Skip to content

NVT 32 353 #10

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
Parent: NVT
wants to merge 2 commits into
base: NVT
Choose a base branch
from
Open

NVT 32 353 #10

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
dcecb98
353K, 32 pairs, 20 ns
PythonFZ Jan 28, 2024
cbfe800
353K, 8 pairs, 20 ns
PythonFZ Jan 30, 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
1 change: 1 addition & 0 deletions config/md.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,3 +8,4 @@ n_inner: 5000 # compiled inner steps
sampling_rate: 200 # dump interval
buffer_size: 1000
dr_threshold: 0.5 # Neighborlist skin
checkpoint_interval: 200
89 changes: 45 additions & 44 deletions dvc.lock
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -27264,24 +27264,24 @@ stages:
depl_Packmol_1:
box:
count:
- 16
- 8
data_ids:
density: 900
pbc: true
tolerance: 2.0
outs:
- path: nodes/depl/Packmol_1/atoms.h5
hash: md5
md5: 7ec77fd6549c61434a9b28b7715027a8
size: 43328
md5: 3cd76ae11c9131c8a7f01264bf5946e4
size: 35776
- path: nodes/depl/Packmol_1/node-meta.json
hash: md5
md5: 4dab86e07acb5e1b620a83587ef489a4
md5: 003a201fcea1010f61324911d4d48619
size: 48
- path: nodes/depl/Packmol_1/packmol
hash: md5
md5: ac2a1f78e24d4acec487ee8d320e3c86.dir
size: 28854
md5: 841037c7ba3625d833250e20c6e49d0e.dir
size: 15413
nfiles: 3
depl_ASEGeoOpt:
cmd: zntrack run ipsuite.nodes.ASEGeoOpt --name depl_ASEGeoOpt
Expand Down Expand Up @@ -27313,16 +27313,16 @@ stages:
size: 8933596
- path: nodes/depl/Packmol_1/atoms.h5
hash: md5
md5: 7ec77fd6549c61434a9b28b7715027a8
size: 43328
md5: 3cd76ae11c9131c8a7f01264bf5946e4
size: 35776
- path: nodes/depl/Packmol_1/node-meta.json
hash: md5
md5: 4dab86e07acb5e1b620a83587ef489a4
md5: 003a201fcea1010f61324911d4d48619
size: 48
- path: nodes/depl/Packmol_1/packmol
hash: md5
md5: ac2a1f78e24d4acec487ee8d320e3c86.dir
size: 28854
md5: 841037c7ba3625d833250e20c6e49d0e.dir
size: 15413
nfiles: 3
params:
params.yaml:
Expand All @@ -27345,12 +27345,12 @@ stages:
nfiles: 1
- path: nodes/depl/ASEGeoOpt/node-meta.json
hash: md5
md5: fe39d4aaaae596691bf44639f50031f0
md5: b792fe7ae1695af8e65a117401229061
size: 48
- path: nodes/depl/ASEGeoOpt/trajectory.h5
hash: md5
md5: 983b66b57f7c4f7f7e5d9043e0e0f8e4
size: 6554344
md5: ac6bf9748958632f4b4ebe0fb7597a86
size: 6590696
depl_ASEMD:
cmd: zntrack run ipsuite.nodes.ASEMD --name depl_ASEMD
deps:
Expand Down Expand Up @@ -27386,12 +27386,12 @@ stages:
nfiles: 1
- path: nodes/depl/ASEGeoOpt/node-meta.json
hash: md5
md5: fe39d4aaaae596691bf44639f50031f0
md5: b792fe7ae1695af8e65a117401229061
size: 48
- path: nodes/depl/ASEGeoOpt/trajectory.h5
hash: md5
md5: 983b66b57f7c4f7f7e5d9043e0e0f8e4
size: 6554344
md5: ac6bf9748958632f4b4ebe0fb7597a86
size: 6590696
params:
params.yaml:
depl_ASEMD:
Expand All @@ -27417,25 +27417,25 @@ stages:
outs:
- path: nodes/depl/ASEMD/metrics_dict.csv
hash: md5
md5: 9eabeb33f3ffd6fd44e887e438258f81
size: 42026
md5: 0691758813e71d9bd9d7321c192e52c8
size: 41980
- path: nodes/depl/ASEMD/model
hash: md5
md5: 64586897446153f477c052dd0e2579ad.dir
size: 11
nfiles: 1
- path: nodes/depl/ASEMD/node-meta.json
hash: md5
md5: 702ac4b90cb94907e6daea3925c92de3
md5: 92853eb5b2db24b1ad4bc26e4fb2f586
size: 48
- path: nodes/depl/ASEMD/steps_before_stopping.json
hash: md5
md5: 6bb61e3b7bce0931da574d19d1d82c88
size: 2
- path: nodes/depl/ASEMD/trajectory.h5
