Skip to content

Mace mp 0 #6

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
wants to merge 7 commits into
base: production
Choose a base branch
from
Open

Mace mp 0 #6

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
7 commits
Select commit Hold shift + click to select a range
c93b8ad
test run
PythonFZ Jan 4, 2024
78bb5ef
prepare AIMD NPT
PythonFZ Jan 4, 2024
48b527b
AIMD failed, commiting 12k steps
PythonFZ Jan 6, 2024
465a476
fix empty files
PythonFZ Jan 6, 2024
254c55f
analyse density
PythonFZ Jan 6, 2024
1278415
MACE-MP-0 wo D3
PythonFZ Jan 6, 2024
d2ce408
MACE-MP-0 + D3
PythonFZ Jan 6, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
513 changes: 513 additions & 0 deletions dvc.lock
View file
Open in desktop

Large diffs are not rendered by default.

290 changes: 229 additions & 61 deletions dvc.yaml
View file
Open in desktop

Large diffs are not rendered by default.

1 change: 1 addition & 0 deletions external/.gitignore
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
/b1799dde-b87b-47c0-9678-af7fcf7b96e7.json
13 changes: 13 additions & 0 deletions external/b1799dde-b87b-47c0-9678-af7fcf7b96e7.json.dvc
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
md5: 91ad8a11f02b807fb20fa5e8a84eae87
frozen: true
deps:
- path: nodes/MACE-MP-0/node-meta.json
repo:
url: https://github.com/RokasEl/MACE-Models.git
rev: MACE-MP-0
rev_lock: 28e8f324aa01ea70653c94865fcc263d39627c85
outs:
- md5: accc8a2fcb83d05845ed506eebcf9623
size: 48
hash: md5
path: b1799dde-b87b-47c0-9678-af7fcf7b96e7.json
77 changes: 76 additions & 1 deletion main.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
import ipsuite as ips
from ase import units
import mace_models

project = ips.Project(automatic_node_names=True)

Expand Down Expand Up @@ -55,6 +56,80 @@
sampling_rate=10,
)

thermostat = ips.calculators.NPTThermostat(
time_step=0.5,
temperature=303,
pressure=1.01325 * units.bar,
ttime=25 * units.fs,
pfactor=(75 * units.fs) ** 2,
tetragonal_strain=True,
)

with project.group("AIMD") as aimd_grp:
start_conf = ips.configuration_selection.IndexSelection(
data.atoms,
indices=[2000,]
)

aimd_model = ips.calculators.CP2KSinglePoint(
data=start_conf.atoms,
cp2k_params="config/cp2k.yaml",
cp2k_files=["GTH_BASIS_SETS", "GTH_POTENTIALS", "dftd3.dat"],
)

aimd = ips.calculators.ASEMD(
data=start_conf.atoms,
data_id=-1,
model=aimd_model,
thermostat=thermostat,
steps=13_200,
sampling_rate=1,
dump_rate=100,
)

density = ips.analysis.AnalyseDensity(data=aimd.atoms)

mace_mp_0_model = mace_models.LoadModel.from_rev("MACE-MP-0", rev="MACE-MP-0", remote="https://github.com/RokasEl/MACE-Models.git")

with project.group("density_md", "MACE-MP-0") as mace_mp_0:
mace_md = ips.calculators.ASEMD(
data=start_conf.atoms,
data_id=-1,
model=mace_mp_0_model,
thermostat=thermostat,
steps=20_000,
sampling_rate=1,
dump_rate=100,
)

density = ips.analysis.AnalyseDensity(data=mace_md.atoms)

mace_d3 = ips.calculators.TorchD3(
data=None,
xc="pbe",
damping="bj",
cutoff=20.0,
cnthr=18.0,
abc=False,
dtype="float32",
)


with project.group("density_md", "MACE-MP-0-d3") as mace_mp_0:
mace_mp_0_model_with_d3 = ips.calculators.MixCalculator(data=start_conf.atoms, calculators=[mace_mp_0_model, mace_d3])

