diff --git a/source/Tutorials/DP-GEN/learnDoc/DP-GEN_handson.md b/source/Tutorials/DP-GEN/learnDoc/DP-GEN_handson.md index d04eead..0d58586 100644 --- a/source/Tutorials/DP-GEN/learnDoc/DP-GEN_handson.md +++ b/source/Tutorials/DP-GEN/learnDoc/DP-GEN_handson.md @@ -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； @@ -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.