-[ 2. How it works](#How-it-works)
+### wfGenes:
+wfGenes is a tool to generate various type of workflow management systems (WMSs) by parsing single workflow configuration file called WConfig.
+Naturally, within wfGenes framework, workflows are defined in human readable format, JSON or YAML, with efficient and concise structure to generate different type of WMSs by performing dependency analysis and automatic code generation for specific WMS.
+This approach enables users to examine different type of WMS based on the application requirement and available computing environment.
-[ 3. Supported WMS](#Supported-WMS)
-
-[ 3. Get Started](#Get-Started)
-
-[ 4. References](#References)
-
-
-
-### WGenerator:
-| -Sample One - - | --Sample Two - - | -
|---|---|
-
-workflow_name: First workflow
-nodes:
-- name: node_1
- id: 1
- tasks:
- - func: [source_1 , module_1]
- input: [input1]
- outputs: [output1_id1]
- kwargs: {}
- - func: [source_1, module_2]
- inputs: [input1, output1_id1]
- outputs: [output2_id1]
- kwargs: {}
-- name: node_2
- id: 2
- tasks:
- - func: [source_1, module_3]
- inputs: [input2, input1]
- outputs: [output1_id2]
- kwargs: {}
-- name: node_3
- id: 3
- tasks:
- - func: [source_2, module_1]
- inputs: [output2_id1, output1_id2]
- outputs: [output1_id3]
- kwargs: {}
-
-
- |
-
-
-workflow_name: Second workflow
-nodes:
-- name: node_1
- id: 1
- tasks:
- - func: [source_1, module_1]
- input: [input1]
- outputs: [output1_id1]
- kwargs: {}
- - func: [source_1, module_2]
- inputs: [input2, output1_id1]
- outputs: [output2_id1 , output3_id1 ]
- kwargs: {}
-- name: node_2
- id: 2
- tasks:
- - func: [source_1, module_3]
- inputs: [input1, output2_id1]
- outputs: [output1_id2]
- kwargs: {}
-- name: node_3
- id: 3
- tasks:
- - func: [source_2, module_1]
- inputs: [input1, output3_id1]
- outputs: [output1_id3]
- kwargs: {}
-
- |
-
- 
-
-
-
Directed Acyclic Graph (DAG) generated by WGenerator for two different mentioned sample
- -* Regardless of target WMS, all instances of WGenerator are validated against schema to assure early stage validation and ease further improvement of the tool during development phase . - - -
- 
-
-
-[ ↥ BACK to TOP](#top)
-
-
-### Supported WMS:
-
-
-
-The main motivation behind developing this tool is to establish a high level approach on top of available WMSs that provides the chance of trustworthy comparison and facilitates interoperability relying on fully automated and multi-step verified approach.
-
-To present the methodology and get started with WGenerator, currently, two different WMS are supported.
-
- 1. Firework: Open-source code which supports YAML/JSON and python as input [1].
-
- 2. SimStack: Commercial WMS featured with Graphical user interface [2].
-
-
-
-[ ↥ BACK to TOP](#top)
-
-
-### Get Started:
-
-
-To get started with WGenerator, a single configuration file should be adopted according to workflow specification. In fact, it is a raw list of input, output and function names that will be feed to WGenerator. Apart from configuration file, additional arguments improve controlability over automation process and output generation.
-
- --workflowconfig
- Path to workflowconfig file that contains data of workflow in YAML/JSON format. i.e. Input/Outputfile, modules and arguments names, the default is workflow.yaml.
-
- --inputpath
- Set input directory of WMS. It is not necessary for all WMS.
-
- --outputpath
- Place the output into outputpath (optional).
-
- --wms
- Choose specific workflow management system.The default behavior produces all supported WMSs. Possible values are firework and simstack.
-
-
- ##### First example:
-
- As a first attempt, we demonstrate how to generate firework workflow using WGenerator. However, this workflow is already implemented in [3], using WGenerator enables us to implement very same workflow in SimStack. This document assumes users clone the repository as a whole and all path will be relative to the repository environment.
-
-The command below generates firework workflow in yaml, as mentioned earlier, the output of WGenerator is validated against schema to guarantee the functionality of final result before any further experiment.
-
-
-
- python wgenerator.py --workflowconfig config_path/workflow_version_one.yaml --inputpath inputpath --wms firework --outputpath output_test
-
-*config_path: workflow_configuration/adsorption_energy_slab*
-
-*inputpath: runtime_input/firework_adsorption_slab_version_one*
-
-
-Following tree shows output directory:
-
-```
-output_test/
-├── energy_slab_ver1/
-└── firework
- └── energy_slab_ver1.yaml
-```
-
-We can generate our next workflow using second configuration file that generates additional directory for new workflow called *workflow_version_two.yaml* :
-
- python wgenerator.py --workflowconfig config_path/workflow_version_two.yaml --inputpath inputpath --wms firework --outputpath output_test
-
-*config_path: workflow_configuration/adsorption_energy_slab*
-
-*inputpath: runtime_input/firework_adsorption_slab_version_two*
-
-
-```
-output_test/
-├── energy_slab_ver1
-│ └── firework
-│ └── energy_slab_ver1.yaml
-└── energy_slab_ver2
- └── firework
- └── energy_slab_ver2.yaml
-```
-
- ##### Second example:
-
-In this example, WGenerator is an intermediate layer between python source code (lower-level) and model based design tool called SimStack [1]. Users are able to generate their desired scientific workflow and perform simulation in highest level of abstraction using provided instruction.
-
-WaNos are stand-alone simulation block in SimStack workflow management tool. Each WaNo contains four main files.
-
-1. Wrapper: Encapsulates python modules and interface files.
-2. XML file: Render graphical user-interface in SimStack.
-3. Environment Script: Set simulation environment.
-4. Run script: Execute all necessary commands to begin simulation.
-
-WGenerator generates all necessary codes for each workflow and provides users with ready-to-use WaNo for performing scientific simulation. Obviously, structure of each workflow, combination of WaNos, may vary in different simulation that can be smoothly adopted using SimStack graphical editor. This guide assumes users have basic background on SimStack tool and workflow terminology. Otherwise, please start completing [4].
-
-Now it is time to generate SimStack version of previous workflows using same procedure **only** with passing simsatck as --wms argument. Please note that no additional modification is needed to generate all necessary codes and files for SimStack, however, completely different output is generated for second workflow. Following tree gives overall view on generated output by WGenerator.
-
- python wgenerator.py --workflowconfig config_path/workflow_version_one.yaml --inputpath inputpath --wms simstack --outputpath output_test
-
-*config_path: workflow_configuration/adsorption_energy_slab*
-
-*inputpath: runtime_input/firework_adsorption_slab_version_one*
-
-
-
-
-```
-output_test/
-└── energy_slab_ver1
- ├── firework
- │ └── energy_slab_ver1.yaml
- └── simstack
- ├── Adsorption_energies
- │ ├── Adsorption_energies_wrapper.py
- │ ├── Adsorption_energies.xml
- │ ├── run_python.sh
- │ └── setenv.sh
- ├── Merge_properties_star_O
- │ ├── Merge_properties_star_O_wrapper.py
- │ ├── Merge_properties_star_O.xml
- │ ├── run_python.sh
- │ └── setenv.sh
- ├── Merge_star
- │ ├── Merge_star_wrapper.py
- │ ├── Merge_star.xml
- │ ├── run_python.sh
- │ └── setenv.sh
- ├── Normal_mode_analysis_star
- │ ├── Normal_mode_analysis_star_wrapper.py
- │ ├── Normal_mode_analysis_star.xml
- │ ├── run_python.sh
- │ └── setenv.sh
- ├── Normal_mode_analysis_star_O
- │ ├── Normal_mode_analysis_star_O_wrapper.py
- │ ├── Normal_mode_analysis_star_O.xml
- │ ├── run_python.sh
- │ └── setenv.sh
- ├── Relax_structure_O_two
- │ ├── Relax_structure_O_two_wrapper.py
- │ ├── Relax_structure_O_two.xml
- │ ├── run_python.sh
- │ └── setenv.sh
- ├── Relax_structure_star
- │ ├── Relax_structure_star_wrapper.py
- │ ├── Relax_structure_star.xml
- │ ├── run_python.sh
- │ └── setenv.sh
- └── Relax_structure_star_O
- ├── Relax_structure_star_O_wrapper.py
- ├── Relax_structure_star_O.xml
- ├── run_python.sh
- └── setenv.sh
-```
-The tree above shows all generated files by WGenerator for two different WMS.
-
-
-
-### References:
-
-
-
-[1] https://www.simstack.de/
-
-[2] https://materialsproject.github.io/fireworks/
-
-[3] https://git.scc.kit.edu/jk7683/multihith
-
-[4] https://git.scc.kit.edu/th7356/simstack_tutorial
-
-
-
-
-
-[ ↥ BACK to TOP](#top)
-
-
\ No newline at end of file
diff --git a/fig/glueblue_logo.png b/fig/glueblue_logo.png
new file mode 100644
index 0000000000000000000000000000000000000000..cb863ea129ab587651d70b48ab242de1ac39f6aa
Binary files /dev/null and b/fig/glueblue_logo.png differ
diff --git a/fig/wfgenes_logo.png b/fig/wfgenes_logo.png
new file mode 100644
index 0000000000000000000000000000000000000000..ded6fe0803ad3d8126934d945da6a239987676e0
Binary files /dev/null and b/fig/wfgenes_logo.png differ
diff --git a/intro_examples/README.md b/intro_examples/foreach_sample/README.md
similarity index 89%
rename from intro_examples/README.md
rename to intro_examples/foreach_sample/README.md
index 4360c025046a91eaa844383bb03323465707ca38..17e486a4cdc9046f5642750804c2111a0af078a2 100644
--- a/intro_examples/README.md
+++ b/intro_examples/foreach_sample/README.md
@@ -8,7 +8,7 @@ wfGenes implements the FOREACH method to support data parallelism in python mode
* modulename(str): a name of module to be imported, the *filename* must be in $PYTHONPATH.
