diff --git a/docs/hands-on/bands.mdx b/docs/hands-on/bands.mdx index 125361a2..f43e0a49 100755 --- a/docs/hands-on/bands.mdx +++ b/docs/hands-on/bands.mdx @@ -3,19 +3,23 @@ title: Bandstructure Calculation sidebar_label: Bandstructure --- +import Mat3raAdmonition from '../../src/apps/mat3ra'; + + + Before we can run `bands` calculation, we need to perform single-point [self consistent field calculation](scf.mdx). We have our input `scf` file with some new parameters: import CodeBlock from '@theme/CodeBlock'; -import si_bands_scf_in from '!!raw-loader!/src/silicon/si_bands_scf.in'; +import si_bands_scf_in from '!!raw-loader!/src/silicon/pw.scf.silicon_bands.in'; -{si_bands_scf_in} +{si_bands_scf_in} Run the `scf` calculation: ```bash -pw.x < si_bands_scf.in > si_bands_scf.out +pw.x < pw.scf.silicon_bands.in > pw.scf.silicon_bands.out ``` Next step is our band calculation (non-self consistent field) calculation. The @@ -33,28 +37,28 @@ also in the unoccupied bands above the Fermi energy. Number of occupied bands can be found in the `scf` output as number of Kohn-Sham states. Below is a sample input file for the band calculation: -import si_bands_in from '!!raw-loader!/src/silicon/si_bands.in'; +import si_bands_in from '!!raw-loader!/src/silicon/pw.bands.silicon.in'; -{si_bands_in} +{si_bands_in} Run `pw.x` with `bands` calculation input file: ```bash -pw.x < si_bands.in > si_bands.out +pw.x < pw.bands.silicon.in > pw.bands.silicon.out ``` After the bands calculation is performed, we need some postprocessing using `bands.x` utility in order to obtain the data in more usable format. Input file for `bands.x` postprocessing: -import si_bands_pp_in from '!!raw-loader!/src/silicon/si_bands_pp.in'; +import si_bands_pp_in from '!!raw-loader!/src/silicon/pp.bands.silicon.in'; -{si_bands_pp_in} +{si_bands_pp_in} Run `bands.x` from post processing (PP) module: ```bash -bands.x < si_bands_pp.in > si_bands_pp.out +bands.x < pp.bands.silicon.in > pp.bands.silicon.out ``` Finally, we run `plotband.x` to visualize bandstructure. We can either run it diff --git a/docs/hands-on/dos.mdx b/docs/hands-on/dos.mdx index 04969d97..56f38eaa 100755 --- a/docs/hands-on/dos.mdx +++ b/docs/hands-on/dos.mdx @@ -21,7 +21,7 @@ of DOS depends on the integration in $k$ space. 3. Finally, the DOS can be determined by integrating the electron density in $k$ space. -I have created a new input file (`si_scf_dos.in`) which is very much the same as +I have created a new input file (`pw.scf.silicon_dos.in`) which is very much the same as our previous scf input file except some parameters are modified. You can find all the input files in my [GitHub repository]( https://github.com/pranabdas/espresso/). We used the lattice constant value that @@ -31,9 +31,13 @@ pseudo-potential, it might result stress in the system. We have increased the `ecutwfc` to have better precision. We run the scf calculation: ```bash -pw.x < si_scf_dos.in > si_scf_dos.out +pw.x < pw.scf.silicon_dos.in > pw.scf.silicon_dos.out ``` +import Mat3raAdmonition from '../../src/apps/mat3ra'; + + + Next, we