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Aug 19, 2022
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update auto-test part of dpgen hands-on #52

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bc11804
Merge pull request #47 from deepmodeling/devel
likefallwind Jul 12, 2022
084bfa2
Merge pull request #51 from deepmodeling/devel
likefallwind Aug 10, 2022
de3ae3e
update dpgen hands on
veritas496 Aug 18, 2022
c365437
update auto test
veritas496 Aug 18, 2022
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307 changes: 305 additions & 2 deletions source/Tutorials/DP-GEN/learnDoc/DP-GEN_handson.md
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Original file line number Diff line number Diff line change
Expand Up @@ -690,9 +690,9 @@ $ cat cat dpgen.log | grep system
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.


### Auto-test
## Auto-test

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
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

- 00.equi:(default task) the equilibrium state；

Expand All @@ -706,6 +706,309 @@ To verify the accuracy of the DP model, users can calculate a simple set of pro

- 05.surf: the surface formation energy.

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:
- `make` prepares all required calculation files and input scripts automatically;
- `run` can help submit calculation tasks to remote calculation plantforms and when calculation tasks are completed, will collect results automatically;
- `post` returns calculation results to local root automatically.

### structure relaxation

#### step1-`make`
Prepare the following files in a separate folder.
```sh
├── machine.json
├── relaxation.json
├── confs
│ ├── mp-3034
```
**IMPORTANT!** The ID number, mp-3034, is in the line with Material Project ID for Al-Mg-Cu.
- 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).
- relaxtion.json

```json
{
"structures": ["confs/mp-3034"],//in this folder, confs/mp-3034, required files and scripts will be generated automatically by `dpgen autotest make relaxation.json`
"interaction": {
"type": "deepmd",
"model": "graph.pb",
"in_lammps": "lammps_input/in.lammps",
"type_map": {"Mg":0,"Al": 1,"Cu":2} //if you calculate other materials, remember to modify element types here.
},
"relaxation": {
"cal_setting":{"etol": 1e-12,
"ftol": 1e-6,
"maxiter": 5000,
"maximal": 500000,
"relax_shape": true,
"relax_vol": true}
}
}
```

Run this command,
```bash
dpgen autotest make relaxation.json
```
and then corresponding files and scripts used for calculation will be generated automatically.

#### step2-`run`
```bash
nohup dpgen autotest run relaxation.json machine.json &
```
After running this command, structures will be relaxed.

#### step3-`post`
```bash
dpgen autotest post relaxation.json
```
### property calculation
#### step1-`make`
The parameters used for property calculations are in property.json.

```json
{
"structures": ["confs/mp-3034"],
"interaction": {
"type": "deepmd",
"model": "graph.pb",
"deepmd_version":"2.1.0",
"type_map": {"Mg":0,"Al": 1,"Cu":2}
},
"properties": [
{
"type": "eos",
"vol_start": 0.9,
"vol_end": 1.1,
"vol_step": 0.01
},
{
"type": "elastic",
"norm_deform": 2e-2,
"shear_deform": 5e-2
},
{
"type": "vacancy",
"supercell": [3, 3, 3],
"start_confs_path": "confs"
},
{
"type": "interstitial",
"supercell": [3, 3, 3],
"insert_ele": ["Mg","Al","Cu"],
"conf_filters":{"min_dist": 1.5},
"cal_setting": {"input_prop": "lammps_input/lammps_high"}
},
{
"type": "surface",
"min_slab_size": 10,
"min_vacuum_size":11,
"max_miller": 2,
"cal_type": "static"
}
]
}
```
Run this command
```bash
dpgen autotest make property.json
```
#### step2-`run`
Run this command
```bash
nohup dpgen autotest run property.json machine.json &
```
#### step3-`post`
```bash
dpgen autotest post property.json
```
In the folder, you can use the command `tree . -L 1` and then you can check results.

```
(base) ➜ mp-3034 tree . -L 1
.
├── dpdispatcher.log
├── dpgen.log
├── elastic_00
├── eos_00
├── eos_00.bk000
├── eos_00.bk001
├── eos_00.bk002
├── eos_00.bk003
├── eos_00.bk004
├── eos_00.bk005
├── graph_new.pb
├── interstitial_00
├── POSCAR
├── relaxation
├── surface_00
└── vacancy_00
```