* FOREACH(str): This enables wfGenes to generate necessary code for **FOREACH** method.
* partitionable(str): The array which **'FOREACH'** traverse in a parallel manner.
-* Partitioning factor(str): The default is **'full'** that provides the maximum level of parallelism. Max = len(partitionable) and min = 1, any value between can be set to achieve optimum performance.
+* Partitioning factor(str): The default is **'full'** that rovides the maximum level of parallelism. Max = len(partitionable) and min = 1, any value between can be set to achieve optimum performance.
* zip_inputs(lst): List of arguments to be partitioned with same factor as split array passed to concurrent function instances.
Both Dask and Parsl return tuple objects for parallel FOREACH operation. Within the wfGenes framework, flat_tuple method is used to map the computed results of function with multiple return objects to separate lists which can be used for further data processing. The flat_list method has the same functionality with much simpler implementation for functions with single return value. The wfGenes is capable to generate code and deploy proper builtin methods in **auxiliary** file placed in **wfGenes_exe** folder in this repository.
diff --git a/intro_examples/foreach_sample/inputs/data.yaml b/intro_examples/foreach_sample/inputs/data.yaml
index a1b301eba659b4c55476c8012ae923b60e3f2127..bdc0d2b927612a915a610ad84d96c3a423a5d976 100644
--- a/intro_examples/foreach_sample/inputs/data.yaml
+++ b/intro_examples/foreach_sample/inputs/data.yaml
@@ -1 +1,12 @@
-[1, 2, 3, 4, 5, 6, 7, 8, 9, 10,11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 3, 40]
+- 1
+- 2
+- 3
+- 4
+- 5
+- 6
+- 7
+- 8
+- 9
+- 10
+- 11
+- 12
diff --git a/intro_examples/foreach_sample/inputs/list_length.yaml b/intro_examples/foreach_sample/inputs/list_length.yaml
index 2edeafb09db0093bae6ff060e2dcd2166f5c9387..3cacc0b93c9c9c03a72da624ca28a09ba5c1336f 100644
--- a/intro_examples/foreach_sample/inputs/list_length.yaml
+++ b/intro_examples/foreach_sample/inputs/list_length.yaml
@@ -1 +1 @@
-20
\ No newline at end of file
+12
\ No newline at end of file
diff --git a/intro_examples/foreach_sample/lib/__pycache__/myfunctions.cpython-37.pyc b/intro_examples/foreach_sample/lib/__pycache__/myfunctions.cpython-37.pyc
deleted file mode 100644
index da81c8f98ac1d8dbd3bb4f68d7733dcd82cf74bc..0000000000000000000000000000000000000000
Binary files a/intro_examples/foreach_sample/lib/__pycache__/myfunctions.cpython-37.pyc and /dev/null differ
diff --git a/intro_examples/foreach_sample/lib/__pycache__/myfunctions.cpython-38.pyc b/intro_examples/foreach_sample/lib/__pycache__/myfunctions.cpython-38.pyc
deleted file mode 100644
index 2697aabfd654795ceee6ce4f45b623df81700d1d..0000000000000000000000000000000000000000
Binary files a/intro_examples/foreach_sample/lib/__pycache__/myfunctions.cpython-38.pyc and /dev/null differ
diff --git a/intro_examples/foreach_sample/lib/myfunctions.py b/intro_examples/foreach_sample/lib/myfunctions.py
index 58ba0a5c17adf270025c290bb6f5306a51fd873c..fe94d7557550898fa38654a3db581b2d981b9b8b 100644
--- a/intro_examples/foreach_sample/lib/myfunctions.py
+++ b/intro_examples/foreach_sample/lib/myfunctions.py
@@ -1,4 +1,4 @@
-from parsl import python_app
+#from parsl import python_app
import time
import yaml
diff --git a/intro_examples/foreach_sample/wconfig.yaml b/intro_examples/foreach_sample/wconfig.yaml
index c165db43534c1a24cc7eda1446f07fe669ab3385..8e1ee8e4eca77dd9dba464fd40c84fc5119903ca 100644
--- a/intro_examples/foreach_sample/wconfig.yaml
+++ b/intro_examples/foreach_sample/wconfig.yaml
@@ -1,4 +1,4 @@
-workflow_name: parallel data jupyter
+workflow_name: parallel data jupyter
nodes:
- name: plus_minus
id: 1
@@ -45,7 +45,6 @@ nodes:
outputs:
- midpoint
kwargs: {}
-
- name: data_generator
id: 4
tasks:
diff --git a/intro_examples/foreach_sample/wconfig_simple.yaml b/intro_examples/foreach_sample/wconfig_simple.yaml
index ca1ce5325ea5754091e62bff6976d00f2678cdb7..db52d12d56f0ff143b8b806f4873a71ad0234484 100644
--- a/intro_examples/foreach_sample/wconfig_simple.yaml
+++ b/intro_examples/foreach_sample/wconfig_simple.yaml
@@ -1,4 +1,4 @@
-workflow_name: simple_test.genes
+workflow_name: simple_test
nodes:
- name: plus_minus
id: 1
diff --git a/intro_examples/model_interface.ipynb b/intro_examples/model_interface.ipynb
new file mode 100644
index 0000000000000000000000000000000000000000..4096e5958f75ec1504be79cc9f7e80f995916d9e
--- /dev/null
+++ b/intro_examples/model_interface.ipynb
@@ -0,0 +1,315 @@
+{
+ "cells": [
+ {
+ "cell_type": "code",
+ "execution_count": 2,
+ "id": "legal-pulse",
+ "metadata": {
+ "tags": []
+ },
+ "outputs": [
+ {
+ "data": {
+ "application/vnd.jupyter.widget-view+json": {
+ "model_id": "1c66b3bfd8294c5a8a2d9edff1c38d7d",
+ "version_major": 2,
+ "version_minor": 0
+ },
+ "text/plain": [
+ "FileChooser(path='..', filename='', title='HTML(value='Path to the python model:')', show_hidden='False…"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "application/vnd.jupyter.widget-view+json": {
+ "model_id": "ca3f083a750b44ec894a135163d685e6",
+ "version_major": 2,
+ "version_minor": 0
+ },
+ "text/plain": [
+ "FileChooser(path='..', filename='', title='HTML(value='Path to the launch directory:')', show_hidden='F…"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "application/vnd.jupyter.widget-view+json": {
+ "model_id": "d8695f182e6a49078339f17e9157d15d",
+ "version_major": 2,
+ "version_minor": 0
+ },
+ "text/plain": [
+ "FileChooser(path='..', filename='', title='HTML(value='Set the environment:')', show_hidden='False', us…"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "application/vnd.jupyter.widget-view+json": {
+ "model_id": "d6b70dda872443bf9cd09245d33216ac",
+ "version_major": 2,
+ "version_minor": 0
+ },
+ "text/plain": [
+ "Dropdown(description='Pool type:', options=('local_threads', 'slurm'), style=DescriptionStyle(descriptio…"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "application/vnd.jupyter.widget-view+json": {
+ "model_id": "d31165cb95b14d858b49de22fa3460ac",
+ "version_major": 2,
+ "version_minor": 0
+ },
+ "text/plain": [
+ "BoundedIntText(value=1, description='Sleep duration (s):', style=DescriptionStyle(description_width='ini…"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "application/vnd.jupyter.widget-view+json": {
+ "model_id": "3034d07c157f4423bd49a154d4c402f8",
+ "version_major": 2,
+ "version_minor": 0
+ },
+ "text/plain": [
+ "HBox(children=(BoundedIntText(value=3, description='Number of nodes:', min=1, style=DescriptionStyle(des…"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "application/vnd.jupyter.widget-view+json": {
+ "model_id": "9aea37ae3d304b95aeeccbedbdea9143",
+ "version_major": 2,
+ "version_minor": 0
+ },
+ "text/plain": [
+ "BoundedIntText(value=24, description='Maximum local threads:', min=1, style=DescriptionStyle(description…"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "application/vnd.jupyter.widget-view+json": {
+ "model_id": "03e0cbc8aa3b432b842aa3d8b945617a",
+ "version_major": 2,
+ "version_minor": 0
+ },
+ "text/plain": [
+ "HBox(children=(Button(description='Run model', icon='play', style=ButtonStyle(), tooltip='Run model'), Button(…"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "application/vnd.jupyter.widget-view+json": {
