Release ob2-1-1

dftbparams · Dec 9, 2024 · 9e0d5cc · 9e0d5cc
commit 9e0d5cc
Show file tree

Hide file tree

Showing 56 changed files with 31,848 additions and 0 deletions.
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -0,0 +1,49 @@
+name: release
+
+on:
+  push:
+    tags:
+      - v[0-9]*-[0-9]*
+
+env:
+  SKF_SET_NAME: "${{ github.event.repository.name }}"
+
+jobs:
+
+  skf-archive:
+
+    runs-on: ubuntu-latest
+
+    steps:
+
+    - name: Checkout sk set
+      uses: actions/checkout@v4
+
+    - name: Get version number
+      run: |
+        GIT_TAG=$(git describe --tags --match 'v[0-9]*-[0-9]*')
+        SKF_SET_VERSION=${GIT_TAG#v}"
+        echo "SKF_SET_VERSION=${SKF_SET_VERSION} >> ${GITHUB_ENV}
+        echo "ARCHIVE_NAME=${SKF_SET_NAME}-${SKF_SET_VERSION}" >> ${GITHUB_ENV}
+
+    - name: Create archive
+      run: |
+        mkdir -p _build/${ARCHIVE_NAME}
+        cp $(find . -maxdepth 1 -not -type 'd') _build/${ARCHIVE_NAME}
+        cp skfiles/*.skf _build/${ARCHIVE_NAME}
+        tar -C _build -c -v -J -f ${ARCHIVE_NAME}.tar.xz ${ARCHIVE_NAME}
+        mkdir -p _build/${ARCHIVE_NAME}-extras
+        cp -r extras/* _build/${ARCHIVE_NAME}-extras
+        tar -C _build -c -v -J -f ${ARCHIVE_NAME}-extras.tar.xz ${ARCHIVE_NAME}-extras
+
+    - name: Create release
+      uses: softprops/action-gh-release@v2
+      with:
+        name: ${{ env.ARCHIVE_NAME }}
+        preserve_order: True
+        files: |
+          ${{ env.ARCHIVE_NAME }}.tar.xz
+          ${{ env.ARCHIVE_NAME }}-extras.tar.xz
+        body_path: RELEASE.md
+
+
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -0,0 +1,5 @@
+# Changelog
+
+## ob2-1-1
+
+First public release under CC-BY-SA license
diff --git a/LICENSE b/LICENSE
diff --git a/README b/README
@@ -0,0 +1,37 @@
+======================================================================
+ob2-1-1
+======================================================================
+
+(c) 2017, Marcus Elstner, Karlsruher Institut für Technologie
+All rights reserved
+
+This work is licensed under the Creative Commons Attribution-ShareAlike 4.0
+International License. To view a copy of this license, consult the LICENSE file
+or visit http://creativecommons.org/licenses/by-sa/4.0/ .
+
+NOTE: The rights holder(s) for this work explicitly require that the attribution
+conditions of this license are enforced. Use in part or in whole of this data is
+permitted only under the condition that the scientific background of the
+Licensed Material will be CITED IN ANY PUBLICATIONS ARISING FROM ITS USE. The
+required references are specified in this file and must be included in resulting
+works.
+
+
+Description
+===========
+
+This set of parameters is part of the Parametrization for Organic and Biological
+Molecules (OB2) has been specifically designed for Long-range Corrected Density
+Functional Tight Binding (LC-DFTB2).  Comprehensive benchmark tests for C-H-N-O
+can be found in J. Chem. Theory Comput., 2018, 14 (1), pp 115–12. Please also
+consult the paper for the details and use cases of the various sets (base,
+shift, split).
+
+The elements should be used with following maximal angular momenta:
+
+H:s, C: p, N: p, O: p
+
+
+PUBLICATIONS TO BE CITED
+[JCTC2018]   J. Chem. Theory Comput., 2018, 14 (1), pp 115–12, 
+             DOI: http://dx.doi.org/10.1021/acs.jctc.7b00947
diff --git a/RELEASE.md b/RELEASE.md
@@ -0,0 +1,12 @@
+# Parameter set ob2-1-1
+
+Density Functional Tight Binding (DFTB) parameter set providing long range corrected parameterization for biological and organic molecules.
+
+Before applying it in your work, **consult the [README](README) file to ensure correct usage**.
+
+
+## License Information
+
+The parameter set is distributed under the [Creative Commons Attribution-ShareAlike 4.0 International (CC-BY-SA)](LICENSE) license.