have prepared the input file for the `nscf` calculation. Where is have added `occupations` in the `&system` card as `tetrahedra` (appropriate for DOS calculation). We have increased the number of k-points to 12 × 12 × 12 with @@ -46,21 +50,21 @@ Kohn-Sham states. ```bash -pw.x < si_nscf_dos.in > si_nscf_dos.out +pw.x < pw.nscf.silicon_dos.in > pw.nscf.silicon_dos.out ``` Now our final step is to calculate the density of states. The DOS input file as follows: import CodeBlock from '@theme/CodeBlock'; -import si_dos_in from '!!raw-loader!/src/silicon/si_dos.in'; +import si_dos_in from '!!raw-loader!/src/silicon/pp.dos.silicon.in'; -{si_dos_in} +{si_dos_in} We run: ```bash -dos.x < si_dos.in > si_dos.out +dos.x < pp.dos.silicon.in > pp.dos.silicon.out ``` The DOS data in the `si_dos.dat` file that we specified in our input file. We diff --git a/docs/hands-on/scf.mdx b/docs/hands-on/scf.mdx index f2f865c7..1fb74d76 100755 --- a/docs/hands-on/scf.mdx +++ b/docs/hands-on/scf.mdx @@ -36,6 +36,10 @@ lines can be added with lines starting with a `!` like in Fortran. Also, parameter names are not case-sensitive, i.e., `&control` and `&CONTROL` are the same. +import ColabBadge from '../../src/apps/colab'; + + + import CodeBlock from '@theme/CodeBlock'; import pw_scf_silicon_in from '!!raw-loader!/src/silicon/pw.scf.silicon.in'; diff --git a/docs/hands-on/wannier.mdx b/docs/hands-on/wannier.mdx index 309ce413..439f9344 100644 --- a/docs/hands-on/wannier.mdx +++ b/docs/hands-on/wannier.mdx @@ -6,7 +6,7 @@ title: Wannier method 1. Perform `scf` calculation using Quantum Espresso `pw.x` -```console +```bash QE_PATH="/workspaces/q-e-qe-7.2/bin" mpirun -np 4 ${QE_PATH}/pw.x -i pw.scf.silicon.in > pw.scf.silicon.out ``` @@ -15,7 +15,7 @@ mpirun -np 4 ${QE_PATH}/pw.x -i pw.scf.silicon.in > pw.scf.silicon.out to provide explicit list of k-points. Such explicit list of k-points can be generated using perl script included in the Wannier package under utility. -```console +```bash WANNIER_PATH="/workspaces/wannier90-3.1.0" # directly append the k-points to the input file ${WANNIER_PATH}/utility/kmesh.pl 4 4 4 >> pw.nscf.silicon.in @@ -23,34 +23,34 @@ ${WANNIER_PATH}/utility/kmesh.pl 4 4 4 >> pw.nscf.silicon.in Run `nscf` calculation: -```console +```bash mpirun -np 4 ${QE_PATH}/pw.x -i pw.nscf.silicon.in > pw.nscf.silicon.out ``` 3. Prepare input file for wannier90 (`silicon.win`). Here we need the k-points list without the weights: -```console +```bash ${WANNIER_PATH}/utility/kmesh.pl 4 4 4 wan ``` 4. Generate nnkp input: -```console +```bash # we can just provide the seedname or seedname.win ${WANNIER_PATH}/wannier90.x -pp silicon ``` 5. Create input file for `pw2wan`, and generate initial projections: -```console +```bash mpirun -np 4 ${WANNIER_PATH}/pw2wannier90.x -i pw2wan.silicon.in > pw2 wan.silicon.out ``` 6. Run wannier calculation: -```console +```bash mpirun -np 4 ${WANNIER_PATH}/wannier90.x silicon ``` diff --git a/package-lock.json b/package-lock.json index 9a446184..1d966d0d 100644 --- a/package-lock.json +++ b/package-lock.json @@ -25,19 +25,31 @@ } }, "node_modules/@algolia/autocomplete-core": { - "version": "1.8.2", - "resolved": "https://registry.npmjs.org/@algolia/autocomplete-core/-/autocomplete-core-1.8.2.tgz", - "integrity": "sha512-mTeshsyFhAqw/ebqNsQpMtbnjr+qVOSKXArEj4K0d7sqc8It1XD0gkASwecm9mF/jlOQ4Z9RNg1HbdA8JPdRwQ==", + "version": "1.9.3", + "resolved": "https://registry.npmjs.org/@algolia/autocomplete-core/-/autocomplete-core-1.9.3.tgz", + "integrity": "sha512-009HdfugtGCdC4JdXUbVJClA0q0zh24yyePn+KUGk3rP7j8FEe/m5Yo/z65gn6nP/cM39PxpzqKrL7A6fP6PPw==", + "dependencies": { + "@algolia/autocomplete-plugin-algolia-insights": "1.9.3", + "@algolia/autocomplete-shared": "1.9.3" + } + }, + "node_modules/@algolia/autocomplete-plugin-algolia-insights": { + "version": "1.9.3", + 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"bonjour-service": "^1.0.11", "chokidar": "^3.5.3", @@ -14500,9 +14606,9 @@ "integrity": "sha512-NM8/P9n3XjXhIZn1lLhkFaACTOURQXjWhV4BA/RnOv8xvgqtqpAX9IO4mRQxSx1Rlo4tqzeqb0sOlruaOy3dug==" }, "node_modules/webpack-dev-server/node_modules/schema-utils": { - "version": "4.0.1", - "resolved": "https://registry.npmjs.org/schema-utils/-/schema-utils-4.0.1.tgz", - "integrity": "sha512-lELhBAAly9NowEsX0yZBlw9ahZG+sK/1RJ21EpzdYHKEs13Vku3LJ+MIPhh4sMs0oCCeufZQEQbMekiA4vuVIQ==", + "version": "4.2.0", + "resolved": "https://registry.npmjs.org/schema-utils/-/schema-utils-4.2.0.tgz", + "integrity": "sha512-L0jRsrPpjdckP3oPug3/VxNKt2trR8TcabrM6FOAAlvC/9Phcmm+cuAgTlxBqdBR1WJx7Naj9WHw+aOmheSVbw==", "dependencies": { "@types/json-schema": "^7.0.9", "ajv": "^8.9.0", @@ -14538,9 +14644,9 @@ } }, "node_modules/webpack-merge": { - "version": "5.8.0", - "resolved": "https://registry.npmjs.org/webpack-merge/-/webpack-merge-5.8.0.tgz", - "integrity": 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----------------------------- SCF CALCULATION ------------------------------ # +# switch to the job working directory +cd $PBS_O_WORKDIR + +BASE_URL='https://github.com/pranabdas/espresso/raw/next/src' +IN_FILE='pw.scf.silicon_bands.in' +PP_FILE='Si.pz-vbc.UPF' + +# get QE input file +wget ${BASE_URL}/silicon/${IN_FILE} -O ${IN_FILE} + +# get pseudopotential file +wget ${BASE_URL}/pseudos/${PP_FILE} -O ${PP_FILE} + +# delete pseudo_dir from input file and specify via ENV +sed -i '/^\s*pseudo_dir/d' ${IN_FILE} +export ESPRESSO_PSEUDO='./' + +# load required module +module add espresso/63-i-174-impi-044 + +# run the calculation +mpirun -np $PBS_NP pw.x -in ${IN_FILE} > ${IN_FILE%*.in}.out + +# ------------------------- BANDS (NSCF) CALCULATION ------------------------- # +IN_FILE='pw.bands.silicon.in' +wget ${BASE_URL}/silicon/${IN_FILE} -O ${IN_FILE} +sed -i '/^\s*pseudo_dir/d' ${IN_FILE} +mpirun -np $PBS_NP pw.x -in ${IN_FILE} > ${IN_FILE%*.in}.out + +# -------------------------- BANDS POST-PROCESSING --------------------------- # +IN_FILE='pp.bands.silicon.in' +wget ${BASE_URL}/silicon/${IN_FILE} -O ${IN_FILE} +mpirun -np $PBS_NP bands.x -in ${IN_FILE} > ${IN_FILE%*.in}.out + +# ----------------------------------- END ------------------------------------ # diff --git a/scripts/mat3ra-pbs/silicon-dos.sh b/scripts/mat3ra-pbs/silicon-dos.sh new file mode 100644 index 00000000..f1957e0a --- /dev/null +++ b/scripts/mat3ra-pbs/silicon-dos.sh @@ -0,0 +1,45 @@ +#!