+ "model_id": "df89f2a22ee443729c40b91985e947e9",
+ "version_major": 2,
+ "version_minor": 0
+ },
+ "text/plain": [
+ "Output()"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "application/vnd.jupyter.widget-view+json": {
+ "model_id": "fed37288c7b54b69adf298b58050947f",
+ "version_major": 2,
+ "version_minor": 0
+ },
+ "text/plain": [
+ "Output()"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "import os\n",
+ "import sys\n",
+ "import ipywidgets as widgets\n",
+ "from ipyfilechooser import FileChooser\n",
+ "from ipywidgets import Button, HBox, VBox\n",
+ "from IPython.display import HTML, display, clear_output, Markdown as md, JSON, FileLink\n",
+ "\n",
+ "\n",
+ "style = {'description_width': 'initial'}\n",
+ "\n",
+ "#Choose python model's path\n",
+ "model_path = FileChooser('')\n",
+ "model_path.default_path= '../'\n",
+ "model_path.use_dir_icons = True\n",
+ "model_path.filter_pattern = ['*.py']\n",
+ "model_path.title = 'Path to the python model:'\n",
+ "display(model_path)\n",
+ "\n",
+ "#Choose laucher's path\n",
+ "launcher_path = FileChooser('')\n",
+ "launcher_path.default_path= '../'\n",
+ "launcher_path.use_dir_icons = True\n",
+ "launcher_path.title = 'Path to the launch directory:'\n",
+ "display(launcher_path)\n",
+ "\n",
+ "#Environment path\n",
+ "env_path = FileChooser('')\n",
+ "env_path.default_path= '../'\n",
+ "env_path.use_dir_icons = True\n",
+ "env_path.filter_pattern = ['*.sh', '*.env']\n",
+ "env_path.title = 'Set the environment:'\n",
+ "display(env_path)\n",
+ "\n",
+ "pool_type = widgets.Dropdown(\n",
+ " options=['local_threads', 'slurm'],\n",
+ " value= 'local_threads',\n",
+ " description='Pool type:',\n",
+ " disabled=False,\n",
+ " style=style\n",
+ ")\n",
+ "display(pool_type)\n",
+ "\n",
+ "sleep_duration = widgets.BoundedIntText(\n",
+ " value=1,\n",
+ " min=0,\n",
+ " step=1,\n",
+ " description='Sleep duration (s):',\n",
+ " disabled=False,\n",
+ " style=style\n",
+ ")\n",
+ "display(sleep_duration)\n",
+ "\n",
+ "scale_nodes = widgets.BoundedIntText(\n",
+ " value=3,\n",
+ " min=1,\n",
+ " step=1,\n",
+ " description='Number of nodes:',\n",
+ " disabled=False,\n",
+ " style=style\n",
+ ")\n",
+ "\n",
+ "workers_nodes = widgets.BoundedIntText(\n",
+ " value=1,\n",
+ " min=1,\n",
+ " step=1,\n",
+ " description='Workers per nodes:',\n",
+ " disabled=False,\n",
+ " style=style\n",
+ ")\n",
+ "\n",
+ "cpu_per_node = widgets.BoundedIntText(\n",
+ " value=1,\n",
+ " min=1,\n",
+ " step=1,\n",
+ " description='CPU cores per worker:',\n",
+ " disabled=False,\n",
+ " style=style\n",
+ ")\n",
+ "\n",
+ "display(HBox([scale_nodes, workers_nodes, cpu_per_node]))\n",
+ "\n",
+ "maximum_threads = widgets.BoundedIntText(\n",
+ " value=24,\n",
+ " min=1,\n",
+ " step=1,\n",
+ " description='Maximum local threads:',\n",
+ " disabled=False,\n",
+ " style=style\n",
+ ")\n",
+ "display(maximum_threads)\n",
+ "\n",
+ "#Button RUN MODEL\n",
+ "run_model = widgets.Button(tooltip='Run model', icon='play', description='Run model', style=style)\n",
+ "output1 = widgets.Output()\n",
+ "def run_model_clicked(b):\n",
+ " with output1:\n",
+ " #Clear cell output\n",
+ " for i in range(10):\n",
+ " clear_output(wait=True)\n",
+ " \n",
+ " %cd {launcher_path.selected}\n",
+ " %run {model_path.selected} --pool {pool_type.value} --sleep {sleep_duration.value} --scale {scale_nodes.value}\\\n",
+ " --worker_per_node {workers_nodes.value} --cpu_per_node {cpu_per_node.value} --maximum_threads {maximum_threads.value}\n",
+ " print('Done')\n",
+ " \n",
+ "#Button RUN TESTS\n",
+ "run_tests = widgets.Button(tooltip='Runs tests for 4 different list lengths', icon='play', description='Run tests', style=style)\n",
+ "output2 = widgets.Output()\n",
+ "def run_tests_clicked(b):\n",
+ " with output2:\n",
+ " #Clear cell output\n",
+ " for i in range(10):\n",
+ " clear_output(wait=True)\n",
+ " length = [1024, 2048, 4096, 8192] #dask and parsl\n",
+ " n = [ 1, 2, 4, 8, 16, 32]\n",
+ " list_path = launcher_path.selected + 'list_length.yaml'\n",
+ " for i in length:\n",
+ " list_length = open(list_path, \"w\")\n",
+ " list_length.write(str(i))\n",
+ " list_length.close()\n",
+ " %cd {launcher_path.selected}\n",
+ " print('Done')\n",
+ " %run {model_path.selected} --pool {pool_type.value} --scale {scale_nodes.value}\\\n",
+ " --worker_per_node {workers_nodes.value} --cpu_per_node {cpu_per_node.value} --maximum_threads {maximum_threads.value} \n",
+ " \n",
+ " print('Done')\n",
+ " \n",
+ "display(HBox([run_model, run_tests]), output1, output2)\n",
+ "run_model.on_click(run_model_clicked)\n",
+ "run_tests.on_click(run_tests_clicked)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "b9e9a8c3-378f-4f12-ab93-27c8fc2061e9",
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 3",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.7.5"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/intro_examples/multihith/output/energy_slab_ver_2/DASK/energy_slab_ver_2_dask.py b/intro_examples/multihith/output/energy_slab_ver_2/DASK/energy_slab_ver_2_dask.py
new file mode 100644
index 0000000000000000000000000000000000000000..a51716a5eaad17d213459008ca19369ea954c58f
--- /dev/null
+++ b/intro_examples/multihith/output/energy_slab_ver_2/DASK/energy_slab_ver_2_dask.py
@@ -0,0 +1,209 @@
+import yaml
+import numpy as np
+from auxiliary import flat_tuple
+from auxiliary import flat_list
+from auxiliary import MERGE
+import dask
+from dask.distributed import Client
+from distributed.client import *
+from dask_jobqueue import SLURMCluster
+import time
+from ueffumax import build_structure_generic
+from ueffumax import structure_relaxation
+from ueffumax import build_structure
+from ueffumax import vibrations
+from ueffumax import reaction_energies
+
+if __name__ == '__main__':
+
+
+ start_time = time.time()
+ #cluster = SLURMCluster(cores=40, memory='150GB', walltime='01:50:00', queue='single', processes=4)
+ #client = Client(cluster)
+ #cluster.scale(1)
+ #print(cluster.job_script())
+ dask.config.set(scheduler='threads')
+ #Read Input #1 from subroutine #1 in routine #0
+ yaml_stream = open('parameters_id0.yaml', 'r')
+ parameters_id0 = yaml.load(yaml_stream, Loader=yaml.Loader)
+
+
+ end_memtime = time.time()
+ #Read Input #2 from subroutine #3 in routine #0
+ yaml_stream = open('zero_point_energy_id0.yaml', 'r')
+ zero_point_energy_id0 = yaml.load(yaml_stream, Loader=yaml.Loader)
+
+
+ end_memtime = time.time()
+ #Read Input #3 from subroutine #3 in routine #0
+ yaml_stream = open('total_entropy_term_id0.yaml', 'r')
+ total_entropy_term_id0 = yaml.load(yaml_stream, Loader=yaml.Loader)
+
+
+ end_memtime = time.time()
+ #Read Input #4 from subroutine #3 in routine #0
+ yaml_stream = open('energy_minimum_id0.yaml', 'r')
+ energy_minimum_id0 = yaml.load(yaml_stream, Loader=yaml.Loader)
+
+
+ end_memtime = time.time()
+ #Read Input #1 from subroutine #1 in routine #1
+ yaml_stream = open('parameters_id1.yaml', 'r')
+ parameters_id1 = yaml.load(yaml_stream, Loader=yaml.Loader)
+
+
+ end_memtime = time.time()
+ #Read Input #1 from subroutine #1 in routine #2
+ yaml_stream = open('parameters_id2.yaml', 'r')