- 01.eos: the equation of state；
```bash
(base) ➜ mp-3034 tree eos_00 -L 1
eos_00
├── 99c07439f6f14399e7785dc783ca5a9047e768a8_flag_if_job_task_fail
├── 99c07439f6f14399e7785dc783ca5a9047e768a8_job_tag_finished
├── 99c07439f6f14399e7785dc783ca5a9047e768a8.sub
├── backup
├── graph.pb -> ../../../graph.pb
├── result.json
├── result.out
├── run_1660558797.sh
├── task.000000
├── task.000001
├── task.000002
├── task.000003
├── task.000004
├── task.000005
├── task.000006
├── task.000007
├── task.000008
├── task.000009
├── task.000010
├── task.000011
├── task.000012
├── task.000013
├── task.000014
├── task.000015
├── task.000016
├── task.000017
├── task.000018
├── task.000019
└── tmp_log
```

The `EOS` calculation results are shown in `eos_00/results.out` file
```bash
(base) ➜ eos_00 cat result.out
conf_dir: /root/1/confs/mp-3034/eos_00
VpA(A^3) EpA(eV)
15.075 -3.2727
15.242 -3.2838
15.410 -3.2935
15.577 -3.3019
15.745 -3.3090
15.912 -3.3148
16.080 -3.3195
16.247 -3.3230
16.415 -3.3254
16.582 -3.3268
16.750 -3.3273
16.917 -3.3268
17.085 -3.3256
17.252 -3.3236
17.420 -3.3208
17.587 -3.3174
17.755 -3.3134
17.922 -3.3087
18.090 -3.3034
18.257 -3.2977
```
- 02.elastic: the elasticity like Young's module；
The `elastic` calculation results are shown in `elastic_00/results.out` file
```bash
(base) ➜ elastic_00 cat result.out
/root/1/confs/mp-3034/elastic_00
124.32 55.52 60.56 0.00 0.00 1.09
55.40 125.82 75.02 0.00 0.00 -0.17
60.41 75.04 132.07 0.00 0.00 7.51
0.00 0.00 0.00 53.17 8.44 0.00
0.00 0.00 0.00 8.34 37.17 0.00
1.06 -1.35 7.51 0.00 0.00 34.43
# Bulk Modulus BV = 84.91 GPa
# Shear Modulus GV = 37.69 GPa
# Youngs Modulus EV = 98.51 GPa
# Poission Ratio uV = 0.31
```
- 03.vacancy: the vacancy formation energy；
The `vacancy` calculation results are shown in `vacancy_00/results.out` file
```bash
(base) ➜ vacancy_00 cat result.out
/root/1/confs/mp-3034/vacancy_00
Structure: Vac_E(eV) E(eV) equi_E(eV)
[3, 3, 3]-task.000000: -10.489 -715.867 -705.378
[3, 3, 3]-task.000001: 4.791 -713.896 -718.687
[3, 3, 3]-task.000002: 4.623 -714.064 -718.687
```
- 04.interstitial: the interstitial formation energy；
The `interstitial` calculation results are shown in `interstitial_00/results.out` file
```bash
(base) ➜ vacancy_00 cat result.out
/root/1/confs/mp-3034/vacancy_00
Structure: Vac_E(eV) E(eV) equi_E(eV)
[3, 3, 3]-task.000000: -10.489 -715.867 -705.378
[3, 3, 3]-task.000001: 4.791 -713.896 -718.687
[3, 3, 3]-task.000002: 4.623 -714.064 -718.687
```
- 05.surf: the surface formation energy.
The `surface` calculation results are shown in `surface_00/results.out` file
```bash
(base) ➜ surface_00 cat result.out
/root/1/confs/mp-3034/surface_00
Miller_Indices: Surf_E(J/m^2) EpA(eV) equi_EpA(eV)
[1, 1, 1]-task.000000: 1.230 -3.102 -3.327
