aiida-raspa

AiiDA plugin for RASPA2.

Installation

If you use pip, you can install it as:

pip install aiida-raspa

If you want to install the plugin in an editable mode, run:

git clone https://github.com/yakutovicha/aiida-raspa
cd aiida-raspa
pip install -e .  # also installs aiida, if missing (but not postgres)

In case the plugin does not appear in verdi calculation plugins list, run

reentry scan

and try again.

Examples

See examples folder for complete examples of setting up a calculation or workflow.

simple calculation:

verdi daemon restart                                   # make sure the daemon is running
cd examples/simple_calculations
verdi run test_raspa_base.py <code_label> --submit     # submit test calculation
verdi calculation list -a -p1                          # check status of calculation

workflow:

verdi daemon restart                                   # make sure the daemon is running
cd examples/workflows
verdi run run_RaspaConverge_workflow.py  <code_label>  # submit test calculation
verdi work list -a -p1                                 # check status of calculation

Analyzing output

$ verdi calculation show 7491
-----------  ------------------------------------
type         RaspaCalculation
pk           7491
uuid         adc178d9-9f7e-4bbf-8283-8768f1964d9a
label
description
ctime        2019-01-10 15:38:20.103794+00:00
mtime        2019-01-10 15:39:24.799300+00:00
computer     [3] deneb
code         raspa
-----------  ------------------------------------
##### INPUTS:
Link label      PK  Type
------------  ----  -------------
parameters    7490  ParameterData
structure     7489  CifData
##### OUTPUTS:
Link label           PK  Type
-----------------  ----  -------------
remote_folder      7492  RemoteData
retrieved          7498  FolderData
output_parameters  7499  ParameterData
component_0        7500  ParameterData

Results that are for the framework and adsorbate can be obtained:

$ verdi calculation res 7491 # same as $ verdi data parameter show 7499
{
  "ads_ads_coulomb_energy_average": 0.0, 
  "ads_ads_coulomb_energy_dev": 0.0, 
  "ads_ads_coulomb_energy_unit": "kJ/mol", 
  "ads_ads_total_energy_average": -4.4408682910929, 
  "ads_ads_total_energy_dev": 1.63152616602518, 
  "ads_ads_total_energy_unit": "kJ/mol", 
  "ads_ads_vdw_energy_average": -4.44086832435076, 
  "ads_ads_vdw_energy_dev": 1.63152614939625, 
  "ads_ads_vdw_energy_unit": "kJ/mol", 
  "adsorbate_density_average": 26.35203, 
  "adsorbate_density_dev": 4.63163, 
  "adsorbate_density_unit": "kg/m^3", 
  "cell_volume_average": 12025.61229, 
  "cell_volume_dev": 0.0, 
  "cell_volume_unit": "A^3", 
  "enthalpy_of_adsorption_average": -2092.24759, 
  "enthalpy_of_adsorption_dev": 315.039138, 
  "enthalpy_of_adsorption_unit": "K", 
  "exceeded_walltime": false, 
  "framework_density": "739.995779685958", 
  "framework_density_unit": "kg/m^3", 
  "framework_heat_capacity_average": 3082.15209, 
  "framework_heat_capacity_dev": 2889.16503, 
  "framework_heat_capacity_unit": "J/mol/K", 
  "host_ads_coulomb_energy_average": 0.0, 
  "host_ads_coulomb_energy_dev": 0.0, 
  "host_ads_coulomb_energy_unit": "kJ/mol", 
  "host_ads_total_energy_average": -176.211538447682, 
  "host_ads_total_energy_dev": 36.0785945303337, 
  "host_ads_total_energy_unit": "kJ/mol", 
  "host_ads_vdw_energy_average": -176.211538455997, 
  "host_ads_vdw_energy_dev": 36.0785944970758, 
  "host_ads_vdw_energy_unit": "kJ/mol", 
  "pressure_average": 0.0, 
  "pressure_dev": 0.0, 
  "pressure_unit": "Pa", 
  "temperature_average": 0.0, 
  "temperature_dev": 0.0, 
  "temperature_unit": "K", 
  "total_energy_average": -21727.4844, 
  "total_energy_dev": 4526.71327, 
  "total_energy_unit": "K"
}

Component specific results can be obtained:

$ verdi data parameter show 7499
{
  "ads_ads_coulomb_energy_average": 0.0, 
  "ads_ads_coulomb_energy_dev": 0.0, 
  "ads_ads_coulomb_energy_unit": "kJ/mol", 
  "ads_ads_total_energy_average": -4.4408682910929, 
  "ads_ads_total_energy_dev": 1.63152616602518, 
  "ads_ads_total_energy_unit": "kJ/mol", 
  "ads_ads_vdw_energy_average": -4.44086832435076, 
  "ads_ads_vdw_energy_dev": 1.63152614939625, 
  "ads_ads_vdw_energy_unit": "kJ/mol", 
  "adsorbate_density_average": 26.35203, 
  "adsorbate_density_dev": 4.63163, 
  "adsorbate_density_unit": "kg/m^3", 
  "cell_volume_average": 12025.61229, 
  "cell_volume_dev": 0.0, 
  "cell_volume_unit": "A^3", 
  "enthalpy_of_adsorption_average": -2092.24759, 
  "enthalpy_of_adsorption_dev": 315.039138, 
  "enthalpy_of_adsorption_unit": "K", 
  "exceeded_walltime": false, 
  "framework_density": "739.995779685958", 
  "framework_density_unit": "kg/m^3", 
  "framework_heat_capacity_average": 3082.15209, 
  "framework_heat_capacity_dev": 2889.16503, 
  "framework_heat_capacity_unit": "J/mol/K", 
  "host_ads_coulomb_energy_average": 0.0, 
  "host_ads_coulomb_energy_dev": 0.0, 
  "host_ads_coulomb_energy_unit": "kJ/mol", 
  "host_ads_total_energy_average": -176.211538447682, 
  "host_ads_total_energy_dev": 36.0785945303337, 
  "host_ads_total_energy_unit": "kJ/mol", 
  "host_ads_vdw_energy_average": -176.211538455997, 
  "host_ads_vdw_energy_dev": 36.0785944970758, 
  "host_ads_vdw_energy_unit": "kJ/mol", 
  "pressure_average": 0.0, 
  "pressure_dev": 0.0, 
  "pressure_unit": "Pa", 
  "temperature_average": 0.0, 
  "temperature_dev": 0.0, 
  "temperature_unit": "K", 
  "total_energy_average": -21727.4844, 
  "total_energy_dev": 4526.71327, 
  "total_energy_unit": "K"
}

Files that are downloaded by the plugin to the local machine:

$ verdi calculation outputls 7491
_scheduler-stderr.txt
_scheduler-stdout.txt
output_framework_1.1.1_300.000000_500000.data
restart_framework_1.1.1_300.000000_500000

Cat the output file:

$ verdi calculation outputcat 7491 -p output_framework_1.1.1_300.000000_500000.data
...
Average adsorption energy <U_gh>_1-<U_h>_0 obtained from Widom-insertion:
(Note: the total heat of adsorption is dH=<U_gh>_1-<U_h>_0 - <U_g> - RT)
=========================================================================

Simulation finished,  1 warnings
WARNING: INAPPROPRIATE NUMBER OF UNIT CELLS USED


Thu Jan 10 16:39:01 2019
Simulation finished on Thursday, January 10.
The end time was 04:39 PM.

License

MIT

Contact

yakutovicha@gmail.com