+
+**Important Note:** The creators of this work require that you **adhere to the attribution requirements** specified by this license. If you use this data, either in part or in full, in any research or publication, you must properly cite the scientific references associated with this material. **The necessary citations are listed in the [README](README) file and must be included in all resulting publications.**
diff --git a/extras/spinw.txt b/extras/spinw.txt
@@ -0,0 +1,15 @@
+H:
+   -0.07925
+C:
+   -0.04559   -0.02930
+   -0.02930   -0.02755
+N:
+   -0.04687   -0.03170
+   -0.03165   -0.03072
+O:
+   -0.04782   -0.03335
+   -0.03335   -0.03307
+S:
+   -0.03533   -0.02130   0.00000
+   -0.02135   -0.01921   0.00000
+    0.00000    0.00000  -0.15488
diff --git a/skfiles/base/C-C.skf b/skfiles/base/C-C.skf
diff --git a/skfiles/base/C-H.skf b/skfiles/base/C-H.skf
diff --git a/skfiles/base/C-N.skf b/skfiles/base/C-N.skf
diff --git a/skfiles/base/C-O.skf b/skfiles/base/C-O.skf
diff --git a/skfiles/base/H-C.skf b/skfiles/base/H-C.skf
diff --git a/skfiles/base/H-H.skf b/skfiles/base/H-H.skf
diff --git a/skfiles/base/H-N.skf b/skfiles/base/H-N.skf
diff --git a/skfiles/base/H-O.skf b/skfiles/base/H-O.skf
diff --git a/skfiles/base/N-C.skf b/skfiles/base/N-C.skf
diff --git a/skfiles/base/N-H.skf b/skfiles/base/N-H.skf
diff --git a/skfiles/base/N-N.skf b/skfiles/base/N-N.skf
diff --git a/skfiles/base/N-O.skf b/skfiles/base/N-O.skf
diff --git a/skfiles/base/O-C.skf b/skfiles/base/O-C.skf
diff --git a/skfiles/base/O-H.skf b/skfiles/base/O-H.skf
diff --git a/skfiles/base/O-N.skf b/skfiles/base/O-N.skf
diff --git a/skfiles/base/O-O.skf b/skfiles/base/O-O.skf
diff --git a/skfiles/base/efit.in b/skfiles/base/efit.in
@@ -0,0 +1,91 @@
+$system:
+ncpus    16
+dftb     lctddftb+
+skgen    skgennode
+#onecent  hfatom
+onecent  hfatom_spin
+twocent  sktwocnt_lr
+outfile  gasefit.log
+libdir   ../libskf
+omega    0.3
+power    4
+dgrid    0.02
+ngrid    500
+grids    grids
+dftb_inp dftb_inp
+rep.in   rep.in
+gasrepfit gasrepfit
+$end
+
+$addHamiltonian:
+  MaxAngularMomentum = {
+    H  = "s"
+    C  = "p"
+    N  = "p"
+    O  = "p"
+  }
+  RangeSep = {
+     Enable = Yes
+     Algorithm = tr{
+       Threshold = 1e-16
+     }
+  }
+$end
+
+$genetic_algrithm:
+ga              1
+popsize         16  
+ngen            1 
+pmut            0.3 
+pcross          0.9
+score_type      1 
+seed            0
+runtest         0
+readr           1
+$end
+
+$atom_types:# name, opt type, lmax, denr (min, guess, max, precision), wr_s (min, guess, max, precision), wr_p (min, guess, max, precision),
+H  1  0  7.7  7.7  7.7  1  2.1  2.1  2.1  1  
+C  2  1  6.1  6.1  6.1  1  2.9  2.9  2.9  1  2.9  2.9  2.9  1  
+N  2  1  4.3  4.3  4.3  1  2.9  2.9  2.9  1  2.9  2.9  2.9  1  
+O  2  1  3.8  3.8  3.8  1  2.8  2.8  2.8  1  2.8  2.8  2.8  1  
+$end
+
+$compounds:#  str, charge, charge type, cweight, cfile, start, end, ref, evweight, evfile
+  ../../../geom_bnl0.3/h2.xyz            0 1 0   ../../../geom_bnl0.3/h2.chg          -1 -1 0 4   ../../../geom_bnl0.3/h2_-1_-1.eig        
+  ../../../geom_bnl0.3/ch4.xyz           0 1 0   ../../../geom_bnl0.3/ch4.chg         -3 -1 0 2   ../../../geom_bnl0.3/ch4_-3_-1.eig       
+  ../../../geom_bnl0.3/hcch.xyz          0 1 0   ../../../geom_bnl0.3/hcch.chg        -4 -1 0 1   ../../../geom_bnl0.3/hcch_-4_-1.eig      