mace_md = ips.calculators.ASEMD(
data=start_conf.atoms,
data_id=-1,
model=mace_mp_0_model_with_d3,
thermostat=thermostat,
steps=20_000,
sampling_rate=1,
dump_rate=100,
)

density = ips.analysis.AnalyseDensity(data=mace_md.atoms)

with project.group("ML0"):
kernel_selection = ips.models.apax.BatchKernelSelection(
data=train_data.excluded_atoms,
Expand Down Expand Up @@ -536,4 +611,4 @@
prediction = ips.analysis.Prediction(data=train_data, model=model)
metrics = ips.analysis.PredictionMetrics(data=prediction)

project.build(nodes=[final])
project.build(nodes=[mace_mp_0])
3 changes: 3 additions & 0 deletions nodes/AIMD/ASEMD/.gitignore
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
/trajectory.h5
/model
/metrics_dict.csv
1 change: 1 addition & 0 deletions nodes/AIMD/ASEMD/node-meta.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
{"uuid": "cd255ff2-aa42-4e16-a6cd-f1a9237ca196"}
1 change: 1 addition & 0 deletions nodes/AIMD/ASEMD/steps_before_stopping.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
-1
2 changes: 2 additions & 0 deletions nodes/AIMD/AnalyseDensity/.gitignore
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
/results.csv
/density.png
4 changes: 4 additions & 0 deletions nodes/AIMD/AnalyseDensity/density.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
{
"density": 1107.791955911932,
"std": 28.05726060677191
}
1 change: 1 addition & 0 deletions nodes/AIMD/AnalyseDensity/node-meta.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
{"uuid": "96360e64-0642-4054-907c-91b59b2655dd"}
2 changes: 2 additions & 0 deletions nodes/AIMD/CP2KSinglePoint/.gitignore
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
/cp2k
/atoms.h5
1 change: 1 addition & 0 deletions nodes/AIMD/CP2KSinglePoint/node-meta.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
{"uuid": "e0f6d873-64a4-4978-9c86-140653846ce9"}
2 changes: 2 additions & 0 deletions nodes/AIMD/ConfigurationSelection/.gitignore
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
/selected_configurations.json
/selection.png
1 change: 1 addition & 0 deletions nodes/AIMD/ConfigurationSelection/node-meta.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
{"uuid": "df38abb8-600a-4b2e-98e2-ce1836470ba6"}
3 changes: 3 additions & 0 deletions nodes/density_md/MACE-MP-0-d3/ASEMD/.gitignore
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
/trajectory.h5
/metrics_dict.csv
/model
1 change: 1 addition & 0 deletions nodes/density_md/MACE-MP-0-d3/ASEMD/node-meta.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
{"uuid": "ee98b853-6718-4974-8ba9-fce701c0a9d9"}
1 change: 1 addition & 0 deletions nodes/density_md/MACE-MP-0-d3/ASEMD/steps_before_stopping.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
-1
2 changes: 2 additions & 0 deletions nodes/density_md/MACE-MP-0-d3/AnalyseDensity/.gitignore
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
/density.png
/results.csv
4 changes: 4 additions & 0 deletions nodes/density_md/MACE-MP-0-d3/AnalyseDensity/density.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
{
"density": 1188.838453792172,
"std": 17.584099869892363
}
1 change: 1 addition & 0 deletions nodes/density_md/MACE-MP-0-d3/AnalyseDensity/node-meta.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
{"uuid": "5da41610-ffe0-4d70-a4a4-a0eadd80928f"}
1 change: 1 addition & 0 deletions nodes/density_md/MACE-MP-0-d3/MixCalculator/.gitignore
