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Merge pull request #52 from veritas496/master
update auto-test part of dpgen hands-on
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‎source/Tutorials/DP-GEN/learnDoc/DP-GEN_handson.md‎

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@@ -690,9 +690,9 @@ $ cat cat dpgen.log | grep system
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It can be found that 3010 structures are generated in `iter.000001`, in which no structure is collected for first-principle calculations. Therefore, the final models are not updated in iter.000002/00.train.
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### Auto-test
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## Auto-test
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To verify the accuracy of the DP model, users can calculate a simple set of properties and compare the results with those of a DFT or traditional empirical force field. DPGEN's autotest module supports the calculation of a variety of properties, such as
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The function, `auto-test`, is only for alloy materials to verify the accuracy of their DP model, users can calculate a simple set of properties and compare the results with those of a DFT or traditional empirical force field. DPGEN's autotest module supports the calculation of a variety of properties, such as
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- 00.equi:(default task) the equilibrium state；
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@@ -706,6 +706,309 @@ To verify the accuracy of the DP model, users can calculate a simple set of pro
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- 05.surf: the surface formation energy.
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In this part, the Al-Mg-Cu DP potential is used to illustrate how to automatically test DP potential of alloy materials. Each `auto-test` task includes three stages:
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- `make` prepares all required calculation files and input scripts automatically;
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- `run` can help submit calculation tasks to remote calculation plantforms and when calculation tasks are completed, will collect results automatically;
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- `post` returns calculation results to local root automatically.
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### structure relaxation
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#### step1-`make`
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Prepare the following files in a separate folder.
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```sh
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├── machine.json
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├── relaxation.json
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├── confs
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│ ├── mp-3034
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```
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**IMPORTANT!** The ID number, mp-3034, is in the line with Material Project ID for Al-Mg-Cu.
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- machine.json is the same with the one used in `init` and `run`. For more information about it, please check this [link](https://bohrium-doc.dp.tech/#/docs/DP-GEN?id=步骤3：准备计算文件).
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- relaxtion.json
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```json
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{
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"structures": ["confs/mp-3034"],//in this folder, confs/mp-3034, required files and scripts will be generated automatically by `dpgen autotest make relaxation.json`
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"interaction": {
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"type": "deepmd",
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"model": "graph.pb",
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"in_lammps": "lammps_input/in.lammps",
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"type_map": {"Mg":0,"Al": 1,"Cu":2} //if you calculate other materials, remember to modify element types here.
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},
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"relaxation": {
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"cal_setting":{"etol": 1e-12,
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"ftol": 1e-6,
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"maxiter": 5000,
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"maximal": 500000,
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"relax_shape": true,
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"relax_vol": true}
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}
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}
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```
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Run this command,
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```bash
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dpgen autotest make relaxation.json
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```
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and then corresponding files and scripts used for calculation will be generated automatically.
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#### step2-`run`
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```bash
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nohup dpgen autotest run relaxation.json machine.json &
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```
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After running this command, structures will be relaxed.
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#### step3-`post`
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```bash
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dpgen autotest post relaxation.json
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```
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### property calculation
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#### step1-`make`
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The parameters used for property calculations are in property.json.
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```json
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{
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"structures": ["confs/mp-3034"],
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"interaction": {
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"type": "deepmd",
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"model": "graph.pb",
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"deepmd_version":"2.1.0",
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"type_map": {"Mg":0,"Al": 1,"Cu":2}
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},
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"properties": [
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{
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"type": "eos",
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"vol_start": 0.9,
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"vol_end": 1.1,
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"vol_step": 0.01
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},
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{
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"type": "elastic",
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"norm_deform": 2e-2,
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"shear_deform": 5e-2
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},
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{
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"type": "vacancy",
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"supercell": [3, 3, 3],
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"start_confs_path": "confs"
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},
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{
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"type": "interstitial",
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"supercell": [3, 3, 3],
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"insert_ele": ["Mg","Al","Cu"],
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"conf_filters":{"min_dist": 1.5},
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"cal_setting": {"input_prop": "lammps_input/lammps_high"}
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},
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{
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"type": "surface",
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"min_slab_size": 10,
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"min_vacuum_size":11,
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"max_miller": 2,
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"cal_type": "static"
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}
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]
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}
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```
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Run this command
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```bash
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dpgen autotest make property.json
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```
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#### step2-`run`
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Run this command
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```bash
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nohup dpgen autotest run property.json machine.json &
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```
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#### step3-`post`
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```bash
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dpgen autotest post property.json
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```
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In the folder, you can use the command `tree . -L 1` and then you can check results.
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```
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(base) ➜ mp-3034 tree . -L 1
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.
