surfflow 1.0.4

Calculate surface energies of arbitrary crystals.

SurfFlow

SurfFlow is a collection of workflows designed to generate surfaces with arbitrary Miller indices and terminations and perform VASP calculations to automatically calculate surface energies and Wulff shapes. surfflow uses the FireWorks framework and relies heavily on pymatgen, atomate, and the Materialsproject in general.

1. Download and Installation
   1. Create a virtual environment for surfflow
   2. Install and configure MongoDB locally if you want your database to run also in conda
   3. Create a folder structure, download and install
   4. Configuring FireWorks
   5. Configuring pymatgen
2. Testing your installation of FireWorks
3. A note about atomate
4. Using surfflow
   1. Running a workflow
   2. Looking at the results

Download and Installation

We recommend installing surfflow inside a virtual python environment. We use mamba in this guide to create and manage environments, but conda, virtualenv, or similar are also possible. We currently recommend mamba because it is essentially conda, but with much faster environment solving and package installation. If you prefer to proceed with conda instead, you can just replace all the mamba commands with conda. In fact, in the later sections of this guide, we use mamba and conda interchangeably in some commands and when referring to environments.

Create a virtual environment for SurfFlow

1. Make sure that you have mamba installed or download and install mambaforge from here. If you already have conda installed, you can also install mamba by running conda install mamba -n base -c conda-forge.
2. Update mamba and then create a new python 3 environment named "surfflow" (or whatever you decide) by typing mamba update mamba followed by mamba create --name surfflow python=3
3. Switch to your new environment: mamba activate surfflow

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Install SurfFlow from PyPi

Simply install surfflow from PyPi with the following command

pip install surfflow

Note: atomate is a dependency of the surfflow package. However, due to some changes that either fix certain bugs or add necessary functionality yet to be implemented in the official atomate version, we use a slightly modified fork of atomate. This fork should be installed with

pip install git+atomate@git+https://github.com/fyalcin/atomate.git

Install and configure MongoDB locally if you want your database to run also in conda environment

This is optional, and you should skip these steps if you already have a database running somewhere that you want to use and can access from the machine you are using. See also this section of the atomate installation instructions.

1. Install the mamba package of MongoDB by simply running mamba install mongodb while the surfflow environment is active.
2. You should now have access to the mongo shell via the mongo command and the daemon via the mongod command. Before we create the database and set up the daemon, we have to prepare a configuration file and decide where the database should be located. The location will be referred to as <YourMongoPath>, and you put the configuration file mongod.conf there. It should look somewhat similar to the yaml file below, but you can also tune it according to the options given here. Important settings are storage.dbPath (where your database will be located), processManagement.fork (If true, the process will run in the background and not block your shell), net.port (use the standard port for MongoDB: 27017), and security.authorization (should be disabled in the beginning to set up the users). Note that you must use spaces and not tabs in YAML!

Example mongod.conf file:

storage:  
   dbPath: "<YourMongoPath>/data/db"  
   journal:  
       enabled: true  
       commitIntervalMs: 100  
   directoryPerDB: true  
   engine: "wiredTiger"  
   wiredTiger:  
       engineConfig:  
          cacheSizeGB: 4.0  
          journalCompressor: "snappy"  
          directoryForIndexes: false  
systemLog:
   verbosity: 0  
   quiet: false  
   traceAllExceptions: false  
   path: "<YourMongoPath>/mongod.log"  
   logAppend: true  
   logRotate: "reopen"  
   destination: "file"  
   component:  
       accessControl:  
           verbosity: 0  
       command:  
           verbosity: 0
processManagement:  
   fork: true  
   pidFilePath: "<YourMongoPath>/pidfile"
net:  
   port: 27017  
   bindIp: localhost # Can also use a comma separated list  
   bindIpAll: false # If true can access from everywhere.  
   ipv6: true  
security:  
   authorization: disabled

3. Now, create the folder to hold the database files by typing:
   cd <YourMongoPath>; mkdir data; mkdir data/db where you can choose <YourMongoPath> however you like, and then start the mongo daemon using the configuration file by executing: mongod --config mongod.conf which should result in something ending with : child process started successfully, parent exiting and produce a mongod.log and a pidfile. If you have some problems, check the logfile.