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
/atoms.h5
1 change: 1 addition & 0 deletions nodes/density_md/MACE-MP-0-d3/MixCalculator/node-meta.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
{"uuid": "d511709c-0b80-45d4-ae7f-620cc847939d"}
3 changes: 3 additions & 0 deletions nodes/density_md/MACE-MP-0/ASEMD/.gitignore
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
/model
/metrics_dict.csv
/trajectory.h5
1 change: 1 addition & 0 deletions nodes/density_md/MACE-MP-0/ASEMD/node-meta.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
{"uuid": "164fb563-1fdd-45af-a345-baf47f39aa36"}
1 change: 1 addition & 0 deletions nodes/density_md/MACE-MP-0/ASEMD/steps_before_stopping.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
-1
2 changes: 2 additions & 0 deletions nodes/density_md/MACE-MP-0/AnalyseDensity/.gitignore
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
/results.csv
/density.png
4 changes: 4 additions & 0 deletions nodes/density_md/MACE-MP-0/AnalyseDensity/density.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
{
"density": 939.3767537051928,
"std": 63.61742932171865
}
1 change: 1 addition & 0 deletions nodes/density_md/MACE-MP-0/AnalyseDensity/node-meta.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
{"uuid": "0e0c8c2d-67e0-44e5-9d85-1f5aa4289767"}
84 changes: 84 additions & 0 deletions params.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,3 +1,30 @@
AIMD_ASEMD:
data_id: -1
dump_rate: 100
pop_last: false
repeat:
- 1
- 1
- 1
sampling_rate: 1
seed: 42
steps: 13200
use_momenta: false
wrap: false
AIMD_ASEMD+thermostat:
pfactor: 54.27299976036698
pressure: 6.324209121801212e-07
temperature: 303
tetragonal_strain: true
time_step: 0.5
ttime: 2.455673697116016
AIMD_AnalyseDensity:
end: null
start: 0
window: 1000
AIMD_ConfigurationSelection:
indices:
- 2000
ML0_ConfigurationSelection:
base_feature_map:
layer_name: dense_2
Expand Down Expand Up @@ -951,6 +978,63 @@ classical_MLModel:
use_energy: true
use_forces: true
use_stresses: false
density_md_MACE-MP-0-d3_ASEMD:
data_id: -1
dump_rate: 100
pop_last: false
repeat:
- 1
- 1
- 1
sampling_rate: 1
seed: 42
steps: 20000
use_momenta: false
wrap: false
density_md_MACE-MP-0-d3_ASEMD+thermostat:
pfactor: 54.27299976036698
pressure: 6.324209121801212e-07
temperature: 303
tetragonal_strain: true
time_step: 0.5
ttime: 2.455673697116016
density_md_MACE-MP-0-d3_AnalyseDensity:
end: null
start: 0
window: 1000
density_md_MACE-MP-0-d3_MixCalculator:
methods: sum
density_md_MACE-MP-0-d3_MixCalculator+calculators+1:
abc: false
cnthr: 18.0
cutoff: 20.0
damping: bj
dtype: float32
xc: pbe
density_md_MACE-MP-0_ASEMD:
data_id: -1
dump_rate: 100
pop_last: false
repeat:
- 1
- 1
- 1
sampling_rate: 1
seed: 42
steps: 20000
use_momenta: false
wrap: false
density_md_MACE-MP-0_ASEMD+thermostat:
pfactor: 54.27299976036698
pressure: 6.324209121801212e-07
temperature: 303
tetragonal_strain: true
time_step: 0.5
ttime: 2.455673697116016
density_md_MACE-MP-0_AnalyseDensity:
end: null
start: 0
window: 1000
final_MLModel:
jax_enable_x64: true
use_energy: true
Expand Down
2 changes: 1 addition & 1 deletion submit_cpu.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
#SBATCH --ntasks=32
#SBATCH --cpus-per-task=8
#SBATCH --time=48:00:00
#SBATCH --mem=32gb
#SBATCH --mem=64gb

source ~/.bashrc

Expand Down
Loading