/bin/bash +# ----------------------------- CLUSTER CONFIGS ------------------------------ # +#PBS -N Silicon-DOS +#PBS -j oe +#PBS -l nodes=1 +#PBS -l ppn=4 +#PBS -q OR +#PBS -l walltime=00:00:30:00 +#PBS -A seminar-espresso-tutorials +# ----------------------------- SCF CALCULATION ------------------------------ # +# switch to the job working directory +cd $PBS_O_WORKDIR + +BASE_URL='https://github.com/pranabdas/espresso/raw/next/src' +IN_FILE='pw.scf.silicon_dos.in' +PP_FILE='Si.pz-vbc.UPF' + +# get QE input file +wget ${BASE_URL}/silicon/${IN_FILE} -O ${IN_FILE} + +# get pseudopotential file +wget ${BASE_URL}/pseudos/${PP_FILE} -O ${PP_FILE} + +# delete pseudo_dir from input file and specify via ENV +sed -i '/^\s*pseudo_dir/d' ${IN_FILE} +export ESPRESSO_PSEUDO='./' + +# load required module +module add espresso/63-i-174-impi-044 + +# run the calculation +mpirun -np $PBS_NP pw.x -in ${IN_FILE} > ${IN_FILE%*.in}.out + +# ----------------------------- NSCF CALCULATION ----------------------------- # +IN_FILE='pw.nscf.silicon_dos.in' +wget ${BASE_URL}/silicon/${IN_FILE} -O ${IN_FILE} +sed -i '/^\s*pseudo_dir/d' ${IN_FILE} +mpirun -np $PBS_NP pw.x -in ${IN_FILE} > ${IN_FILE%*.in}.out + +# ----------------------------- DOS CALCULATION ------------------------------ # +IN_FILE='pp.dos.silicon.in' +wget ${BASE_URL}/silicon/${IN_FILE} -O ${IN_FILE} +mpirun -np $PBS_NP dos.x -in ${IN_FILE} > ${IN_FILE%*.in}.out + +# ----------------------------------- END ------------------------------------ # diff --git a/scripts/mat3ra-pbs/silicon-scf.sh b/scripts/mat3ra-pbs/silicon-scf.sh new file mode 100644 index 00000000..d3478f39 --- /dev/null +++ b/scripts/mat3ra-pbs/silicon-scf.sh @@ -0,0 +1,35 @@ +#!/bin/bash +# ----------------------------- CLUSTER CONFIGS ------------------------------ # +#PBS -N Silicon-SCF +#PBS -j oe +#PBS -l nodes=1 +#PBS -l ppn=4 +#PBS -q OR +#PBS -l walltime=00:00:30:00 +#PBS -A seminar-espresso-tutorials +# ------------------------------- INPUT FILES -------------------------------- # +# switch to the job working directory +cd $PBS_O_WORKDIR + +BASE_URL='https://github.com/pranabdas/espresso/raw/next/src' +IN_FILE='pw.scf.silicon.in' +PP_FILE='Si.pz-vbc.UPF' + +# get QE input file +wget ${BASE_URL}/silicon/${IN_FILE} -O ${IN_FILE} + +# get pseudopotential file +wget ${BASE_URL}/pseudos/${PP_FILE} -O ${PP_FILE} + +# delete pseudo_dir from input file and specify via ENV +sed -i '/^\s*pseudo_dir/d' ${IN_FILE} +export ESPRESSO_PSEUDO='./' + +# --------------------------------- RUN JOB ---------------------------------- # +# load required module +module add espresso/63-i-174-impi-044 + +# run the calculation +mpirun -np $PBS_NP pw.x -in ${IN_FILE} > ${IN_FILE%*.in}.out + +# ----------------------------------- END ------------------------------------ # diff --git a/src/apps/colab.jsx b/src/apps/colab.jsx new file mode 100644 index 00000000..8b7cbe39 --- /dev/null +++ b/src/apps/colab.jsx @@ -0,0 +1,14 @@ +import React from "react"; + +const ColabBadge = ({ notebook }) => { + const url = "https://colab.research.google.com/github/pranabdas/espresso/blob/main/notebooks/" + notebook; + return ( +
