aiida-lammps 0.4.0b3

aiida lammps插件

这是用于AiiDA的lammps插件。 此插件包含4种代码类型：

• lammps.forces：原子单点力计算
• lammps.optimize：晶体结构优化
• lammps.md：分子动力学计算
• lammps.combinate：使用lammps md轨迹的dynaphopy计算（当前未测试）

注：lammps.combinate需要aiida-phonopy（https://github.com/abelcarreras/aiida-phonopy） 插件工作，dynaphopy可以在：https://github.com/abelcarreras/aiida-phonopy

• AiiDA LAMMPS plugin
  • Built-in Potential Support
  • Examples
    • Code Setup
    • Structure Setup
    • Potential Setup
    • Force Calculation
    • Optimisation Calculation
    • MD Calculation

内置潜在支持

• EAM
• 伦纳德·琼斯
• 特索夫
• reaxff

示例

更多示例计算可在文件夹/examples中找到， 在/aiida lammps/tests/test_calculations中有许多测试示例。

代码设置

fromaiida_lammps.tests.utilsimport(get_or_create_local_computer,get_or_create_code)fromaiida_lammps.tests.utilsimportlammps_versioncomputer_local=get_or_create_local_computer('work_directory','localhost')code_lammps_force=get_or_create_code('lammps.force',computer_local,'lammps')code_lammps_opt=get_or_create_code('lammps.optimize',computer_local,'lammps')code_lammps_md=get_or_create_code('lammps.md',computer_local,'lammps')meta_options={"resources":{"num_machines":1,"num_mpiprocs_per_machine":1}}

结构设置

fromaiida.pluginsimportDataFactoryimportnumpyasnpcell=[[3.1900000572,0,0],[-1.5950000286,2.762621076,0],[0.0,0,5.1890001297]]positions=[(0.6666669,0.3333334,0.0000000),(0.3333331,0.6666663,0.5000000),(0.6666669,0.3333334,0.3750000),(0.3333331,0.6666663,0.8750000)]symbols=names=['Ga','Ga','N','N']structure=DataFactory('structure')(cell=cell)forposition,symbol,nameinzip(positions,symbols,names):position=np.dot(position,cell).tolist()structure.append_atom(position=position,symbols=symbol,name=name)structure

<StructureData: uuid: 96f9c02b-77c7-4889-9de2-dbda27bb03fa (unstored)>

电位设置

pair_style='tersoff'potential_dict={'Ga Ga Ga':'1.0 0.007874 1.846 1.918000 0.75000 -0.301300 1.0 1.0 1.44970 410.132 2.87 0.15 1.60916 535.199','N  N  N':'1.0 0.766120 0.000 0.178493 0.20172 -0.045238 1.0 1.0 2.38426 423.769 2.20 0.20 3.55779 1044.77','Ga Ga N':'1.0 0.001632 0.000 65.20700 2.82100 -0.518000 1.0 0.0 0.00000 0.00000 2.90 0.20 0.00000 0.00000','Ga N  N':'1.0 0.001632 0.000 65.20700 2.82100 -0.518000 1.0 1.0 2.63906 3864.27 2.90 0.20 2.93516 6136.44','N  Ga Ga':'1.0 0.001632 0.000 65.20700 2.82100 -0.518000 1.0 1.0 2.63906 3864.27 2.90 0.20 2.93516 6136.44','N  Ga N ':'1.0 0.766120 0.000 0.178493 0.20172 -0.045238 1.0 0.0 0.00000 0.00000 2.20 0.20 0.00000 0.00000','N  N  Ga':'1.0 0.001632 0.000 65.20700 2.82100 -0.518000 1.0 0.0 0.00000 0.00000 2.90 0.20 0.00000 0.00000','Ga N  Ga':'1.0 0.007874 1.846 1.918000 0.75000 -0.301300 1.0 0.0 0.00000 0.00000 2.87 0.15 0.00000 0.00000'}potential=DataFactory("lammps.potential")(structure=structure,type=pair_style,data=potential_dict)potential.attributes

{'kind_elements':['Ga','N'],'potential_type':'tersoff','atom_style':'atomic','default_units':'metal','potential_md5':'b3b7d45ae7b92eba05ed99ffe69810d0','input_lines_md5':'3145644a408a6d464e80866b833115a2'}

力计算

fromaiida.engineimportrun_get_nodeparameters=DataFactory('dict')(dict={'lammps_version':lammps_version(),'output_variables':["temp","etotal","pe","ke"],'thermo_keywords':[]})builder=code_lammps_force.get_builder()builder.metadata.options=meta_optionsbuilder.structure=structurebuilder.potential=potentialbuilder.parameters=parametersresult,calc_node=run_get_node(builder)