hash: md5
md5: ed7e9f3b3286701eb4ee6d025a1c72e1
size: 50790792
md5: 476eb5dd9ca4ec982f6a62cfbb685f75
size: 25409160
depl_ASEMD_1:
cmd: zntrack run ipsuite.nodes.ASEMD --name depl_ASEMD_1
deps:
Expand Down Expand Up @@ -27466,25 +27466,25 @@ stages:
size: 8933596
- path: nodes/depl/ASEMD/metrics_dict.csv
hash: md5
md5: 9eabeb33f3ffd6fd44e887e438258f81
size: 42026
md5: 0691758813e71d9bd9d7321c192e52c8
size: 41980
- path: nodes/depl/ASEMD/model
hash: md5
md5: 64586897446153f477c052dd0e2579ad.dir
size: 11
nfiles: 1
- path: nodes/depl/ASEMD/node-meta.json
hash: md5
md5: 702ac4b90cb94907e6daea3925c92de3
md5: 92853eb5b2db24b1ad4bc26e4fb2f586
size: 48
- path: nodes/depl/ASEMD/steps_before_stopping.json
hash: md5
md5: 6bb61e3b7bce0931da574d19d1d82c88
size: 2
- path: nodes/depl/ASEMD/trajectory.h5
hash: md5
md5: ed7e9f3b3286701eb4ee6d025a1c72e1
size: 50790792
md5: 476eb5dd9ca4ec982f6a62cfbb685f75
size: 25409160
params:
params.yaml:
depl_ASEMD_1:
Expand All @@ -27507,25 +27507,25 @@ stages:
outs:
- path: nodes/depl/ASEMD_1/metrics_dict.csv
hash: md5
md5: 1d7fedd953d3070286a7f7eb3145a04f
size: 41972
md5: 180d59b898aa5ca11eee252c37769b33
size: 41946
- path: nodes/depl/ASEMD_1/model
hash: md5
md5: 64586897446153f477c052dd0e2579ad.dir
size: 11
nfiles: 1
- path: nodes/depl/ASEMD_1/node-meta.json
hash: md5
md5: b9dc78a7b957ee3fa6edf192a9587642
md5: 07e0fd3e41ce717e8375a4ab8c2f296c
size: 48
- path: nodes/depl/ASEMD_1/steps_before_stopping.json
hash: md5
md5: 6bb61e3b7bce0931da574d19d1d82c88
size: 2
- path: nodes/depl/ASEMD_1/trajectory.h5
hash: md5
md5: 96704554effb815f0a6f29808461916e
size: 50790792
md5: 005cd53b37325a87bbec0fbaec8bf4ce
size: 25409160
ML17_training_MLModel_4:
cmd: zntrack run ipsuite.nodes.Apax --name ML17_training_MLModel_4
deps:
Expand Down Expand Up @@ -27813,25 +27813,25 @@ stages:
size: 8933596
- path: nodes/depl/ASEMD_1/metrics_dict.csv
hash: md5
md5: 1d7fedd953d3070286a7f7eb3145a04f
size: 41972
md5: 180d59b898aa5ca11eee252c37769b33
size: 41946
- path: nodes/depl/ASEMD_1/model
hash: md5
md5: 64586897446153f477c052dd0e2579ad.dir
size: 11
nfiles: 1
- path: nodes/depl/ASEMD_1/node-meta.json
hash: md5
md5: b9dc78a7b957ee3fa6edf192a9587642
md5: 07e0fd3e41ce717e8375a4ab8c2f296c
size: 48
- path: nodes/depl/ASEMD_1/steps_before_stopping.json
hash: md5
md5: 6bb61e3b7bce0931da574d19d1d82c88
size: 2
- path: nodes/depl/ASEMD_1/trajectory.h5
hash: md5
md5: 96704554effb815f0a6f29808461916e
size: 50790792
md5: 005cd53b37325a87bbec0fbaec8bf4ce
size: 25409160
params:
params.yaml:
depl_ApaxJaxMD:
Expand All @@ -27840,6 +27840,7 @@ stages:
repeat:
config/md.yaml:
buffer_size: 1000
checkpoint_interval: 200
dr_threshold: 0.5
duration: 20000000
ensemble:
Expand All @@ -27851,14 +27852,14 @@ stages:
outs:
- path: nodes/depl/ApaxJaxMD/initial_structure.extxyz
hash: md5
md5: d8e66e3ed64784648957086d9c12796c
size: 50550
md5: 9a12f22898f77175697adc600bf17e17
size: 25344
- path: nodes/depl/ApaxJaxMD/md
hash: md5
md5: c90a3eb0c501822a60b483f4bcba4a4a.dir
size: 7914518180
nfiles: 2
md5: 0cdc69409922ed8449606e3297224156.dir
size: 4117321789
nfiles: 6
- path: nodes/depl/ApaxJaxMD/node-meta.json
hash: md5
md5: 449f50cd73381549536365afb653a8ef
size: 65
md5: 386f7edcfa74df85ab0d1264322eb244
size: 48
2 changes: 1 addition & 1 deletion main.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -959,7 +959,7 @@

