update /compile-vasp-m1-mac post to sync with gist

update deps, update oss.yml

.pre-commit-config.yaml

@@ -13,7 +13,6 @@ repos:
       - id: check-symlinks
       - id: check-yaml
       - id: destroyed-symlinks
-      - id: double-quote-string-fixer
       - id: end-of-file-fixer
       - id: mixed-line-ending
       - id: trailing-whitespace
@@ -37,7 +36,7 @@ repos:
         args: [--ignore-words-list, 'ist,yau,te,manuel', --check-filenames]
 
   - repo: https://github.com/pre-commit/mirrors-eslint
-    rev: v9.0.0-beta.1
+    rev: v9.0.0-rc.0
     hooks:
       - id: eslint
         types: [file]

package.json

@@ -29,10 +29,10 @@
     "@iconify/svelte": "^3.1.6",
     "@rollup/plugin-yaml": "^4.1.2",
     "@sveltejs/adapter-static": "^3.0.1",
-    "@sveltejs/kit": "^2.5.1",
+    "@sveltejs/kit": "^2.5.5",
     "@sveltejs/vite-plugin-svelte": "^3.0.2",
-    "@typescript-eslint/eslint-plugin": "^7.0.2",
-    "@typescript-eslint/parser": "^7.0.2",
+    "@typescript-eslint/eslint-plugin": "^7.4.0",
+    "@typescript-eslint/parser": "^7.4.0",
     "devalue": "^4.3.2",
     "elementari": "^0.2.3",
     "eslint": "^8.57.0",
@@ -41,22 +41,22 @@
     "hast-util-select": "^6.0.2",
     "hastscript": "^9.0.0",
     "js-yaml": "^4.1.0",
-    "katex": "^0.16.9",
+    "katex": "^0.16.10",
     "mdsvex": "^0.11.0",
     "prettier": "^3.2.5",
-    "prettier-plugin-svelte": "^3.2.1",
+    "prettier-plugin-svelte": "^3.2.2",
     "rehype-autolink-headings": "^7.1.0",
     "rehype-katex-svelte": "^1.2.0",
     "rehype-slug": "^6.0.0",
     "remark-math": "3.0.0",
     "svelte": "^4.2.12",
-    "svelte-check": "^3.6.4",
+    "svelte-check": "^3.6.8",
     "svelte-multiselect": "^10.2.0",
     "svelte-preprocess": "^5.1.3",
     "svelte-preprocess-import-assets": "^1.1.0",
     "svelte-zoo": "^0.4.10",
-    "svelte2tsx": "^0.7.1",
-    "typescript": "^5.3.3",
-    "vite": "^5.1.4"
+    "svelte2tsx": "^0.7.5",
+    "typescript": "^5.4.3",
+    "vite": "^5.2.7"
   }
 }