4. Now, we will use the mongo shell to create two users for the databases. We start by going in the shell and switching to the admin database (which we will use for authorization):
   mongo use admin Now we will create an adminUser and a readOnlyUser by typing: db.createUser({user: "<RootUser>", pwd: "<RootPassword>", roles: [{role: "root", db: "admin" }]}) and db.createUser({user: "<ReadUser>", pwd: "<ReadPassword>", roles: [{role:"readAnyDatabase", db: "admin" }]}) Now exit the mongo shell: exit

5. Stop the mongo daemon by executing mongod --shutdown --dbpath <YoutMongoPath>/data/db and activate authorization in the mongod.conf file by changing the last line to authorization: enabled. Now, your database is password-protected, and you have to the username and password you created before in the mongo shell. To do that, while in the mongo shell, switch to the admin database by executing use admin and then authenticate with db.auth(<RootUser>, <RootPassword>). Then exit the mongo shell again.

6. It might be a good idea to define some aliases in your .bashrc or .myaliases files to start and stop the mongod daemon, so you can do it quickly if needed. E.g.:

alias mongo_start="mongod -f <YourMongoPath>/mongod.conf"
alias mongo_stop="mongod --shutdown --dbpath <YourMongoPath>/data/db"

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Installing surfflow

1. You have two options here. For both options, first make sure that you are in the surfflow environment you created. If you want to install the latest published version of surfflow, you can simply run pip install surfflow. If you want to install the latest development version however, you can clone the repository by typing git clone https://github.com/fyalcin/surfflow.git and then run pip install -e . in the root directory of the repository. This will install the package in editable mode, so you can make changes to the code and see the changes immediately.
2. Select a location where you want to have your surfflow files located. We will assume this is <YourPath>. Now create two subfolders: <YourPath>/config for your configuration files and <YourPath>/pps for your pseudopotentials.

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Configuration Files

surfflow comes with a nifty command line tool to make the generation of configuration files easy for the end user. After you have installed surfflow, you can use the command surfflow_tool config init to start the configuration wizard that will run you through the process of defining the configuration files and setting necessary conda environment variables. This tool creates a directory depending on user input (default is at ~/config), and all the necessary configuration files will be placed in this folder. This folder from now on will be referred to as <ConfigPath>.

If you already have configuration files for fireworks in a directory, you can still use this tool to set the necessary conda environment variables by pointing to this folder and skipping the config file generation part of the wizard. You can also use the command surfflow_tool config init --help to see the options for the configuration wizard.

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Configuring FireWorks for Job Schedulers

If the computer or cluster where you are installing surfflow has a job scheduler, you have to set up a file called my_qadapter.yaml in the <ConfigPath> directory. <SchedulerType> can be PBS/Torque, SLURM, SGE, or IBM LoadLeveler. pre_rocket and post_rocket are optional commands to be run in the job script before and after the workflow is executed; this is e.g. useful for loading and unloading modules. You probably will have to activate your conda environment here. The --timeout option tells the job to stop pulling new FireWorks from the Launchpad after <sec> number of seconds, which should of course be smaller than the walltime. E.g. if you have an allowed walltime of 72 hours, set the --timeout option to e.g. 172800 (2 days in seconds).
It is important to note that this type of rocket_launch will only work if the compute nodes on your cluster can access the MongoDB database, which is a problem for many clusters since only the login nodes have access to the internet and firewall rules are strict. Possible solutions are described here. The my_qadapter.yaml file might look something like this:

_fw_name: CommonAdapter  
_fw_q_type: <SchedulerType>
rocket_launch: rlaunch -c <YourPath>/config rapidfire --timeout <sec>
nodes: <NrOfNodes>
walltime: <hh:mm:ss>
queue: null  
account: null  
job_name: null  
pre_rocket: <Custom commands to load modules and conda etc.>
post_rocket: <Custom commands to unload modules etc.>
logdir: <YourPath>/logs

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Configuring pymatgen

When running VASP calculations FireWorks relies heavily on pymatgen and Custodian. Some configuration of pymatgen is required:

1. We assume that you have a folder <EXTRACTED_VASP_POTCAR> where you have the VASP pseudopotentials (delivered with the VASP package) already extracted. Type pmg config -p <EXTRACTED_VASP_POTCAR> <YourPath>/pps to put these potentials in an order where pymatgen can find them. The final file structure should look something like this (you maybe have to rename the directories in the pps folder):

pps
├── POT_GGA_PAW_PBE  
│   ├── POTCAR.Ac.gz  
│   ├── POTCAR.Ac_s.gz  
│   ├── POTCAR.Ag.gz  
│   └── ...  
├── POT_GGA_PAW_PW91  
│   ├── POTCAR.Ac.gz  
│   ├── POTCAR.Ac_s.gz  
│   ├── POTCAR.Ag.gz  
│   └── ...  
└── POT_LDA_PAW  
    ├── POTCAR.Ac.gz  
    ├── POTCAR.Ac_s.gz  
    ├── POTCAR.Ag.gz  
    └── ...