+ parameters_id2 = yaml.load(yaml_stream, Loader=yaml.Loader)
+
+
+ end_memtime = time.time()
+ #Read Input #1 from subroutine #1 in routine #3
+ yaml_stream = open('parameters_id3.yaml', 'r')
+ parameters_id3 = yaml.load(yaml_stream, Loader=yaml.Loader)
+
+
+ end_memtime = time.time()
+ #Read Input #5 from subroutine #2 in routine #3
+ yaml_stream = open('rotational_entropy_term_id3.yaml', 'r')
+ rotational_entropy_term_id3 = yaml.load(yaml_stream, Loader=yaml.Loader)
+
+
+ end_memtime = time.time()
+ #Read Input #6 from subroutine #2 in routine #3
+ yaml_stream = open('translational_entropy_term_id3.yaml', 'r')
+ translational_entropy_term_id3 = yaml.load(yaml_stream, Loader=yaml.Loader)
+
+
+ end_memtime = time.time()
+ #Read Input #1 from subroutine #1 in routine #4
+ yaml_stream = open('parameters_id4.yaml', 'r')
+ parameters_id4 = yaml.load(yaml_stream, Loader=yaml.Loader)
+
+
+ end_memtime = time.time()
+ #Read Input #1 from subroutine #1 in routine #5
+ yaml_stream = open('parameters_id5.yaml', 'r')
+ parameters_id5 = yaml.load(yaml_stream, Loader=yaml.Loader)
+
+
+ end_memtime = time.time()
+ #Read Input #1 from subroutine #1 in routine #6
+ yaml_stream = open('parameters_id6.yaml', 'r')
+ parameters_id6 = yaml.load(yaml_stream, Loader=yaml.Loader)
+
+
+ end_memtime = time.time()
+ #Read Input #5 from subroutine #2 in routine #6
+ yaml_stream = open('rotational_entropy_term_id6.yaml', 'r')
+ rotational_entropy_term_id6 = yaml.load(yaml_stream, Loader=yaml.Loader)
+
+
+ end_memtime = time.time()
+ #Read Input #6 from subroutine #2 in routine #6
+ yaml_stream = open('translational_entropy_term_id6.yaml', 'r')
+ translational_entropy_term_id6 = yaml.load(yaml_stream, Loader=yaml.Loader)
+
+
+ end_memtime = time.time()
+ #Read Input #2 from subroutine #2 in routine #7
+ yaml_stream = open('reactions.yaml', 'r')
+ reactions = yaml.load(yaml_stream, Loader=yaml.Loader)
+
+
+ end_memtime = time.time()
+
+ #### Start Step #1
+ # Call subroutine #1 from routine #0
+
+ lazy_build_structure_generic = dask.delayed(nout=1)(build_structure_generic)(parameters_id0)
+ # Call subroutine #1 from routine #1
+
+ lazy_build_structure = dask.delayed(nout=1)(build_structure)(parameters_id1)
+ # Call subroutine #1 from routine #4
+
+ lazy_build_structure_id4 = dask.delayed(nout=1)(build_structure)(parameters_id4)
+
+ #### Start Step #2
+ # Call subroutine #2 from routine #0
+
+ lazy_structure_relaxation = dask.delayed(nout=4)(structure_relaxation)(parameters_id0, lazy_build_structure_generic )
+ # Call subroutine #1 from routine #2
+
+ lazy_structure_relaxation_id2 = dask.delayed(nout=4)(structure_relaxation)(parameters_id2, lazy_build_structure)
+ # Call subroutine #1 from routine #5
+
+ lazy_structure_relaxation_id5 = dask.delayed(nout=4)(structure_relaxation)(parameters_id5, lazy_build_structure_id4)
+
+ #### Start Step #3
+ # Call subroutine #3 from routine #0
+
+ lazy_o_two_id0 = dask.delayed(MERGE)(energy_id0=lazy_structure_relaxation[1] , zero_point_energy_id0=zero_point_energy_id0, total_entropy_term_id0=total_entropy_term_id0, energy_minimum_id0=energy_minimum_id0)
+ # Call subroutine #1 from routine #3
+
+ lazy_vibrations = dask.delayed(nout=7)(vibrations)(parameters_id3, lazy_structure_relaxation_id2[0] )
+ # Call subroutine #1 from routine #6
+
+ lazy_vibrations_id6 = dask.delayed(nout=7)(vibrations)(parameters_id6, lazy_structure_relaxation_id5[0] )
+ # Call subroutine #1 from routine #8
+
+ lazy_vibrations_id8 = dask.delayed(nout=7)(vibrations)(parameters_id6, lazy_structure_relaxation_id5[0] )
+ # Call subroutine #1 from routine #9
+
+ lazy_vibrations_id9 = dask.delayed(nout=7)(vibrations)(parameters_id6, lazy_structure_relaxation_id5[0] )
+ # Call subroutine #1 from routine #10
+
+ lazy_vibrations_id10 = dask.delayed(nout=7)(vibrations)(parameters_id6, lazy_structure_relaxation_id5[0] )
+ # Call subroutine #1 from routine #11
+
+ lazy_vibrations_id11 = dask.delayed(nout=7)(vibrations)(parameters_id6, lazy_structure_relaxation_id5[0] )
+ # Call subroutine #1 from routine #12
+
+ lazy_vibrations_id12 = dask.delayed(nout=7)(vibrations)(parameters_id6, lazy_structure_relaxation_id5[0] )
+ # Call subroutine #1 from routine #13
+
+ lazy_vibrations_id13 = dask.delayed(nout=7)(vibrations)(parameters_id6, lazy_structure_relaxation_id5[0] )
+
+ #### Start Step #4
+ # Call subroutine #2 from routine #3
+
+ lazy_star_o_id3 = dask.delayed(MERGE)(energy_minimum_id3=lazy_vibrations[6] , energy_id2=lazy_structure_relaxation_id2[1],zero_point_energy_id3=lazy_vibrations[4] , vibrational_entropy_term_id3=lazy_vibrations[2] , rotational_entropy_term_id3=rotational_entropy_term_id3, translational_entropy_term_id3=translational_entropy_term_id3)
+ # Call subroutine #2 from routine #6
+
+ lazy_star_id6 = dask.delayed(MERGE)(energy_minimum_id6=lazy_vibrations_id6[6] , energy_id5=lazy_structure_relaxation_id5[1],zero_point_energy_id6=lazy_vibrations_id6[4] , vibrational_entropy_term_id6=lazy_vibrations_id6[2] , rotational_entropy_term_id6=rotational_entropy_term_id6, translational_entropy_term_id6=translational_entropy_term_id6)
+ # Call subroutine #2 from routine #8
+
+ lazy_star_id6 = dask.delayed(MERGE)(energy_minimum_id6=lazy_vibrations_id8[6] , energy_id5=lazy_structure_relaxation_id5[1],zero_point_energy_id6=lazy_vibrations_id8[4] , vibrational_entropy_term_id6=lazy_vibrations_id8[2] , rotational_entropy_term_id6=rotational_entropy_term_id6, translational_entropy_term_id6=translational_entropy_term_id6)
+ # Call subroutine #2 from routine #9
+
+ lazy_star_id6 = dask.delayed(MERGE)(energy_minimum_id6=lazy_vibrations_id9[6] , energy_id5=lazy_structure_relaxation_id5[1],zero_point_energy_id6=lazy_vibrations_id9[4] , vibrational_entropy_term_id6=lazy_vibrations_id9[2] , rotational_entropy_term_id6=rotational_entropy_term_id6, translational_entropy_term_id6=translational_entropy_term_id6)
+ # Call subroutine #2 from routine #10
+
+ lazy_star_id6 = dask.delayed(MERGE)(energy_minimum_id6=lazy_vibrations_id10[6] , energy_id5=lazy_structure_relaxation_id5[1],zero_point_energy_id6=lazy_vibrations_id10[4] , vibrational_entropy_term_id6=lazy_vibrations_id10[2] , rotational_entropy_term_id6=rotational_entropy_term_id6, translational_entropy_term_id6=translational_entropy_term_id6)
+ # Call subroutine #2 from routine #11
+
+ lazy_star_id6 = dask.delayed(MERGE)(energy_minimum_id6=lazy_vibrations_id11[6] , energy_id5=lazy_structure_relaxation_id5[1],zero_point_energy_id6=lazy_vibrations_id11[4] , vibrational_entropy_term_id6=lazy_vibrations_id11[2] , rotational_entropy_term_id6=rotational_entropy_term_id6, translational_entropy_term_id6=translational_entropy_term_id6)
+ # Call subroutine #2 from routine #12
+
+ lazy_star_id6 = dask.delayed(MERGE)(energy_minimum_id6=lazy_vibrations_id12[6] , energy_id5=lazy_structure_relaxation_id5[1],zero_point_energy_id6=lazy_vibrations_id12[4] , vibrational_entropy_term_id6=lazy_vibrations_id12[2] , rotational_entropy_term_id6=rotational_entropy_term_id6, translational_entropy_term_id6=translational_entropy_term_id6)
+ # Call subroutine #2 from routine #13
+