structure = ips.configuration_generation.Packmol(
data=[single_structure.atoms],
count=[16], # 16, 32, 64
count=[8], # 16, 32, 64
density=900,
)

Expand Down
2 changes: 1 addition & 1 deletion nodes/depl/ASEGeoOpt/node-meta.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1 +1 @@
{"uuid": "0d584356-51f5-4a5f-ace8-5a4c3eaacc1f"}
{"uuid": "c9925b2d-5f73-4164-b289-a9da5d04f16f"}
2 changes: 1 addition & 1 deletion nodes/depl/ASEMD/node-meta.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1 +1 @@
{"uuid": "7762021a-481c-40bc-a25f-268c2bce0a4a"}
{"uuid": "10ac38e8-734f-4413-bd60-cbfb03b000e2"}
2 changes: 1 addition & 1 deletion nodes/depl/ASEMD_1/node-meta.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1 +1 @@
{"uuid": "c30fb88b-5e00-49a3-bd12-99d258c289f5"}
{"uuid": "ebc1231a-d151-46d1-b95f-8dce92b2d7e5"}
2 changes: 1 addition & 1 deletion nodes/depl/ApaxJaxMD/node-meta.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1 +1 @@
{"uuid": "f9c6d9bb-61a2-45fd-9e7a-51ee968fbdd2", "run_count": 1}
{"uuid": "6980bfa0-7655-4bb7-b315-81dd2b24a625"}
2 changes: 1 addition & 1 deletion nodes/depl/Packmol_1/node-meta.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1 +1 @@
{"uuid": "12b972d9-3c62-4873-a260-c2a25705c182"}
{"uuid": "0248a570-e2cb-4513-9f64-cc86ca028215"}
2 changes: 1 addition & 1 deletion params.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1296,7 +1296,7 @@ depl_Packmol:
depl_Packmol_1:
box: null
count:
- 16
- 8
data_ids: null
density: 900
pbc: true
Expand Down
17 changes: 0 additions & 17 deletions submit_cpu.sh
View file
Open in desktop

This file was deleted.

14 changes: 14 additions & 0 deletions submit_ehlers.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,14 @@
#!/bin/bash
#SBATCH --partition=dgx
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --time=12:00:00
#SBATCH --gres=gpu:1
#SBATCH --mem=32gb
#SBATCH --job-name=353K-8Pairs

source ~/.bashrc
conda activate ips

# dvc repro
zntrack run ipsuite.nodes.ApaxJaxMD --name depl_ApaxJaxMD
18 changes: 0 additions & 18 deletions submit_gpu.sh
View file
Open in desktop

This file was deleted.

18 changes: 0 additions & 18 deletions submit_single_multi.sh
View file
Open in desktop

This file was deleted.