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Running metadynamics with PLUMED and metatensor-defined collective variables #88

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Running metadynamics with PLUMED and metatensor-defined collective variables #88

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3591057
Start working on a PLUMED + metatensor tutorial
Luthaf Oct 11, 2024
2682b7e
Added i-PI inputs and tweaked model parameters
ceriottm Oct 12, 2024
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3 changes: 3 additions & 0 deletions examples/metatensor-plumed/.gitignore
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extensions/
custom-cv.pt
HILLS
4 changes: 4 additions & 0 deletions examples/metatensor-plumed/README.rst
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Using machine learning collective variables in PLUMED with metatensor
=====================================================================

TODO
39 changes: 39 additions & 0 deletions examples/metatensor-plumed/data/input-md.xml
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<simulation safe_stride='10' verbosity='medium'>
<ffsocket mode='unix' name='driver'>
<latency> 1.00000000e-04</latency> <address>lj-driver</address>
</ffsocket>
<total_steps>5000</total_steps>
<output prefix="base-md">
<trajectory stride="10" filename="pos" cell_units="atomic_unit">positions{atomic_unit}</trajectory>
<properties stride="10">
[ step, time, conserved, temperature, kinetic_md, potential, ensemble_bias ]
</properties>
</output>
<prng>
<seed>18885</seed>
</prng>
<system>
<forces>
<force forcefield="driver"></force>
</forces>
<initialize nbeads="1">
<file mode="xyz">data/lj38.xyz</file>
<masses mode="manual"> [ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]</masses>
<cell>
[ 100, 0, 0, 0, 100, 0, 0, 0, 100 ]
</cell>
</initialize>
<ensemble>
<temperature units="atomic_unit"> 0.30 </temperature>
</ensemble>
<motion mode="dynamics">
<fixcom> False </fixcom>
<dynamics mode="nvt">
<timestep units="atomic_unit"> 0.02 </timestep>
<thermostat mode="langevin">
<tau units="atomic_unit"> 10 </tau>
</thermostat>
</dynamics>
</motion>
</system>
</simulation>
51 changes: 51 additions & 0 deletions examples/metatensor-plumed/data/input-meta.xml
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<simulation safe_stride='10' verbosity='medium'>
<ffsocket mode='unix' name='driver'>
<latency> 1.00000000e-04</latency> <address>lj-driver</address>
</ffsocket>
<ffplumed name="plumed">
<file mode="xyz">data/lj38.xyz</file>
<plumeddat> data/plumed.dat </plumeddat>
<plumed_extras> [cv1, cv2, mtd.bias ] </plumed_extras>
</ffplumed>
<total_steps>5000</total_steps>
<output prefix="meta-md">
<trajectory stride="10" filename="pos" cell_units="atomic_unit">positions{atomic_unit}</trajectory>
<trajectory stride="10" filename="colvar" bead="0" extra_type="cv1,cv2,mtd.bias"> extras_bias </trajectory>
<properties stride="10">
[ step, time, conserved, temperature, kinetic_md, potential, ensemble_bias ]
</properties>
</output>
<prng>
<seed>18885</seed>
</prng>
<system>
<forces>
<force forcefield="driver"></force>
</forces>
<initialize nbeads="1">
<file mode="xyz">data/lj38.xyz</file>
<masses mode="manual"> [ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]</masses>
<cell>
[ 100, 0, 0, 0, 100, 0, 0, 0, 100 ]
</cell>
</initialize>
<ensemble>
<temperature units="atomic_unit"> 0.30 </temperature>
<bias>
<force forcefield="plumed"/>
</bias>
</ensemble>
<motion mode="dynamics">
<fixcom> False </fixcom>