+ lazy_star_id6 = dask.delayed(MERGE)(energy_minimum_id6=lazy_vibrations_id13[6] , energy_id5=lazy_structure_relaxation_id5[1],zero_point_energy_id6=lazy_vibrations_id13[4] , vibrational_entropy_term_id6=lazy_vibrations_id13[2] , rotational_entropy_term_id6=rotational_entropy_term_id6, translational_entropy_term_id6=translational_entropy_term_id6)
+
+ #### Start Step #5
+ # Call subroutine #1 from routine #7
+
+ lazy_properties = dask.delayed(MERGE)(star_id6=lazy_star_id6, star_o_id3=lazy_star_o_id3, o_two_id0=lazy_o_two_id0 )
+
+ #### Start Step #6
+ # Call subroutine #2 from routine #7
+
+ lazy_reaction_energies = dask.delayed(nout=1)(reaction_energies)(lazy_properties, reactions)
+ #task_graph = Prefered_task.visualize(filename = 'mywf_test.png')
+ print(lazy_reaction_energies_id13.compute())
+ end_time = time.time()
+ total_time = end_time - start_time
+ total_memtime = end_memtime - start_time
+ print(' The total time is' , round(total_time, 2), 'seconds')
+ print(' The total memory load time is' , round(total_memtime, 2), 'seconds')
\ No newline at end of file
diff --git a/intro_examples/multihith/output/energy_slab_ver_2/DOT/energy_slab_ver_2.dot b/intro_examples/multihith/output/energy_slab_ver_2/DOT/energy_slab_ver_2.dot
new file mode 100644
index 0000000000000000000000000000000000000000..5ca1e6914449eb4796f5c2575952065c170d3c38
--- /dev/null
+++ b/intro_examples/multihith/output/energy_slab_ver_2/DOT/energy_slab_ver_2.dot
@@ -0,0 +1,72 @@
+digraph {
+ graph[
+ name=energy_slab_ver_2
+ ];
+0 [
+state=NONE
+name=Relax_structure_o_two
+label=Relax_structure_o_two
+ ];
+1 [
+state=NONE
+name=Build_structure_star_O
+label=Build_structure_star_O
+ ];
+2 [
+state=NONE
+name=Relax_structure_star_O
+label=Relax_structure_star_O
+ ];
+3 [
+state=NONE
+name=Normal_mode_analysis_star_O
+label=Normal_mode_analysis_star_O
+ ];
+4 [
+state=NONE
+name=Build_structure_star
+label=Build_structure_star
+ ];
+5 [
+state=NONE
+name=Relax_structure_star
+label=Relax_structure_star
+ ];
+6 [
+state=NONE
+name=Normal_mode_analysis_star
+label=Normal_mode_analysis_star
+ ];
+7 [
+state=NONE
+name=Adsorption_energies
+label=Adsorption_energies
+ ];
+1->2[
+label=structure
+ ];
+2->3[
+label=relaxed_structure
+ ];
+2->3[
+label=energy
+ ];
+4->5[
+label=structure
+ ];
+5->6[
+label=relaxed_structure
+ ];
+5->6[
+label=energy
+ ];
+6->7[
+label=star
+ ];
+3->7[
+label=star_o
+ ];
+0->7[
+label=o_two
+ ];
+ }
diff --git a/intro_examples/multihith/output/energy_slab_ver_2/DOT/energy_slab_ver_2.pdf b/intro_examples/multihith/output/energy_slab_ver_2/DOT/energy_slab_ver_2.pdf
new file mode 100644
index 0000000000000000000000000000000000000000..12c053566c4e87d3f222d86571caec3b2e792e5b
Binary files /dev/null and b/intro_examples/multihith/output/energy_slab_ver_2/DOT/energy_slab_ver_2.pdf differ
diff --git a/intro_examples/multihith/output/energy_slab_ver_2/DOT/energy_slab_ver_2.png b/intro_examples/multihith/output/energy_slab_ver_2/DOT/energy_slab_ver_2.png
new file mode 100644
index 0000000000000000000000000000000000000000..d819feed61cfc178dae5cc49cf7c01aaf455ecb7
Binary files /dev/null and b/intro_examples/multihith/output/energy_slab_ver_2/DOT/energy_slab_ver_2.png differ
diff --git a/intro_examples/multihith/output/energy_slab_ver_2/PARSL/energy_slab_ver_2_parsl.py b/intro_examples/multihith/output/energy_slab_ver_2/PARSL/energy_slab_ver_2_parsl.py
new file mode 100644
index 0000000000000000000000000000000000000000..c4555f5d1c54e3f5e5c564a45a2980e1fdd7b6a2
--- /dev/null
+++ b/intro_examples/multihith/output/energy_slab_ver_2/PARSL/energy_slab_ver_2_parsl.py
@@ -0,0 +1,264 @@
+import yaml
+import numpy as np
+from auxiliary import MERGE
+from auxiliary import flat_tuple
+from auxiliary import flat_list
+import time
+from parsl.addresses import address_by_hostname
+from parsl.providers import LocalProvider
+from parsl.channels import LocalChannel
+from parsl.config import Config
+from parsl.executors import HighThroughputExecutor
+from parsl.monitoring.monitoring import MonitoringHub
+import parsl
+
+from parsl.providers import SlurmProvider
+from parsl.launchers import SrunLauncher
+
+from parsl.data_provider.files import File
+from parsl.data_provider.file_noop import NoOpFileStaging
+from ueffumax import build_structure_generic
+from ueffumax import structure_relaxation
+from ueffumax import build_structure
+from ueffumax import vibrations
+from ueffumax import reaction_energies
+
+if __name__ == '__main__':
+
+
+ start_time = time.time()
+
+ config_slurm = Config(
+ executors=[
+ HighThroughputExecutor(
+ label="frontera_htex",
+ address=address_by_hostname(),
+ max_workers=56,
+ provider=SlurmProvider(
+ channel=LocalChannel(),
+ nodes_per_block=1,
+ init_blocks=1,
+ partition='single',
+ walltime = '00:30:00',
+ launcher=SrunLauncher(),
+ ),
+ )
+ ],
+
+ monitoring=MonitoringHub(
+ hub_address=address_by_hostname(),
+ monitoring_debug=False,
+ workflow_name = 'slab_1_slurm',
+ resource_monitoring_interval=1,
+ ),
+ strategy = None
+ )
+
+ config_local = Config(
+ executors=[
+ HighThroughputExecutor(
+ label = "frontera_htex",
+ cores_per_worker = 2,
+ max_workers = 40,
+ storage_access=[NoOpFileStaging()],
+ provider = LocalProvider(
+ parallelism = 1,
+ ),
+
+ )
+ ],
+
+ monitoring=MonitoringHub(
+ hub_address=address_by_hostname(),
+ workflow_name = 'slab_1_local',
+ monitoring_debug=False,
+ resource_monitoring_interval=1,
+ ),
+ strategy = None
+ )
+
+ parsl.load(config_local)
+ #Read Input #1from subroutine #1 in routine #0
+ yaml_stream = open('parameters_id0.yaml', 'r')
+ parameters_id0 = yaml.load(yaml_stream, Loader=yaml.Loader)
+
+
+ end_memtime = time.time()
+ #Read Input #2from subroutine #3 in routine #0
+ yaml_stream = open('zero_point_energy_id0.yaml', 'r')
+ zero_point_energy_id0 = yaml.load(yaml_stream, Loader=yaml.Loader)
+
+
+ end_memtime = time.time()
+ #Read Input #3from subroutine #3 in routine #0
+ yaml_stream = open('total_entropy_term_id0.yaml', 'r')
+ total_entropy_term_id0 = yaml.load(yaml_stream, Loader=yaml.Loader)
+
+
+ end_memtime = time.time()
+ #Read Input #4from subroutine #3 in routine #0
+ yaml_stream = open('energy_minimum_id0.yaml', 'r')
+ energy_minimum_id0 = yaml.load(yaml_stream, Loader=yaml.Loader)
+
+
+ end_memtime = time.time()
+ #Read Input #1from subroutine #1 in routine #1
+ yaml_stream = open('parameters_id1.yaml', 'r')
+ parameters_id1 = yaml.load(yaml_stream, Loader=yaml.Loader)
+
+
+ end_memtime = time.time()
+ #Read Input #1from subroutine #1 in routine #2
+ yaml_stream = open('parameters_id2.yaml', 'r')
+ parameters_id2 = yaml.load(yaml_stream, Loader=yaml.Loader)
+
+
+ end_memtime = time.time()
+ #Read Input #1from subroutine #1 in routine #3
+ yaml_stream = open('parameters_id3.yaml', 'r')
+ parameters_id3 = yaml.load(yaml_stream, Loader=yaml.Loader)
+
+
+ end_memtime = time.time()
+ #Read Input #5from subroutine #2 in routine #3
+ yaml_stream = open('rotational_entropy_term_id3.yaml', 'r')
+ rotational_entropy_term_id3 = yaml.load(yaml_stream, Loader=yaml.Loader)
+
+
+ end_memtime = time.time()
+ #Read Input #6from subroutine #2 in routine #3
+ yaml_stream = open('translational_entropy_term_id3.yaml', 'r')
+ translational_entropy_term_id3 = yaml.load(yaml_stream, Loader=yaml.Loader)
+
+
+ end_memtime = time.time()
+ #Read Input #1from subroutine #1 in routine #4
+ yaml_stream = open('parameters_id4.yaml', 'r')
