18, 2024
a193ab1
Better comments for the heat capacity recipe
frostedoyster Sep 18, 2024
f46401c
Fix estimator mess
frostedoyster Sep 18, 2024
3d82def
Fix linter?
frostedoyster Sep 18, 2024
8e35bd7
Small tweaks
frostedoyster Sep 18, 2024
80a0506
Set manually the fd_delta value for the sc estimator
ceriottm Sep 19, 2024
4001506
Tweaked parameters to get better finite-difference accuracy
ceriottm Sep 20, 2024
8fcf8ad
Error estimates
frostedoyster Sep 21, 2024
4b3466c
More explanation
frostedoyster Sep 21, 2024
77597cf
Updated heat capacity example to my satisfaction
ceriottm Sep 21, 2024
f17b62c
Merge branch 'heat-capacity' of github.com:lab-cosmo/software-cookboo…
ceriottm Sep 21, 2024
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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
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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