src/lib/oss.yml

@@ -9,8 +9,8 @@ projects:
       - Python
       - Cython
       - Jupyter Notebook
-    stars: 1266
-    commits: 948
+    stars: 1336
+    commits: 979
   - name: Matbench Discovery
     url: https://matbench-discovery.materialsproject.org
     logo: https://janosh.github.io/matbench-discovery/favicon.svg
@@ -25,8 +25,8 @@ projects:
       - TypeScript
       - JavaScript
       - HTML
-    stars: 57
-    commits: 315
+    stars: 66
+    commits: 318
   - name: CHGNet
     url: https://chgnet.lbl.gov
     repo: https://github.com/CederGroupHub/chgnet
@@ -43,16 +43,16 @@ projects:
       - HTML
       - JavaScript
       - TypeScript
-    stars: 174
-    commits: 169
+    stars: 184
+    commits: 175
   - name: MACE
     url: https://mace-docs.readthedocs.io
     repo: https://github.com/ACEsuit/mace
     role: Contributor
     paper: riebesell_foundation_2023
     description: Fast and accurate machine learning interatomic potentials with higher order equivariant message passing.
     logo: https://avatars.githubusercontent.com/u/68508620
-    stars: 313
+    stars: 345
     commits: 21
     languages:
       - Python
@@ -68,7 +68,7 @@ projects:
       - Python
       - JavaScript
       - HTML
-    stars: 113
+    stars: 118
     commits: 174
   - name: pymatviz
     url: https://pymatviz.janosh.dev
@@ -82,8 +82,8 @@ projects:
       - TypeScript
       - HTML
       - JavaScript
-    stars: 104
-    commits: 237
+    stars: 111
+    commits: 242
   - name: Tensorboard Reducer
     repo: https://github.com/janosh/tensorboard-reducer
     logo: https://raw.githubusercontent.com/janosh/tensorboard-reducer/main/assets/tensorboard-reducer-square.svg
@@ -92,15 +92,15 @@ projects:
     languages:
       - Python
       - TeX
-    stars: 61
+    stars: 65
     commits: 79
   - name: Normalizing Flows
     repo: https://github.com/janosh/awesome-normalizing-flows
     logo: https://api.iconify.design/logos:awesome.svg?color=%23888888
     description: Curated list of resources for learning and using normalizing flows, a powerful tool in ML for modeling probability distributions.
     languages:
       - Python
-    stars: 1265
+    stars: 1283
     commits: 72
   - name: atomate2
     repo: https://github.com/materialsproject/atomate2
@@ -112,8 +112,8 @@ projects:
       potential-powered structure relaxation workflows.
     languages:
       - Python
-    stars: 116
-    commits: 353
+    stars: 119
+    commits: 357
   - name: jobflow
     repo: https://github.com/materialsproject/jobflow
     role: Maintainer
@@ -124,8 +124,8 @@ projects:
     languages:
       - Python
       - TeX
-    stars: 81
-    commits: 100
+    stars: 83
+    commits: 115
   - name: Aviary
     repo: https://github.com/CompRhys/aviary
     role: Maintainer
@@ -134,7 +134,7 @@ projects:
     pypi: https://pypi.org/project/tensorboard-reducer
     languages:
       - Python
-    stars: 38
+    stars: 39
     commits: 234
   - name: MatCalc
     url: https://materialsvirtuallab.github.io/matcalc
@@ -144,13 +144,13 @@ projects:
     description: A Python library for calculating materials properties from ML force field potential energy surfaces.
     languages:
       - Python
-    stars: 40
-    commits: 68
+    stars: 41
+    commits: 72
   - name: TikZ
     url: https://tikz.janosh.dev
     repo: https://github.com/janosh/tikz
     description: Collection TikZ figures for concepts in physics/chemistry/ML.
-    stars: 170
+    stars: 174
     commits: 187
     languages:
       - TeX
@@ -168,7 +168,7 @@ projects:
     logo: https://github.com/janosh/tikz/raw/main/assets/plate-capacitor/plate-capacitor.svg
     paper: riebesell_pushing_2024
     stars: 7
-    commits: 12
+    commits: 14
     languages:
       - Python
       - ReScript
@@ -183,5 +183,5 @@ projects:
       - CSS
       - HTML
       - JavaScript
-    stars: 253
-    commits: 270
+    stars: 263
+    commits: 271

src/routes/+page.svelte

@@ -42,7 +42,7 @@
 </address>
 
 <p style="max-width: min(40em, 80vw); margin: auto;">
-  Interested in<br />
+  I'm interested in<br />
   <a href={mbd?.repo}>🔎 computational materials discovery&emsp;</a>
   <a href="https://arxiv.org/abs/2401.00096v1">🤖 machine learning</a><br />
   <a href={pmg?.repo}>💻 software engineering&emsp;</a>

src/routes/posts/compile-vasp-m1-mac/+page.md → src/routes/posts/compiling-vasp-m1-mac/+page.md

@@ -2,7 +2,7 @@
 title: Compile VASP on M1 Mac
 date: 2022-03-28
 cover:
-  img: compile-vasp-m1-mac.svg
+  img: compiling-vasp-m1-mac.svg
 tags:
   - Guide
   - Fortran
@@ -12,48 +12,50 @@ tags:
 
 > This post started out [as a gist](https://gist.github.com/janosh/a484f3842b600b60cd575440e99455c0). There's some Q&A there that may be useful.
 
-**Courtesy of Alex Ganose [@utf](https://github.com/utf) with additions from yours truly [@janosh](https://github.com/janosh).**
+**Written by Alex Ganose [@utf](https://github.com/utf) and Janosh Riebesell [@janosh](https://github.com/janosh). Last updated on 2024-03-30.**
 
-1. Install Xcode command line tools
+Follow these steps to compile VASP on an M1 Mac:
+
+1. Install Xcode command line tools:
 
    ```sh
    xcode-select --install
    ```
 
-2. Install gcc, OpenMPI and OpenMP using homebrew
+2. Install dependencies using Homebrew:
 
    ```sh
    brew install gcc openmpi scalapack fftw qd openblas
    ```
 
-   Consider appending `hdf5` if you want to compile [VASP with HDF5 support][vasp-hdf5].
+   Optionally, add `hdf5` for [HDF5 support in VASP][vasp-hdf5].
 