+ parameters_id4 = yaml.load(yaml_stream, Loader=yaml.Loader)
+
+
+ end_memtime = time.time()
+ #Read Input #1from subroutine #1 in routine #5
+ yaml_stream = open('parameters_id5.yaml', 'r')
+ parameters_id5 = yaml.load(yaml_stream, Loader=yaml.Loader)
+
+
+ end_memtime = time.time()
+ #Read Input #1from subroutine #1 in routine #6
+ yaml_stream = open('parameters_id6.yaml', 'r')
+ parameters_id6 = yaml.load(yaml_stream, Loader=yaml.Loader)
+
+
+ end_memtime = time.time()
+ #Read Input #5from subroutine #2 in routine #6
+ yaml_stream = open('rotational_entropy_term_id6.yaml', 'r')
+ rotational_entropy_term_id6 = yaml.load(yaml_stream, Loader=yaml.Loader)
+
+
+ end_memtime = time.time()
+ #Read Input #6from subroutine #2 in routine #6
+ yaml_stream = open('translational_entropy_term_id6.yaml', 'r')
+ translational_entropy_term_id6 = yaml.load(yaml_stream, Loader=yaml.Loader)
+
+
+ end_memtime = time.time()
+ #Read Input #2from subroutine #2 in routine #7
+ yaml_stream = open('reactions.yaml', 'r')
+ reactions = yaml.load(yaml_stream, Loader=yaml.Loader)
+
+
+ end_memtime = time.time()
+
+ #### Start Step #1
+ # Call subroutine #1 from routine #0
+
+ parsl_build_structure_generic = build_structure_generic(parameters_id0)
+ # Call subroutine #1 from routine #1
+
+ parsl_build_structure = build_structure(parameters_id1)
+ # Call subroutine #1 from routine #4
+
+ parsl_build_structure_id4 = build_structure(parameters_id4)
+
+ #### Start Step #2
+ # Call subroutine #2 from routine #0
+
+ parsl_structure_relaxation = structure_relaxation(parameters_id0, parsl_build_structure_generic)
+ # Call subroutine #1 from routine #2
+
+ parsl_structure_relaxation_id2 = structure_relaxation(parameters_id2, parsl_build_structure)
+ # Call subroutine #1 from routine #5
+
+ parsl_structure_relaxation_id5 = structure_relaxation(parameters_id5, parsl_build_structure_id4)
+
+ #### Start Step #3
+ # Call subroutine #3 from routine #0
+
+ parsl_o_two_id0 = MERGE(energy_id0=parsl_structure_relaxation.result()[1] , zero_point_energy_id0=zero_point_energy_id0, total_entropy_term_id0=total_entropy_term_id0, energy_minimum_id0=energy_minimum_id0)
+ # Call subroutine #1 from routine #3
+
+ parsl_vibrations = vibrations(parameters_id3, parsl_structure_relaxation_id2.result()[0])
+ # Call subroutine #1 from routine #6
+
+ parsl_vibrations_id6 = vibrations(parameters_id6, parsl_structure_relaxation_id5.result()[0])
+ # Call subroutine #1 from routine #8
+
+ parsl_vibrations_id8 = vibrations(parameters_id6, parsl_structure_relaxation_id5.result()[0])
+ # Call subroutine #1 from routine #9
+
+ parsl_vibrations_id9 = vibrations(parameters_id6, parsl_structure_relaxation_id5.result()[0])
+ # Call subroutine #1 from routine #10
+
+ parsl_vibrations_id10 = vibrations(parameters_id6, parsl_structure_relaxation_id5.result()[0])
+ # Call subroutine #1 from routine #11
+
+ parsl_vibrations_id11 = vibrations(parameters_id6, parsl_structure_relaxation_id5.result()[0])
+ # Call subroutine #1 from routine #12
+
+ parsl_vibrations_id12 = vibrations(parameters_id6, parsl_structure_relaxation_id5.result()[0])
+ # Call subroutine #1 from routine #13
+
+ parsl_vibrations_id13 = vibrations(parameters_id6, parsl_structure_relaxation_id5.result()[0])
+
+ #### Start Step #4
+ # Call subroutine #2 from routine #3
+
+ parsl_star_o_id3 = MERGE(energy_minimum_id3=parsl_vibrations.result()[6] , energy_id2=parsl_structure_relaxation_id2.result()[1], zero_point_energy_id3=parsl_vibrations.result()[4] , vibrational_entropy_term_id3=parsl_vibrations.result()[2] , rotational_entropy_term_id3=rotational_entropy_term_id3, translational_entropy_term_id3=translational_entropy_term_id3)
+ # Call subroutine #2 from routine #6
+
+ parsl_star_id6 = MERGE(energy_minimum_id6=parsl_vibrations_id6.result()[6] , energy_id5=parsl_structure_relaxation_id5.result()[1], zero_point_energy_id6=parsl_vibrations_id6.result()[4] , vibrational_entropy_term_id6=parsl_vibrations_id6.result()[2] , rotational_entropy_term_id6=rotational_entropy_term_id6, translational_entropy_term_id6=translational_entropy_term_id6)
+ # Call subroutine #2 from routine #8
+
+ parsl_star_id6 = MERGE(energy_minimum_id6=parsl_vibrations_id8.result()[6] , energy_id5=parsl_structure_relaxation_id5.result()[1], zero_point_energy_id6=parsl_vibrations_id8.result()[4] , vibrational_entropy_term_id6=parsl_vibrations_id8.result()[2] , rotational_entropy_term_id6=rotational_entropy_term_id6, translational_entropy_term_id6=translational_entropy_term_id6)
+ # Call subroutine #2 from routine #9
+
+ parsl_star_id6 = MERGE(energy_minimum_id6=parsl_vibrations_id9.result()[6] , energy_id5=parsl_structure_relaxation_id5.result()[1], zero_point_energy_id6=parsl_vibrations_id9.result()[4] , vibrational_entropy_term_id6=parsl_vibrations_id9.result()[2] , rotational_entropy_term_id6=rotational_entropy_term_id6, translational_entropy_term_id6=translational_entropy_term_id6)
+ # Call subroutine #2 from routine #10
+
+ parsl_star_id6 = MERGE(energy_minimum_id6=parsl_vibrations_id10.result()[6] , energy_id5=parsl_structure_relaxation_id5.result()[1], zero_point_energy_id6=parsl_vibrations_id10.result()[4] , vibrational_entropy_term_id6=parsl_vibrations_id10.result()[2] , rotational_entropy_term_id6=rotational_entropy_term_id6, translational_entropy_term_id6=translational_entropy_term_id6)
+ # Call subroutine #2 from routine #11
+
+ parsl_star_id6 = MERGE(energy_minimum_id6=parsl_vibrations_id11.result()[6] , energy_id5=parsl_structure_relaxation_id5.result()[1], zero_point_energy_id6=parsl_vibrations_id11.result()[4] , vibrational_entropy_term_id6=parsl_vibrations_id11.result()[2] , rotational_entropy_term_id6=rotational_entropy_term_id6, translational_entropy_term_id6=translational_entropy_term_id6)
+ # Call subroutine #2 from routine #12
+
+ parsl_star_id6 = MERGE(energy_minimum_id6=parsl_vibrations_id12.result()[6] , energy_id5=parsl_structure_relaxation_id5.result()[1], zero_point_energy_id6=parsl_vibrations_id12.result()[4] , vibrational_entropy_term_id6=parsl_vibrations_id12.result()[2] , rotational_entropy_term_id6=rotational_entropy_term_id6, translational_entropy_term_id6=translational_entropy_term_id6)
+ # Call subroutine #2 from routine #13
+
+ parsl_star_id6 = MERGE(energy_minimum_id6=parsl_vibrations_id13.result()[6] , energy_id5=parsl_structure_relaxation_id5.result()[1], zero_point_energy_id6=parsl_vibrations_id13.result()[4] , vibrational_entropy_term_id6=parsl_vibrations_id13.result()[2] , rotational_entropy_term_id6=rotational_entropy_term_id6, translational_entropy_term_id6=translational_entropy_term_id6)
+
+ #### Start Step #5
+ # Call subroutine #1 from routine #7
+
+ parsl_properties = MERGE(star_id6=parsl_star_id6, star_o_id3=parsl_star_o_id3, o_two_id0=parsl_o_two_id0 )
+
+ #### Start Step #6
+ # Call subroutine #2 from routine #7
+
+ parsl_reaction_energies = reaction_energies(parsl_properties, reactions)
+ print(parsl_reaction_energies_id13.compute())
+ end_time = time.time()
+ total_time = end_time - start_time
+ total_memtime = end_memtime - start_time
+ print(' The total time is' , round(total_time, 2), 'seconds')
+ print(' The total memory load time is' , round(total_memtime, 2), 'seconds')
+ print('PARSL based workflow')
\ No newline at end of file