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├── dpdispatcher.log
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├── dpgen.log
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├── elastic_00
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├── eos_00
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├── eos_00.bk000
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├── eos_00.bk001
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├── eos_00.bk002
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├── eos_00.bk003
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├── eos_00.bk004
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├── eos_00.bk005
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├── graph_new.pb
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├── interstitial_00
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├── POSCAR
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├── relaxation
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├── surface_00
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└── vacancy_00
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```
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- 01.eos: the equation of state；
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```bash
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(base) ➜ mp-3034 tree eos_00 -L 1
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eos_00
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├── 99c07439f6f14399e7785dc783ca5a9047e768a8_flag_if_job_task_fail
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├── 99c07439f6f14399e7785dc783ca5a9047e768a8_job_tag_finished
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├── 99c07439f6f14399e7785dc783ca5a9047e768a8.sub
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├── backup
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├── graph.pb -> ../../../graph.pb
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├── result.json
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├── result.out
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├── run_1660558797.sh
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├── task.000000
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├── task.000001
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├── task.000002
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├── task.000003
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├── task.000004
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├── task.000005
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├── task.000006
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├── task.000007
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├── task.000008
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├── task.000009
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├── task.000010
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├── task.000011
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├── task.000012
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├── task.000013
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├── task.000014
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├── task.000015
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├── task.000016
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├── task.000017
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├── task.000018
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├── task.000019
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└── tmp_log
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```
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The `EOS` calculation results are shown in `eos_00/results.out` file
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```bash
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(base) ➜ eos_00 cat result.out
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conf_dir: /root/1/confs/mp-3034/eos_00
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VpA(A^3) EpA(eV)
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15.075 -3.2727
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15.242 -3.2838
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15.410 -3.2935
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15.577 -3.3019
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15.745 -3.3090
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15.912 -3.3148
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16.080 -3.3195
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16.247 -3.3230
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16.415 -3.3254
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16.582 -3.3268
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16.750 -3.3273
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16.917 -3.3268
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17.085 -3.3256
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17.252 -3.3236
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17.420 -3.3208
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17.587 -3.3174
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17.755 -3.3134
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17.922 -3.3087
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18.090 -3.3034
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18.257 -3.2977
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```
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- 02.elastic: the elasticity like Young's module；
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The `elastic` calculation results are shown in `elastic_00/results.out` file
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```bash
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(base) ➜ elastic_00 cat result.out
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/root/1/confs/mp-3034/elastic_00
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124.32 55.52 60.56 0.00 0.00 1.09
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55.40 125.82 75.02 0.00 0.00 -0.17
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60.41 75.04 132.07 0.00 0.00 7.51
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0.00 0.00 0.00 53.17 8.44 0.00
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0.00 0.00 0.00 8.34 37.17 0.00
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1.06 -1.35 7.51 0.00 0.00 34.43
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# Bulk Modulus BV = 84.91 GPa
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# Shear Modulus GV = 37.69 GPa
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# Youngs Modulus EV = 98.51 GPa
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# Poission Ratio uV = 0.31
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```
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- 03.vacancy: the vacancy formation energy；
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The `vacancy` calculation results are shown in `vacancy_00/results.out` file
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```bash
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(base) ➜ vacancy_00 cat result.out
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/root/1/confs/mp-3034/vacancy_00
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Structure: Vac_E(eV) E(eV) equi_E(eV)
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[3, 3, 3]-task.000000: -10.489 -715.867 -705.378
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[3, 3, 3]-task.000001: 4.791 -713.896 -718.687
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[3, 3, 3]-task.000002: 4.623 -714.064 -718.687
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```
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- 04.interstitial: the interstitial formation energy；
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The `interstitial` calculation results are shown in `interstitial_00/results.out` file
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```bash
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(base) ➜ vacancy_00 cat result.out
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/root/1/confs/mp-3034/vacancy_00
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Structure: Vac_E(eV) E(eV) equi_E(eV)
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[3, 3, 3]-task.000000: -10.489 -715.867 -705.378
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[3, 3, 3]-task.000001: 4.791 -713.896 -718.687
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[3, 3, 3]-task.000002: 4.623 -714.064 -718.687
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```
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- 05.surf: the surface formation energy.