2. Now, we have to set a config variable (it will be a file .pmgrc.yaml in your home folder) so pymatgen can find the potentials and add your default functional as well (this could also be PBE_54) if you have this potential family and did not rename the folders in the previous step):
   pmg config --add PMG_VASP_PSP_DIR <YourPath>/pps pmg config --add PMG_DEFAULT_FUNCTIONAL PBE
3. For the integration of the Materials Project REST API, you should register for free at the website https://materialsproject.org/ and get an API Key from your dashboard there. Put it in the configuration file:
   pmg config --add PMG_MAPI_KEY <Your_API_Key>

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Testing your installation of FireWorks

• Try to load a workflow (for a simple structure relaxation of Si) to the launchpad with atwf add -l vasp -p wf_structure_optimization -m mp-149 and check that it has been added with lpad get_wflows. This should result in something like:

[  
 {  
  "state": "READY",  
  "name": "Si—1",  
  "created_on": "2020-02-27T14:44:42.634000",  
  "states_list": "REA"  
 },  
]

• Navigate to a scratch directory and run the workflow (without a scheduler) with rlaunch rapidfire
• Afterwards, you can run lpad get_wflows again to see that the state has changed from "READY" to "COMPLETED"
• It would probably be a good idea to continue with the tutorial of Atomate if you are not familiar with it already, but you can also jump straight into surfflow in the next section.

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A note about atomate

Atomate supplies a bunch of Fireworks and workflows that are used in surfflow. However, we have added a little more custom functionality to it. Mainly enabling the copy of the vdw_kernel.bindat file for OptimizeFW, StaticFW and TransmuterFW completely analogous to the way it was implemented in ScanOptimizeFW already. Another small modification concerns the copying of WAVECAR files from a relaxation to a StaticFW, which was not possible. surfflow automatically installs atomate from a forked repo, so those changes are implemented automatically during installation. Of course, this is not an ideal solution, and we strive to have something similar implemented in the official atomate version, but so far, we were not successful.

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Using surfflow

Running a workflow

Main workflow is located in the surfflow.workflows.main module. One can submit workflows by either defining some input parameters in a script and calling the workflow from this module, or by using the same command line tool we used for the configuration files. The latter is the recommended way but we still provide a short example of the former in the surfflow.tests.surface_energy_test module. The command for submitting workflows is surfflow_tool submit and has the following options:

  -h, --help            show this help message and exit
  -m MPID, --mpid MPID  MPID of the material to submit.
  --miller MILLER [MILLER ...]
                        Miller indices of the surface to submit.
  -f FILENAME, --file FILENAME
                        Path to the file containing the input parameters to use.
  -sg SG_PARAMS, --sg-params SG_PARAMS
                        SlabGenerator parameters given in a dict format.

The --mpid option is the only mandatory one. It is the Materials Project ID of the material to submit. The --miller option is a list of Miller indices of the surface to submit. If not given, all surfaces up to a max_index of the material will be submitted. The --file option is the path to a file containing the input parameters to use. The --sg-params option is a dictionary of parameters that define the slab geometries.

We provide an example of an input file that can be used with the --file option in surfflow/tests/inp.yaml, which you can submit with the command surfflow_tool submit --file <FullPathToInputFile>.

For all the options, the inputs are checked against default values defined in surfflow/defaults.json and set accordingly if not supplied by the user. If one wants to override the defaults given, the recommended way is to create a file user_defaults.json in <ConfigPath> and change the values there. User may refer to the surfflow/defaults.json for the correct format for defining these parameters.