-3. Compile VASP
+3. Compile VASP:
 
-   These instructions are for VASP 6.3.0; they should be transferable to other versions of VASP but the variable names may be different
+   These instructions are for VASP 6.4.1 but should work with minor adjustments for other versions.
 
    ```sh
    cd /path/to/vasp-6.x.y
    cp arch/makefile.include.gnu_omp makefile.include
    ```
 
-   Then edit `makefile.include` as follows:
+   Edit `makefile.include` in the VASP `src` directory:
 
-   - Add the following to CPP_OPTIONS:
+   - Add to `CPP_OPTIONS`:
 
      ```make
      -D_OPENMP \
      -Dqd_emulate
      ```
 
-   - Change all instances of `gcc` to `gcc-11` and `g++` to `g++-11`
+   - Change all instances of `gcc` to `gcc-13` and `g++` to `g++-13`
 
-   - Add the following lines after `LLIBS       = -lstdc++`. This is necessary to emulate quad precision.
+   - Add after `LLIBS = -lstdc++` to emulate quad precision:
 
      ```make
-     QD         ?= /opt/homebrew/
-     LLIBS      += -L$(QD)/lib -lqdmod -lqd
-     INCS       += -I$(QD)/include/qd
+     QD ?= /opt/homebrew/
+     LLIBS += -L$(QD)/lib -lqdmod -lqd
+     INCS += -I$(QD)/include/qd
      ```
 
    - Set `SCALAPACK_ROOT ?= /opt/homebrew`
@@ -71,6 +73,45 @@ tags:
      INCS       += -I$(HDF5_ROOT)/include
      ```
 
+   - Append `getshmem.o` to `OBJECTS_LIB` in `makefile.include` ([VASP wiki](https://www.vasp.at/wiki/index.php/Shared_memory))
+
+     ```diff
+     - OBJECTS_LIB = linpack_double.o
+     + OBJECTS_LIB = linpack_double.o getshmem.o
+     ```
+
+   - In `src/parser/makefile`, change (as noted by [@zhuligs](https://gist.github.com/janosh/a484f3842b600b60cd575440e99455c0?permalink_comment_id=4323518#gistcomment-4323518)):
+
+     ```diff
+     - ar vq libparser.a $(CPPOBJ_PARS) $(COBJ_PARS) locproj.tab.h
+     + ar vq libparser.a $(CPPOBJ_PARS) $(COBJ_PARS)
+     ```
+
+     Do not replace the tab at the beginning of the line with spaces!
+
+   - In `src/lib/getshmem.c`, add the line `#define SHM_NORESERVE 0` ([VASP forum](https://www.vasp.at/forum/viewtopic.php?t=15106)):
+
+     ```c
+     /*output: shmem id
+     */
+     #define SHM_NORESERVE 0 // this line was added
+
+     void getshmem_C(size_t _size, int *_id)
+     ```
+
+   - In `makefile.include`, update the parser section ([VASP forum](https://www.vasp.at/forum/viewtopic.php?f=2&t=17477)):
+
+     ```diff
+     # For the parser library
+     CXX_PARS = g++-13
+     - LLIBS = -lstdc++
+     + LIBS += parser
+     + LLIBS = -Lparser -lparser -lstdc++
+     QD ?= /opt/homebrew
+     LLIBS += -L$(QD)/lib -lqdmod -lqd
+     INCS += -I$(QD)/include/qd
+     ```
+
 4. Finally, run:
 
    ```sh
@@ -81,9 +122,15 @@ tags:
 
    > Fatal Error: `string.mod` not found
 
+If successful, the VASP binaries will be in `src/bin`. Test with `make test`.
+
+## Last Tested on 2024-03-30
+
+Confirmed working with VASP 6.4.1 on M1 Pro with Sonoma 14.2.1 and `gcc@13.2.0`.
+
 ## Resulting `makefile.include` with all modifications
 
-See `makefile.include` below.
+See [`makefile.include`](https://gist.github.com/janosh/a484f3842b600b60cd575440e99455c0#file-makefile-include).
 
 ## Benchmarking