[1, 1, 1]-task.000001: 1.148 -3.117 -3.327
[2, 2, 1]-task.000002: 1.160 -3.120 -3.327
[2, 2, 1]-task.000003: 1.118 -3.127 -3.327
[1, 1, 0]-task.000004: 1.066 -3.138 -3.327
[2, 1, 2]-task.000005: 1.223 -3.118 -3.327
[2, 1, 2]-task.000006: 1.146 -3.131 -3.327
[2, 1, 1]-task.000007: 1.204 -3.081 -3.327
[2, 1, 1]-task.000008: 1.152 -3.092 -3.327
[2, 1, 1]-task.000009: 1.144 -3.093 -3.327
[2, 1, 1]-task.000010: 1.147 -3.093 -3.327
[2, 1, 0]-task.000011: 1.114 -3.103 -3.327
[2, 1, 0]-task.000012: 1.165 -3.093 -3.327
[2, 1, 0]-task.000013: 1.137 -3.098 -3.327
[2, 1, 0]-task.000014: 1.129 -3.100 -3.327
[1, 0, 1]-task.000015: 1.262 -3.124 -3.327
[1, 0, 1]-task.000016: 1.135 -3.144 -3.327
[1, 0, 1]-task.000017: 1.113 -3.148 -3.327
[1, 0, 1]-task.000018: 1.119 -3.147 -3.327
[1, 0, 1]-task.000019: 1.193 -3.135 -3.327
[2, 0, 1]-task.000020: 1.201 -3.089 -3.327
[2, 0, 1]-task.000021: 1.189 -3.092 -3.327
[2, 0, 1]-task.000022: 1.175 -3.094 -3.327
[1, 0, 0]-task.000023: 1.180 -3.100 -3.327
[1, 0, 0]-task.000024: 1.139 -3.108 -3.327
[1, 0, 0]-task.000025: 1.278 -3.081 -3.327
[1, 0, 0]-task.000026: 1.195 -3.097 -3.327
[2, -1, 2]-task.000027: 1.201 -3.121 -3.327
[2, -1, 2]-task.000028: 1.121 -3.135 -3.327
[2, -1, 2]-task.000029: 1.048 -3.147 -3.327
[2, -1, 2]-task.000030: 1.220 -3.118 -3.327
[2, -1, 1]-task.000031: 1.047 -3.169 -3.327
[2, -1, 1]-task.000032: 1.308 -3.130 -3.327
[2, -1, 1]-task.000033: 1.042 -3.170 -3.327
[2, -1, 0]-task.000034: 1.212 -3.154 -3.327
[2, -1, 0]-task.000035: 1.137 -3.165 -3.327
[2, -1, 0]-task.000036: 0.943 -3.192 -3.327
[2, -1, 0]-task.000037: 1.278 -3.144 -3.327
[1, -1, 1]-task.000038: 1.180 -3.118 -3.327
[1, -1, 1]-task.000039: 1.252 -3.105 -3.327
[1, -1, 1]-task.000040: 1.111 -3.130 -3.327
[1, -1, 1]-task.000041: 1.032 -3.144 -3.327
[1, -1, 1]-task.000042: 1.177 -3.118 -3.327
[2, -2, 1]-task.000043: 1.130 -3.150 -3.327
[2, -2, 1]-task.000044: 1.221 -3.135 -3.327
[2, -2, 1]-task.000045: 1.001 -3.170 -3.327
[1, -1, 0]-task.000046: 0.911 -3.191 -3.327
[1, -1, 0]-task.000047: 1.062 -3.168 -3.327
[1, -1, 0]-task.000048: 1.435 -3.112 -3.327
[1, -1, 0]-task.000049: 1.233 -3.143 -3.327
[1, 1, 2]-task.000050: 1.296 -3.066 -3.327
[1, 1, 2]-task.000051: 1.146 -3.097 -3.327
[1, 0, 2]-task.000052: 1.192 -3.085 -3.327
[1, 0, 2]-task.000053: 1.363 -3.050 -3.327
[1, 0, 2]-task.000054: 0.962 -3.132 -3.327
[1, -1, 2]-task.000055: 1.288 -3.093 -3.327
[1, -1, 2]-task.000056: 1.238 -3.102 -3.327
[1, -1, 2]-task.000057: 1.129 -3.122 -3.327
[1, -1, 2]-task.000058: 1.170 -3.115 -3.327
[0, 0, 1]-task.000059: 1.205 -3.155 -3.327
[0, 0, 1]-task.000060: 1.188 -3.158 -3.327
```

## Summary
Now, users have learned the basic usage of the DP-GEN. For further information, please refer to the recommended links.
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