diff --git a/intro_examples/multihith/output/energy_slab_ver_2/firework/energy_slab_ver_2.yaml b/intro_examples/multihith/output/energy_slab_ver_2/firework/energy_slab_ver_2.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..ba9a1614dca49ab45ec4fca744d33ba9e18ebc2e
--- /dev/null
+++ b/intro_examples/multihith/output/energy_slab_ver_2/firework/energy_slab_ver_2.yaml
@@ -0,0 +1,894 @@
+fws:
+- fw_id: 0
+ name: Relax_structure_o_two
+ spec:
+ _tasks:
+ - _fw_name: PyTask
+ func: ueffumax.build_structure_generic
+ inputs:
+ - parameters_id0
+ outputs:
+ - structure_id0
+ - _fw_name: PyTask
+ func: ueffumax.structure_relaxation
+ inputs:
+ - parameters_id0
+ - structure_id0
+ outputs:
+ - relaxed_structure_id0
+ - energy_id0
+ - forces_id0
+ - dipole_id0
+ - _fw_name: JoinDictTask
+ inputs:
+ - energy_id0
+ - zero_point_energy_id0
+ - total_entropy_term_id0
+ - energy_minimum_id0
+ output: o_two_id0
+ energy_minimum_id0: true
+ parameters_id0:
+ calculator:
+ name: vasp
+ optimize: true
+ parameters:
+ algo: Fast
+ ediff: 1.0e-06
+ ediffg: -0.05
+ encut: 400.0
+ ibrion: 2
+ icharg: 2
+ ismear: 0
+ ispin: 2
+ istart: 0
+ kpts:
+ - 1
+ - 1
+ - 1
+ lcharg: false
+ lreal: Auto
+ lwave: false
+ nelm: 250
+ nsw: 500
+ potim: 0.2
+ prec: Normal
+ sigma: 0.05
+ xc: PBE
+ structure:
+ atoms:
+ cell:
+ - - 12.0
+ - 0.0
+ - 0.0
+ - - 0.0
+ - 12.0
+ - 0.0
+ - - 0.0
+ - 0.0
+ - 12.0
+ constraints:
+ - kwargs:
+ a: 0
+ direction:
+ - 0.0
+ - 0.0
+ - 1.0
+ name: FixedLine
+ - kwargs:
+ a: 1
+ direction:
+ - 0.0
+ - 0.0
+ - 1.0
+ name: FixedLine
+ numbers:
+ - 8
+ - 8
+ pbc:
+ - true
+ - true
+ - true
+ positions:
+ - - 0.0
+ - 0.0
+ - 0.0
+ - - 0.0
+ - 0.0
+ - 1.234
+ total_entropy_term_id0: 0.637
+ zero_point_energy_id0: 0.098
+- fw_id: 1
+ name: Build_structure_star_O
+ spec:
+ _tasks:
+ - _fw_name: PyTask
+ func: ueffumax.build_structure
+ inputs:
+ - parameters_id1
+ outputs:
+ - structure_id1
+ parameters_id1:
+ adsorbates:
+ - adsorbate:
+ numbers:
+ - 8
+ positions:
+ - - 0.0
+ - 0.0
+ - 0.0
+ height: 1.3
+ offset:
+ - 0
+ - 0
+ position: fcc
+ substrate:
+ constraints:
+ layers:
+ - 3
+ construct:
+ method:
+ args:
+ - Ni
+ - - 2
+ - 2
+ - 3
+ kwargs:
+ a: 3.518
+ orthogonal: false
+ vacuum: 12.0
+ name: fcc111
+ type: surface
+- fw_id: 2
+ name: Relax_structure_star_O
+ spec:
+ _tasks:
+ - _fw_name: PyTask
+ func: ueffumax.structure_relaxation
+ inputs:
+ - parameters_id2
+ - structure_id1
+ outputs:
+ - relaxed_structure_id2
+ - energy_id2
+ - forces_id2
+ - dipole_id2
+ parameters_id2:
+ calculator:
+ name: vasp
+ optimize: true
+ parameters:
+ algo: Fast
+ ediff: 1.0e-06
+ ediffg: -0.05
+ encut: 400.0
+ ibrion: 2
+ icharg: 2
+ ismear: 1
+ ispin: 2
+ istart: 0
+ kpts:
+ - 5
+ - 5
+ - 1
+ lcharg: false
+ lreal: Auto
+ lwave: false
+ ncore: 20
+ nelm: 250
+ nsw: 500
+ potim: 0.2
+ prec: Normal
+ sigma: 0.2
+ xc: PBE
+- fw_id: 3
+ name: Normal_mode_analysis_star_O
+ spec:
+ _tasks:
+ - _fw_name: PyTask
+ func: ueffumax.vibrations
+ inputs:
+ - parameters_id3
+ - relaxed_structure_id2
+ outputs:
+ - vibrational_energies_id3
+ - vibrational_entropy_id3
+ - vibrational_entropy_term_id3
+ - vibrational_partition_func_id3
+ - zero_point_energy_id3
+ - transition_state_id3
+ - energy_minimum_id3
+ - _fw_name: JoinDictTask
+ inputs:
+ - energy_minimum_id3
+ - energy_id2
+ - zero_point_energy_id3
+ - vibrational_entropy_term_id3
+ - rotational_entropy_term_id3
+ - translational_entropy_term_id3
+ output: star_o_id3
+ parameters_id3:
+ calculator:
+ name: vasp
+ optimize: false
+ parameters:
+ algo: Fast
+ ediff: 1.0e-08
+ encut: 400.0
+ ibrion: 5
+ icharg: 2
+ ismear: 1
+ ispin: 2
+ istart: 0
+ kpts:
+ - 5
+ - 5
+ - 1
+ lcharg: false
+ lreal: Auto
+ lwave: false
+ nelm: 250
+ nfree: 2
+ nsw: 1
+ potim: 0.005
+ prec: Normal
+ sigma: 0.2
+ xc: PBE
+ normal mode analysis:
+ constraints:
+ - kwargs:
+ indices:
+ - 0
+ - 1
+ - 2
+ - 3
+ - 4
+ - 5
+ - 6
+ - 7
+ - 8
+ - 9
+ - 10
+ - 11
+ name: FixAtoms
+ parameters: {}
+ temperature: 298.15
+ rotational_entropy_term_id3: 0.0
+ translational_entropy_term_id3: 0.0
+- fw_id: 4
+ name: Build_structure_star
+ spec:
+ _tasks:
+ - _fw_name: PyTask
+ func: ueffumax.build_structure
+ inputs:
+ - parameters_id4
+ outputs:
+ - structure_id4
+ parameters_id4:
+ adsorbates: []
+ substrate:
+ constraints:
+ layers:
+ - 3
+ construct:
+ method:
+ args:
+ - Ni
+ - - 2
+ - 2
+ - 3
+ kwargs:
+ a: 3.518
+ orthogonal: false
+ vacuum: 12.0
+ name: fcc111
+ type: surface
+- fw_id: 5
+ name: Relax_structure_star
+ spec:
+ _tasks:
+ - _fw_name: PyTask
+ func: ueffumax.structure_relaxation
+ inputs:
+ - parameters_id5
+ - structure_id4
+ outputs:
+ - relaxed_structure_id5
+ - energy_id5
+ - forces_id5
+ - dipole_id5
+ parameters_id5:
+ calculator:
+ name: vasp
+ optimize: true
+ parameters:
+ algo: Fast
+ ediff: 1.0e-06
+ ediffg: -0.05
+ encut: 400.0
+ ibrion: 2
+ icharg: 2
+ ismear: 1
+ ispin: 2
+ istart: 0
+ kpts:
+ - 5
+ - 5
+ - 1
+ lcharg: false
+ lreal: Auto
+ lwave: false
+ ncore: 20
+ nelm: 250
+ nsw: 500
+ potim: 0.2
+ prec: Normal
+ sigma: 0.2
+ xc: PBE
+- fw_id: 6
+ name: Normal_mode_analysis_star
+ spec:
+ _tasks:
+ - _fw_name: PyTask
+ func: ueffumax.vibrations
+ inputs:
+ - parameters_id6
+ - relaxed_structure_id5
+ outputs:
+ - vibrational_energies_id6
+ - vibrational_entropy_id6
+ - vibrational_entropy_term_id6
+ - vibrational_partition_func_id6
+ - zero_point_energy_id6
+ - transition_state_id6
+ - energy_minimum_id6
+ - _fw_name: JoinDictTask
+ inputs:
+ - energy_minimum_id6
+ - energy_id5
+ - zero_point_energy_id6
+ - vibrational_entropy_term_id6
+ - rotational_entropy_term_id6
+ - translational_entropy_term_id6
+ output: star_id6
+ parameters_id6:
+ calculator:
+ name: vasp
+ optimize: false
+ parameters:
+ algo: Fast
+ ediff: 1.0e-08
+ encut: 400.0
+ ibrion: 5
+ icharg: 2
+ ismear: 1
+ ispin: 2
+ istart: 0
+ kpts:
+ - 5
+ - 5
+ - 1
+ lcharg: false
+ lreal: Auto
+ lwave: false
+ nelm: 250
+ nfree: 2
+ nsw: 1
+ potim: 0.005
+ prec: Normal
+ sigma: 0.2
+ normal mode analysis:
+ constraints:
+ - kwargs:
+ indices:
+ - 0
+ - 1
+ - 2
+ - 3
+ - 4
+ - 5
+ - 6
+ - 7
+ - 8
+ - 9
+ - 10
+ - 11
+ name: FixAtoms
+ parameters: {}
+ temperature: 298.15
+ rotational_entropy_term_id6: 0.0
+ translational_entropy_term_id6: 0.0
+- fw_id: 7
+ name: Adsorption_energies
+ spec:
+ _tasks:
+ - _fw_name: JoinDictTask
+ inputs:
+ - star_id6
+ - star_o_id3
+ - o_two_id0
+ output: properties
+ - _fw_name: PyTask
+ func: ueffumax.reaction_energies
+ inputs:
+ - properties
+ - reactions
+ outputs:
+ - reaction_properties
+ reactions:
+ - electrons: 0
+ equation:
+ - coefficient: -1.0
+ species: star
+ - coefficient: -0.5
+ species: o_two
+ - coefficient: 1.0
+ species: star_o
+- fw_id: 8
+ name: Normal_mode_analysis_star
+ spec:
+ _tasks:
+ - _fw_name: PyTask
+ func: ueffumax.vibrations
+ inputs:
+ - parameters_id6
+ - relaxed_structure_id5
+ outputs:
+ - vibrational_energies_id6
+ - vibrational_entropy_id6
+ - vibrational_entropy_term_id6
+ - vibrational_partition_func_id6
+ - zero_point_energy_id6
+ - transition_state_id6
+ - energy_minimum_id6
+ - _fw_name: JoinDictTask
+ inputs:
+ - energy_minimum_id6
+ - energy_id5
+ - zero_point_energy_id6
+ - vibrational_entropy_term_id6
+ - rotational_entropy_term_id6