$ verdi process list -D desc -a -l 1  PK  Created    Process label     Process State    Process status----  ---------  ----------------  ---------------  ----------------2480  32s ago    ForceCalculation  Finished [0]Total results: 1Info: last time an entry changed state: 28s ago (at 02:02:36 on 2019-06-21)$ verdi process show 2480Property       Value-------------  ------------------------------------type           CalcJobNodepk             2480uuid           c754f044-b190-4505-b121-776b79d2d1c8labeldescriptionctime          2019-06-21 02:02:32.894858+00:00mtime          2019-06-21 02:02:33.297377+00:00process state  Finishedexit status    0computer       [2] localhostInputs        PK  Type----------  ----  ------------------code        1351  Codeparameters  2479  Dictpotential   2478  EmpiricalPotentialstructure   2477  StructureDataOutputs          PK  Type-------------  ----  ----------arrays         2483  ArrayDataremote_folder  2481  RemoteDataresults        2484  Dictretrieved      2482  FolderData

calc_node.outputs.results.attributes

{'parser_version':'0.4.0b3','parser_class':'ForceParser','errors':[],'warnings':'','distance_units':'Angstroms','force_units':'eV/Angstrom','energy_units':'eV','energy':-18.1098859130104,'final_variables':{'ke':0.0,'pe':-18.1098859130104,'etotal':-18.1098859130104,'temp':0.0},'units_style':'metal'}

calc_node.outputs.arrays.attributes

{'array|forces':[1,4,3]}

优化计算

fromaiida.engineimportrun_get_nodeparameters=DataFactory('dict')(dict={'lammps_version':lammps_version(),'output_variables':["temp","etotal","pe","ke"],'thermo_keywords':[],'units':'metal','relax':{'type':'iso','pressure':0.0,'vmax':0.001,},"minimize":{'style':'cg','energy_tolerance':1.0e-25,'force_tolerance':1.0e-25,'max_evaluations':100000,'max_iterations':50000}})builder=code_lammps_opt.get_builder()builder.metadata.options=meta_optionsbuilder.structure=structurebuilder.potential=potentialbuilder.parameters=parametersresult,calc_node=run_get_node(builder)

$ verdi process list -D desc -a -l 1  PK  Created    Process label        Process State    Process status----  ---------  -------------------  ---------------  ----------------2486  1m ago     OptimizeCalculation  ⏹ Finished [0]Total results: 1Info: last time an entry changed state: 1m ago (at 02:09:54 on 2019-06-21)$ verdi process show 2486Property       Value-------------  ------------------------------------type           CalcJobNodepk             2486uuid           5c64433d-6337-4352-a0a8-0acb4083a0c3labeldescriptionctime          2019-06-21 02:09:50.872336+00:00mtime          2019-06-21 02:09:51.128639+00:00process state  Finishedexit status    0computer       [2] localhostInputs        PK  Type----------  ----  ------------------code        1344  Codeparameters  2485  Dictpotential   2478  EmpiricalPotentialstructure   2477  StructureDataOutputs          PK  Type-------------  ----  -------------arrays         2490  ArrayDataremote_folder  2487  RemoteDataresults        2491  Dictretrieved      2488  FolderDatastructure      2489  StructureData

calc_node.outputs.results.attributes

{'parser_version':'0.4.0b3','parser_class':'OptimizeParser','errors':[],'warnings':'','stress_units':'bars','distance_units':'Angstroms','force_units':'eV/Angstrom','energy_units':'eV','energy':-18.1108516231423,'final_variables':{'ke':0.0,'pe':-18.1108516231423,'etotal':-18.1108516231423,'temp':0.0},'units_style':'metal'}

calc_node.outputs.arrays.attributes

{'array|positions':[56,4,3],'array|stress':[3,3],'array|forces':[56,4,3]}

md计算

fromaiida.engineimportsubmitparameters=DataFactory('dict')(dict={'lammps_version':lammps_version(),'output_variables':["temp","etotal","pe","ke"],'thermo_keywords':[],'units':'metal','timestep':0.001,'integration':{'style':'nvt','constraints':{'temp':[300,300,0.5]}},"neighbor":[0.3,"bin"],"neigh_modify":{"every":1,"delay":0,"check":False},'equilibrium_steps':100,'total_steps':1000,'dump_rate':10,'restart':100})builder=code_lammps_md.get_builder()builder.metadata.options=meta_optionsbuilder.structure=structurebuilder.potential=potentialbuilder.parameters=parametersresult,calc_node=run_get_node(builder)

$ verdi process list -D desc -a -l 1  PK  Created    Process label    Process State    Process status----  ---------  ---------------  ---------------  ----------------2493  12s ago    MdCalculation    ⏹ Finished [0]Total results: 1Info: last time an entry changed state: 4s ago (at 02:15:02 on 2019-06-21)$ verdi process show 2493Property       Value-------------  ------------------------------------type           CalcJobNodepk             2493uuid           351b4721-10ff-406c-8f1c-951317091524labeldescriptionctime          2019-06-21 02:14:54.986384+00:00mtime          2019-06-21 02:14:55.282272+00:00process state  Finishedexit status    0computer       [2] localhostInputs        PK  Type----------  ----  ------------------code        1540  Codeparameters  2492  Dictpotential   2478  EmpiricalPotentialstructure   2477  StructureDataOutputs            PK  Type---------------  ----  --------------remote_folder    2494  RemoteDataresults          2496  Dictretrieved        2495  FolderDatasystem_data      2498  ArrayDatatrajectory_data  2497  TrajectoryData

calc_node.outputs.results.attributes

{'parser_version':'0.4.0b3','parser_class':'MdParser','errors':[],'warnings':'','time_units':'picoseconds','distance_units':'Angstroms','energy':-17.8464193488116,'units_style':'metal'}

calc_node.outputs.system_data.attributes

{'units_style':'metal','array|step':[100],'array|ke':[100],'array|pe':[100],'array|etotal':[100],'array|temp':[100]}

calc_node.outputs.trajectory_data.attributes

{'array|times':[101],'array|cells':[101,3,3],'array|steps':[101],'array|positions':[101,4,3],'symbols':['Ga','Ga','N','N']}

标签：

• 插件
• node
• builder
• aiida
• structure
• potential
• units
• ga
• lammps
• lamps

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