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The `surface` calculation results are shown in `surface_00/results.out` file
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```bash
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(base) ➜ surface_00 cat result.out
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/root/1/confs/mp-3034/surface_00
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Miller_Indices: Surf_E(J/m^2) EpA(eV) equi_EpA(eV)
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[1, 1, 1]-task.000000: 1.230 -3.102 -3.327
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[1, 1, 1]-task.000001: 1.148 -3.117 -3.327
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[2, 2, 1]-task.000002: 1.160 -3.120 -3.327
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[2, 2, 1]-task.000003: 1.118 -3.127 -3.327
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[1, 1, 0]-task.000004: 1.066 -3.138 -3.327
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[2, 1, 2]-task.000005: 1.223 -3.118 -3.327
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[2, 1, 2]-task.000006: 1.146 -3.131 -3.327
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[2, 1, 1]-task.000007: 1.204 -3.081 -3.327
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[2, 1, 1]-task.000008: 1.152 -3.092 -3.327
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[2, 1, 1]-task.000009: 1.144 -3.093 -3.327
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[2, 1, 1]-task.000010: 1.147 -3.093 -3.327
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[2, 1, 0]-task.000011: 1.114 -3.103 -3.327
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[2, 1, 0]-task.000012: 1.165 -3.093 -3.327
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[2, 1, 0]-task.000013: 1.137 -3.098 -3.327
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[2, 1, 0]-task.000014: 1.129 -3.100 -3.327
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[1, 0, 1]-task.000015: 1.262 -3.124 -3.327
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[1, 0, 1]-task.000016: 1.135 -3.144 -3.327
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[1, 0, 1]-task.000017: 1.113 -3.148 -3.327
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[1, 0, 1]-task.000018: 1.119 -3.147 -3.327
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[1, 0, 1]-task.000019: 1.193 -3.135 -3.327
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[2, 0, 1]-task.000020: 1.201 -3.089 -3.327
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[2, 0, 1]-task.000021: 1.189 -3.092 -3.327
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[2, 0, 1]-task.000022: 1.175 -3.094 -3.327
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[1, 0, 0]-task.000023: 1.180 -3.100 -3.327
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[1, 0, 0]-task.000024: 1.139 -3.108 -3.327
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[1, 0, 0]-task.000025: 1.278 -3.081 -3.327
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[1, 0, 0]-task.000026: 1.195 -3.097 -3.327
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[2, -1, 2]-task.000027: 1.201 -3.121 -3.327
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[2, -1, 2]-task.000028: 1.121 -3.135 -3.327
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[2, -1, 2]-task.000029: 1.048 -3.147 -3.327
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[2, -1, 2]-task.000030: 1.220 -3.118 -3.327
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[2, -1, 1]-task.000031: 1.047 -3.169 -3.327
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[2, -1, 1]-task.000032: 1.308 -3.130 -3.327
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[2, -1, 1]-task.000033: 1.042 -3.170 -3.327
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[2, -1, 0]-task.000034: 1.212 -3.154 -3.327
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[2, -1, 0]-task.000035: 1.137 -3.165 -3.327
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[2, -1, 0]-task.000036: 0.943 -3.192 -3.327
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[2, -1, 0]-task.000037: 1.278 -3.144 -3.327
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[1, -1, 1]-task.000038: 1.180 -3.118 -3.327
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[1, -1, 1]-task.000039: 1.252 -3.105 -3.327
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[1, -1, 1]-task.000040: 1.111 -3.130 -3.327
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[1, -1, 1]-task.000041: 1.032 -3.144 -3.327
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[1, -1, 1]-task.000042: 1.177 -3.118 -3.327
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[2, -2, 1]-task.000043: 1.130 -3.150 -3.327
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[2, -2, 1]-task.000044: 1.221 -3.135 -3.327
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[2, -2, 1]-task.000045: 1.001 -3.170 -3.327
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[1, -1, 0]-task.000046: 0.911 -3.191 -3.327
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[1, -1, 0]-task.000047: 1.062 -3.168 -3.327
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[1, -1, 0]-task.000048: 1.435 -3.112 -3.327
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[1, -1, 0]-task.000049: 1.233 -3.143 -3.327
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[1, 1, 2]-task.000050: 1.296 -3.066 -3.327
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[1, 1, 2]-task.000051: 1.146 -3.097 -3.327
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[1, 0, 2]-task.000052: 1.192 -3.085 -3.327
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[1, 0, 2]-task.000053: 1.363 -3.050 -3.327
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[1, 0, 2]-task.000054: 0.962 -3.132 -3.327
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[1, -1, 2]-task.000055: 1.288 -3.093 -3.327
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[1, -1, 2]-task.000056: 1.238 -3.102 -3.327
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[1, -1, 2]-task.000057: 1.129 -3.122 -3.327
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[1, -1, 2]-task.000058: 1.170 -3.115 -3.327
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[0, 0, 1]-task.000059: 1.205 -3.155 -3.327
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[0, 0, 1]-task.000060: 1.188 -3.158 -3.327
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```
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## Summary
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Now, users have learned the basic usage of the DP-GEN. For further information, please refer to the recommended links.

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