+ - translational_entropy_term_id6
+ output: star_id6
+ parameters_id6:
+ calculator:
+ name: vasp
+ optimize: false
+ parameters:
+ algo: Fast
+ ediff: 1.0e-08
+ encut: 400.0
+ ibrion: 5
+ icharg: 2
+ ismear: 1
+ ispin: 2
+ istart: 0
+ kpts:
+ - 5
+ - 5
+ - 1
+ lcharg: false
+ lreal: Auto
+ lwave: false
+ nelm: 250
+ nfree: 2
+ nsw: 1
+ potim: 0.005
+ prec: Normal
+ sigma: 0.2
+ normal mode analysis:
+ constraints:
+ - kwargs:
+ indices:
+ - 0
+ - 1
+ - 2
+ - 3
+ - 4
+ - 5
+ - 6
+ - 7
+ - 8
+ - 9
+ - 10
+ - 11
+ name: FixAtoms
+ parameters: {}
+ temperature: 298.15
+ rotational_entropy_term_id6: 0.0
+ translational_entropy_term_id6: 0.0
+- fw_id: 9
+ name: Normal_mode_analysis_star
+ spec:
+ _tasks:
+ - _fw_name: PyTask
+ func: ueffumax.vibrations
+ inputs:
+ - parameters_id6
+ - relaxed_structure_id5
+ outputs:
+ - vibrational_energies_id6
+ - vibrational_entropy_id6
+ - vibrational_entropy_term_id6
+ - vibrational_partition_func_id6
+ - zero_point_energy_id6
+ - transition_state_id6
+ - energy_minimum_id6
+ - _fw_name: JoinDictTask
+ inputs:
+ - energy_minimum_id6
+ - energy_id5
+ - zero_point_energy_id6
+ - vibrational_entropy_term_id6
+ - rotational_entropy_term_id6
+ - translational_entropy_term_id6
+ output: star_id6
+ parameters_id6:
+ calculator:
+ name: vasp
+ optimize: false
+ parameters:
+ algo: Fast
+ ediff: 1.0e-08
+ encut: 400.0
+ ibrion: 5
+ icharg: 2
+ ismear: 1
+ ispin: 2
+ istart: 0
+ kpts:
+ - 5
+ - 5
+ - 1
+ lcharg: false
+ lreal: Auto
+ lwave: false
+ nelm: 250
+ nfree: 2
+ nsw: 1
+ potim: 0.005
+ prec: Normal
+ sigma: 0.2
+ normal mode analysis:
+ constraints:
+ - kwargs:
+ indices:
+ - 0
+ - 1
+ - 2
+ - 3
+ - 4
+ - 5
+ - 6
+ - 7
+ - 8
+ - 9
+ - 10
+ - 11
+ name: FixAtoms
+ parameters: {}
+ temperature: 298.15
+ rotational_entropy_term_id6: 0.0
+ translational_entropy_term_id6: 0.0
+- fw_id: 10
+ name: Normal_mode_analysis_star
+ spec:
+ _tasks:
+ - _fw_name: PyTask
+ func: ueffumax.vibrations
+ inputs:
+ - parameters_id6
+ - relaxed_structure_id5
+ outputs:
+ - vibrational_energies_id6
+ - vibrational_entropy_id6
+ - vibrational_entropy_term_id6
+ - vibrational_partition_func_id6
+ - zero_point_energy_id6
+ - transition_state_id6
+ - energy_minimum_id6
+ - _fw_name: JoinDictTask
+ inputs:
+ - energy_minimum_id6
+ - energy_id5
+ - zero_point_energy_id6
+ - vibrational_entropy_term_id6
+ - rotational_entropy_term_id6
+ - translational_entropy_term_id6
+ output: star_id6
+ parameters_id6:
+ calculator:
+ name: vasp
+ optimize: false
+ parameters:
+ algo: Fast
+ ediff: 1.0e-08
+ encut: 400.0
+ ibrion: 5
+ icharg: 2
+ ismear: 1
+ ispin: 2
+ istart: 0
+ kpts:
+ - 5
+ - 5
+ - 1
+ lcharg: false
+ lreal: Auto
+ lwave: false
+ nelm: 250
+ nfree: 2
+ nsw: 1
+ potim: 0.005
+ prec: Normal
+ sigma: 0.2
+ normal mode analysis:
+ constraints:
+ - kwargs:
+ indices:
+ - 0
+ - 1
+ - 2
+ - 3
+ - 4
+ - 5
+ - 6
+ - 7
+ - 8
+ - 9
+ - 10
+ - 11
+ name: FixAtoms
+ parameters: {}
+ temperature: 298.15
+ rotational_entropy_term_id6: 0.0
+ translational_entropy_term_id6: 0.0
+- fw_id: 11
+ name: Normal_mode_analysis_star
+ spec:
+ _tasks:
+ - _fw_name: PyTask
+ func: ueffumax.vibrations
+ inputs:
+ - parameters_id6
+ - relaxed_structure_id5
+ outputs:
+ - vibrational_energies_id6
+ - vibrational_entropy_id6
+ - vibrational_entropy_term_id6
+ - vibrational_partition_func_id6
+ - zero_point_energy_id6
+ - transition_state_id6
+ - energy_minimum_id6
+ - _fw_name: JoinDictTask
+ inputs:
+ - energy_minimum_id6
+ - energy_id5
+ - zero_point_energy_id6
+ - vibrational_entropy_term_id6
+ - rotational_entropy_term_id6
+ - translational_entropy_term_id6
+ output: star_id6
+ parameters_id6:
+ calculator:
+ name: vasp
+ optimize: false
+ parameters:
+ algo: Fast
+ ediff: 1.0e-08
+ encut: 400.0
+ ibrion: 5
+ icharg: 2
+ ismear: 1
+ ispin: 2
+ istart: 0
+ kpts:
+ - 5
+ - 5
+ - 1
+ lcharg: false
+ lreal: Auto
+ lwave: false
+ nelm: 250
+ nfree: 2
+ nsw: 1
+ potim: 0.005
+ prec: Normal
+ sigma: 0.2
+ normal mode analysis:
+ constraints:
+ - kwargs:
+ indices:
+ - 0
+ - 1
+ - 2
+ - 3
+ - 4
+ - 5
+ - 6
+ - 7
+ - 8
+ - 9
+ - 10
+ - 11
+ name: FixAtoms
+ parameters: {}
+ temperature: 298.15
+ rotational_entropy_term_id6: 0.0
+ translational_entropy_term_id6: 0.0
+- fw_id: 12
+ name: Normal_mode_analysis_star
+ spec:
+ _tasks:
+ - _fw_name: PyTask
+ func: ueffumax.vibrations
+ inputs:
+ - parameters_id6
+ - relaxed_structure_id5
+ outputs:
+ - vibrational_energies_id6
+ - vibrational_entropy_id6
+ - vibrational_entropy_term_id6
+ - vibrational_partition_func_id6
+ - zero_point_energy_id6
+ - transition_state_id6
+ - energy_minimum_id6
+ - _fw_name: JoinDictTask
+ inputs:
+ - energy_minimum_id6
+ - energy_id5
+ - zero_point_energy_id6
+ - vibrational_entropy_term_id6
+ - rotational_entropy_term_id6
+ - translational_entropy_term_id6
+ output: star_id6
+ parameters_id6:
+ calculator:
+ name: vasp
+ optimize: false
+ parameters:
+ algo: Fast
+ ediff: 1.0e-08
+ encut: 400.0
+ ibrion: 5
+ icharg: 2
+ ismear: 1
+ ispin: 2
+ istart: 0
+ kpts:
+ - 5
+ - 5
+ - 1
+ lcharg: false
+ lreal: Auto
+ lwave: false
+ nelm: 250
+ nfree: 2
+ nsw: 1
+ potim: 0.005
+ prec: Normal
+ sigma: 0.2
+ normal mode analysis:
+ constraints:
+ - kwargs:
+ indices:
+ - 0
+ - 1
+ - 2
+ - 3
+ - 4
+ - 5
+ - 6
+ - 7
+ - 8
+ - 9
+ - 10
+ - 11
+ name: FixAtoms
+ parameters: {}
+ temperature: 298.15
+ rotational_entropy_term_id6: 0.0
+ translational_entropy_term_id6: 0.0
+- fw_id: 13
+ name: Normal_mode_analysis_star
+ spec:
+ _tasks:
+ - _fw_name: PyTask
+ func: ueffumax.vibrations
+ inputs:
+ - parameters_id6
+ - relaxed_structure_id5
+ outputs:
+ - vibrational_energies_id6
+ - vibrational_entropy_id6
+ - vibrational_entropy_term_id6
+ - vibrational_partition_func_id6
+ - zero_point_energy_id6
+ - transition_state_id6
+ - energy_minimum_id6
+ - _fw_name: JoinDictTask
+ inputs:
+ - energy_minimum_id6
+ - energy_id5
+ - zero_point_energy_id6
+ - vibrational_entropy_term_id6
+ - rotational_entropy_term_id6
+ - translational_entropy_term_id6
+ output: star_id6
+ parameters_id6:
+ calculator:
+ name: vasp
+ optimize: false
+ parameters:
+ algo: Fast
+ ediff: 1.0e-08
+ encut: 400.0
+ ibrion: 5
+ icharg: 2
+ ismear: 1
+ ispin: 2
+ istart: 0
+ kpts:
+ - 5
+ - 5
+ - 1
+ lcharg: false
+ lreal: Auto
+ lwave: false
+ nelm: 250
+ nfree: 2
+ nsw: 1
+ potim: 0.005
+ prec: Normal
+ sigma: 0.2
+ normal mode analysis:
+ constraints:
+ - kwargs:
+ indices:
+ - 0
+ - 1
+ - 2
+ - 3
+ - 4
+ - 5
+ - 6
+ - 7
+ - 8
+ - 9
+ - 10
+ - 11
+ name: FixAtoms
+ parameters: {}
+ temperature: 298.15
+ rotational_entropy_term_id6: 0.0
+ translational_entropy_term_id6: 0.0
+links:
+ '0':
+ - 7
+ '1':
+ - 2
+ '10': []
+ '11': []
+ '12': []
+ '13':
+ - 7
+ '2':
+ - 3
+ '3':
+ - 7
+ '4':
+ - 5
+ '5':
+ - 6
+ - 8
+ - 9
+ - 10
+ - 11
+ - 12
+ - 13
+ '6': []
+ '7': []
+ '8': []
+ '9': []
+metadata: {}
+name: energy_slab_ver_2_wfGenes
diff --git a/intro_examples/multihith/output/energy_slab_ver_2/simstack/simstack.xml b/intro_examples/multihith/output/energy_slab_ver_2/simstack/simstack.xml
new file mode 100644
index 0000000000000000000000000000000000000000..145fb49c96929ba229a664f11532bdc5404a4fd8
--- /dev/null
+++ b/intro_examples/multihith/output/energy_slab_ver_2/simstack/simstack.xml
@@ -0,0 +1,16 @@
+