Explanation of input parameters

Here, we will go over the input parameters in the surfflow/defaults.json file

• comp_params - Parameters used in VASP calculations

  • use_vdw: Whether to use the VdW-DF functional. If true, the vdw_kernel.bindat file will be copied to the working directory of the calculation. Default: false
  • functional: The functional to use. Default: PBE
  • use_spin: Whether to use spin-polarized calculations. Default: true
  • encut: The cutoff energy in eV. Default: 520
  • k_dens: The k-point density in Å^-1. Default: 6
  • is_metal: Whether the material is a metal. Default: null
  • epsilon: The dielectric constant of the material. Default: null

• sg_params - Parameters used in surface generation

  • symmetrize: Whether to symmetrize the slab. Default: false
  • slab_thick: The thickness of the slab in number of layers. Default: 10
  • vac_thick: The thickness of the vacuum in Å. Default: 20
  • primitive: Whether to perform a primitive cell transformationon the slabs. Default: true
  • lll_reduce: Whether to perform a LLL reduction on the slabs. Default: false
  • tol: The tolerance for determining the layers in Å. Default: 0.1
  • max_index: The maximum Miller index to consider if miller isn't supplied. Default: 3
  • max_normal_search: The maximum number of normal vectors to search for the slab. Default: max (highest absolute value of individual Miller indices)
  • resize: Whether to resize the slabs to the desired thickness. Default: true
  • preserve_terminations: Whether to preserve the terminations of the slabs while resizing. Default: true
  • min_thick_A: The minimum thickness of slabs in Å. Default: 10
  • minimize_structures: Whether to try all combinations of primitive, lll_reduce, and max_normal_search to find the smallest slabs. Default: true
  • match_ouc_lattice: Whether to match the lattice of the slab to the lattice of the oriented bulk structure. Default: true
  • calculate_bonds: Whether to calculate the bonds broken while generating the slabs. Default: true
  • max_nsites: The maximum number of sites in the slabs. Default: 100
  • nn_method: The method to use for finding the nearest neighbors. Default: all
  • weight: The weight of the bonds broken while generating the slabs. Default: BVS

• sg_filter: Dictionary of options to filter the slabs.

  • method: Method to use for filtering the slabs based on the bonds broken. Default: all, which means nothing is filtered out. Available methods are bvs_threshold, bvs_min_N, and bvs_min_N_hkl.
    • bvs_threshold: Percentage based filtering. Only slabs with BVS values within a given percentage of the minimum BVS slab are kept.
    • bvs_min_N: Number based filtering. Slabs are ordered by BVS values and the slabs with the lowest N BVS values are kept.
    • bvs_min_N_hkl: Number based filtering within each Miller index. Same thing as bvs_min_N but the slabs are grouped by Miller index first and the slabs with the lowest N BVS values are kept for each group.
  • bvs_param: Parameter N to use for all the methods. Should be given as a fraction for bvs_threshold and an integer for the other methods.

• bulk_coll_suffix: The suffix to use for the bulk collection. Default: bulk_data

• surfflow_coll_suffix: The suffix to use for the surfflow collection. Default: surfflow_data

• db_file: The path to the database file. Default: auto (uses the db_file in the FW_CONFIG_FILE)

• high_level: Name of the high_level database to save the results to. Default: true (uses the high_level in the FW_CONFIG_FILE)

• functional: The functional to use for the high-level calculations. Default: PBE (this is repeated but it is required for now for the workflow to work)

• fake_vasp: Whether to use fake VASP. Instead of running VASP, it copies inputs and outputs from a directory in the module path. Will give nonsense results for surface energies. Commonly used for testing purposes. Use this if you haven't set up VASP yet but would like to test the workflow. Default: false

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Looking at the results

The results of surfflow are saved in a separate MongoDB database, which nevertheless is hosted on the same server (note that the directoryPerDB: true line in mongod.conf assures that the results are stored in a different folder). This database of results is set in the db.json file under the key "high_level", while the "database" database is used by FireWorks to store all kinds of stuff. The results are stored in different collections, separated for the functional used ( PBE, or SCAN) and then split between bulk, slab, and interfaces results. Data in the surfflow database can be queried, of course, directly from the mongo shell, but it is probably more useful to use the python interface to MongoDB, pymongo. Some functions to aid with this are provided in the surfflow.utils module. To look quickly at single results or get a feel for how the data is structured in the database, it might be beneficial to install a GUI for MongoDB, like Compass. (Note that you can use the web-GUI of Atlas when you are using this cloud-based solution instead of a local installation of MongoDB.)

Also, note that there is a web-GUI provided by FireWorks where you can check out the Workflows and Fireworks in your FireWorks database. Just type lpad web_gui for that.

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