+ + Colab badge + +
+ ); +}; + +export default ColabBadge; diff --git a/src/apps/mat3ra.jsx b/src/apps/mat3ra.jsx new file mode 100644 index 00000000..5fe12095 --- /dev/null +++ b/src/apps/mat3ra.jsx @@ -0,0 +1,46 @@ +import React from "react"; +import Admonition from "@theme/Admonition"; +import styles from "./styles.module.css"; + +const Mat3raAdmonition = ({ url }) => { + return ( + +

+ Review, clone, modify, and run this calculation on{" "} + +

+
+ What is Mat3ra? +

Mat3ra is a cloud platform to organize, run, share and + collaborate on your high performance computing projects. There are + several ways we can run Quantum Espresso jobs on Mat3ra.

+
    +
  1. Web Interface: If you are new to various command line + tools and programming languages, this option is the easiest way to + get started. Here is an example.
    2. + +
  2. Bash script: You can define your jobs using bash script and + submit them via web interface. See an example here.
    3. + +
  3. REST API: Mat3ra also provides REST API to most of its + features. In this way we can access Mat3ra directly from a Jupyter + Notebook. Fine more here.
    4. + +
  4. CLI via SSH: If you are experienced user, you can directly + access Mat3ra cluster infra from you terminal. Here is an example.
    5. +
+

Find more at mat3ra.com.

+
+ + ); +}; + +export const Mat3raButton = ({ url }) => { + return ( + + + + ); +}; + +export default Mat3raAdmonition; diff --git a/src/apps/styles.module.css b/src/apps/styles.module.css new file mode 100644 index 00000000..007d6d51 --- /dev/null +++ b/src/apps/styles.module.css @@ -0,0 +1,68 @@ +.mat3ra { + appearance: none; + border: 1px solid rgba(27, 31, 35, 0.15); + border-radius: 6px; + box-shadow: rgba(27, 31, 35, 0.1) 0 1px 0; + box-sizing: border-box; + color: #fff; + cursor: pointer; + display: inline-block; + font-size: 14px; + font-weight: 600; + line-height: 18px; + padding: 4px 12 px; + position: relative; + text-align: center; + text-decoration: none; + user-select: none; + -webkit-user-select: none; + touch-action: manipulation; + vertical-align: middle; + white-space: nowrap; + background: url('../../static/img/mat3ra-logo.svg') no-repeat; + height: 24px; + width: 94px; + background-color: #3f2a98; +} + +.mat3ra:hover { + background-color: purple; +} + +details { + color: grey; +} + +summary { + font-weight: normal; + cursor: pointer; + padding-bottom: 0; +} + +summary:hover { + color: var(--ifm-font-color-base); +} + +details[open] { + color: var(--ifm-font-color-base); +} + +details[open] summary { + margin-bottom: 0.5em; + border: grey; + border-radius: 5px; + border-style: solid; +} + +.colab:hover { + cursor: pointer; +} + +.colab { + padding-top: 