<dynamics mode="nvt">
<timestep units="atomic_unit"> 0.02 </timestep>
<thermostat mode="langevin">
<tau units="atomic_unit"> 10 </tau>
</thermostat>
</dynamics>
</motion>
</system>
<smotion mode="metad">
<metad> <metaff> [ plumed ] </metaff> </metad>
</smotion>
</simulation>
40 changes: 40 additions & 0 deletions examples/metatensor-plumed/data/lj38.xyz
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38
# Step 100000000
Ar 1.4267876E+000 2.9212078E+000 1.0701605E+000
Ar -6.1336159E-001 1.3366171E+000 9.8967797E-001
Ar -7.1959392E-002 1.9963731E+000 2.9199481E-001
Ar 1.4336444E+000 1.1270242E+000 1.0450441E+000
Ar 2.2149714E+000 1.7976783E+000 2.1410531E+000
Ar 1.3734694E+000 2.6020966E+000 2.6952938E+000
Ar 9.1665725E-001 1.3886509E-001 1.2365719E+000
Ar 3.1414994E-001 3.7667848E+000 2.3424693E+000
Ar 9.8263797E-001 2.0201570E+000 6.6390178E-001
Ar 4.1439813E-001 1.0970310E+000 7.5153475E-001
Ar -1.0887056E+000 5.8302904E-001 1.8687178E+000
Ar 2.8615674E-001 2.9154779E+000 7.1026823E-001
Ar -3.3917867E-001 3.4038120E+000 1.4536682E+000
Ar -3.8905351E-001 1.9077154E+000 3.1118603E+000
Ar -6.7077782E-001 3.3591081E+000 2.6207557E+000
Ar -1.1449957E-001 5.0378829E-001 1.5028689E+000
Ar -5.4573740E-001 3.8732958E-001 2.8483650E+000
Ar 1.6481073E-001 1.9170175E+000 1.3753046E+000
Ar 5.1444560E-001 1.9761151E+000 2.4004309E+000
Ar -6.9012030E-001 2.4364761E+000 1.0438342E+000
Ar -1.3149162E+000 3.0291069E+000 1.8041757E+000
Ar 2.1566535E+000 2.0243254E+000 9.8121294E-001
Ar 1.3838741E+000 3.6177568E+000 2.0154838E+000
Ar 2.1685344E+000 2.8098050E+000 1.8275828E+000
Ar -1.3254347E+000 1.2746350E+000 2.7507219E+000
Ar 1.3956249E+000 1.3881537E+000 2.6916380E+000
Ar -1.3201815E+000 2.4262575E+000 2.6909376E+000
Ar 3.4406330E-001 1.0391058E+000 2.9605370E+000
Ar 3.0221745E-001 2.8678386E+000 2.9556254E+000
Ar 5.7627097E-001 2.8893057E+000 1.8005862E+000
Ar 7.7447852E-001 2.0078518E+000 3.4195584E+000
Ar 6.2013735E-001 4.8378593E-002 2.3725838E+000
Ar 1.2838145E+000 2.0173886E+000 1.6958543E+000
Ar -1.2221551E+000 1.8286569E+000 1.7668366E+000
Ar 7.0190189E-001 3.8124480E+000 1.2117366E+000
Ar -3.5844585E-001 1.3234871E+000 2.1555337E+000
Ar 7.0158765E-001 1.0394241E+000 1.8553935E+000
Ar -4.3723088E-001 2.3968664E+000 2.1187988E+000
12 changes: 12 additions & 0 deletions examples/metatensor-plumed/data/plumed.dat
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# default (nm, kJ/mol) to atomic
UNITS LENGTH=0.052917721 ENERGY=0.00038087988
cv: METATENSOR MODEL=custom-cv.pt EXTENSIONS_DIRECTORY=./extensions/ SPECIES1=1-38 SPECIES_TO_TYPES=18
# extract the different components from METATENSOR output into scalar
# (METAD only accepts scalars, and METATENSOR output is a vector here)
cv1: SELECT_COMPONENTS ARG=cv COMPONENTS=1
cv2: SELECT_COMPONENTS ARG=cv COMPONENTS=2
# run metadynamics with this collective variable
mtd: METAD ARG=cv1,cv2 HEIGHT=0.05 PACE=50 SIGMA=1,2.5 GRID_MIN=-20,-40 GRID_MAX=20,40 GRID_BIN=500,500 BIASFACTOR=5 FILE=HILLS TEMP=0.18
# prints out trajectory
PRINT ARG=cv1,cv2,mtd.* STRIDE=10 FILE=COLVAR
FLUSH STRIDE=1
15 changes: 15 additions & 0 deletions examples/metatensor-plumed/environment.yml
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channels:
- conda-forge
dependencies:
- python=3.12
- pip
- plumed
- py-plumed
- pip:
- ase
- numpy
- chemiscope
- metatensor[torch]
- rascaline-torch @ git+https://github.com/Luthaf/rascaline@b14477f#subdirectory=python/rascaline-torch
variables:
PLUMED_KERNEL:
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