5px; + padding-bottom: 5px; +} + +.colab img { + margin-right: auto; +} diff --git a/src/silicon/si_bands_pp.in b/src/silicon/pp.bands.silicon.in similarity index 100% rename from src/silicon/si_bands_pp.in rename to src/silicon/pp.bands.silicon.in diff --git a/src/silicon/si_dos.in b/src/silicon/pp.dos.silicon.in similarity index 100% rename from src/silicon/si_dos.in rename to src/silicon/pp.dos.silicon.in diff --git a/src/silicon/si_bands.in b/src/silicon/pw.bands.silicon.in similarity index 95% rename from src/silicon/si_bands.in rename to src/silicon/pw.bands.silicon.in index 07e8a5ce..a1f52bf8 100644 --- a/src/silicon/si_bands.in +++ b/src/silicon/pw.bands.silicon.in @@ -3,7 +3,7 @@ restart_mode = 'from_scratch', prefix = 'silicon', outdir = './tmp/' - pseudo_dir = './pseudos/' + pseudo_dir = '../pseudos/' verbosity = 'high' / diff --git a/src/silicon/si_nscf_dos.in b/src/silicon/pw.nscf.silicon_dos.in similarity index 93% rename from src/silicon/si_nscf_dos.in rename to src/silicon/pw.nscf.silicon_dos.in index 38f7e971..62703759 100644 --- a/src/silicon/si_nscf_dos.in +++ b/src/silicon/pw.nscf.silicon_dos.in @@ -3,7 +3,7 @@ restart_mode = 'from_scratch', prefix = 'silicon', outdir = './tmp/' - pseudo_dir = './pseudos/' + pseudo_dir = '../pseudos/' verbosity = 'high' / diff --git a/src/silicon/pw.scf.silicon.in b/src/silicon/pw.scf.silicon.in index 1e0eb88c..105ca178 100644 --- a/src/silicon/pw.scf.silicon.in +++ b/src/silicon/pw.scf.silicon.in @@ -6,10 +6,10 @@ prefix = 'silicon', ! output directory. Note that it is deprecated. - outdir = './tmp/silicon/' + outdir = './tmp/' ! directory for the pseudo potential directory - pseudo_dir = './pseudos/' + pseudo_dir = '../pseudos/' ! verbosity high will give more details on the output file verbosity = 'high' diff --git a/src/silicon/si_bands_scf.in b/src/silicon/pw.scf.silicon_bands.in similarity index 94% rename from src/silicon/si_bands_scf.in rename to src/silicon/pw.scf.silicon_bands.in index 9f9caec8..a7df5ead 100644 --- a/src/silicon/si_bands_scf.in +++ b/src/silicon/pw.scf.silicon_bands.in @@ -3,7 +3,7 @@ restart_mode = 'from_scratch', prefix = 'silicon', outdir = './tmp/' - pseudo_dir = './pseudos/' + pseudo_dir = '../pseudos/' verbosity = 'high' / diff --git a/src/silicon/si_scf_dos.in b/src/silicon/pw.scf.silicon_dos.in similarity index 93% rename from src/silicon/si_scf_dos.in rename to src/silicon/pw.scf.silicon_dos.in index 2675c063..263b810a 100644 --- a/src/silicon/si_scf_dos.in +++ b/src/silicon/pw.scf.silicon_dos.in @@ -3,7 +3,7 @@ restart_mode = 'from_scratch', prefix = 'silicon', outdir = './tmp/' - pseudo_dir = './pseudos/' + pseudo_dir = '../pseudos/' verbosity = 'high' / diff --git a/static/img/colab-badge.webp b/static/img/colab-badge.webp new file mode 100644 index 00000000..2c76d2af Binary files /dev/null and b/static/img/colab-badge.webp differ diff --git a/static/img/mat3ra-logo.svg b/static/img/mat3ra-logo.svg new file mode 100644 index 00000000..ebe91eed --- /dev/null +++ b/static/img/mat3ra-logo.svg @@ -0,0 +1,10 @@ + + + + + + + + + +