+  ../../../geom_bnl0.3/h2cchch3.xyz      0 1 0   ../../../geom_bnl0.3/h2cchch3.chg    -4 -1 0 1   ../../../geom_bnl0.3/h2cchch3_-4_-1.eig  
+  ../../../geom_bnl0.3/h3cch2ch3.xyz     0 1 0   ../../../geom_bnl0.3/h3cch2ch3.chg   -4 -1 0 1   ../../../geom_bnl0.3/h3cch2ch3_-4_-1.eig 
+  ../../../geom_bnl0.3/h3cch3.xyz        0 1 0   ../../../geom_bnl0.3/h3cch3.chg      -4 -1 0 1   ../../../geom_bnl0.3/h3cch3_-4_-1.eig    
+  ../../../geom_bnl0.3/c6h6.xyz          0 1 0   ../../../geom_bnl0.3/c6h6.chg        -4 -1 0 1   ../../../geom_bnl0.3/c6h6_-4_-1.eig      
+  ../../../geom_bnl0.3/h2cch2.xyz        0 1 0   ../../../geom_bnl0.3/h2cch2.chg      -4 -1 0 1   ../../../geom_bnl0.3/h2cch2_-4_-1.eig    
+  ../../../geom_bnl0.3/n2.xyz            0 1 0   ../../../geom_bnl0.3/n2.chg          -4 -1 0 1   ../../../geom_bnl0.3/n2_-4_-1.eig        
+  ../../../geom_bnl0.3/hcn.xyz           0 1 0   ../../../geom_bnl0.3/hcn.chg         -4 -1 0 1   ../../../geom_bnl0.3/hcn_-4_-1.eig       
+  ../../../geom_bnl0.3/nh3.xyz           0 1 0   ../../../geom_bnl0.3/nh3.chg         -3 -1 0 2   ../../../geom_bnl0.3/nh3_-3_-1.eig       
+  ../../../geom_bnl0.3/hn_ch3_2.xyz      0 1 0   ../../../geom_bnl0.3/hn_ch3_2.chg    -4 -1 0 1   ../../../geom_bnl0.3/hn_ch3_2_-4_-1.eig  
+  ../../../geom_bnl0.3/n_ch3_3.xyz       0 1 0   ../../../geom_bnl0.3/n_ch3_3.chg     -4 -1 0 1   ../../../geom_bnl0.3/n_ch3_3_-4_-1.eig   
+  ../../../geom_bnl0.3/h2nnh2.xyz        0 1 0   ../../../geom_bnl0.3/h2nnh2.chg      -4 -1 0 1   ../../../geom_bnl0.3/h2nnh2_-4_-1.eig    
+  ../../../geom_bnl0.3/hnnh.xyz          0 1 0   ../../../geom_bnl0.3/hnnh.chg        -4 -1 0 1   ../../../geom_bnl0.3/hnnh_-4_-1.eig      
+  ../../../geom_bnl0.3/hnch2.xyz         0 1 0   ../../../geom_bnl0.3/hnch2.chg       -4 -1 0 1   ../../../geom_bnl0.3/hnch2_-4_-1.eig     
+  ../../../geom_bnl0.3/h2nch3.xyz        0 1 0   ../../../geom_bnl0.3/h2nch3.chg      -4 -1 0 1   ../../../geom_bnl0.3/h2nch3_-4_-1.eig    
+  ../../../geom_bnl0.3/pyridine.xyz      0 1 0   ../../../geom_bnl0.3/pyridine.chg    -4 -1 0 1   ../../../geom_bnl0.3/pyridine_-4_-1.eig  
+  ../../../geom_bnl0.3/hoch3.xyz         0 1 0   ../../../geom_bnl0.3/hoch3.chg       -4 -1 0 1   ../../../geom_bnl0.3/hoch3_-4_-1.eig     
+  ../../../geom_bnl0.3/h3coch3.xyz       0 1 0   ../../../geom_bnl0.3/h3coch3.chg     -4 -1 0 1   ../../../geom_bnl0.3/h3coch3_-4_-1.eig   
+  ../../../geom_bnl0.3/h2noch3.xyz       0 1 0   ../../../geom_bnl0.3/h2noch3.chg     -4 -1 0 1   ../../../geom_bnl0.3/h2noch3_-4_-1.eig   
+  ../../../geom_bnl0.3/hcooh.xyz         0 1 0   ../../../geom_bnl0.3/hcooh.chg       -4 -1 0 1   ../../../geom_bnl0.3/hcooh_-4_-1.eig     
+  ../../../geom_bnl0.3/h2o.xyz           0 1 0   ../../../geom_bnl0.3/h2o.chg         -3 -1 0 2   ../../../geom_bnl0.3/h2o_-3_-1.eig       
+  ../../../geom_bnl0.3/co.xyz            0 1 0   ../../../geom_bnl0.3/co.chg          -4 -1 0 1   ../../../geom_bnl0.3/co_-4_-1.eig        
+  ../../../geom_bnl0.3/d24.xyz           0 1 0   ../../../geom_bnl0.3/d24.chg         -4 -1 0 1   ../../../geom_bnl0.3/d24_-4_-1.eig       
+  ../../../geom_bnl0.3/o2.xyz            0 1 0   ../../../geom_bnl0.3/o2.chg          -4 -1 0 1   ../../../geom_bnl0.3/o2_-4_-1.eig        
+  ../../../geom_bnl0.3/h3cno2.xyz        0 1 0   ../../../geom_bnl0.3/h3cno2.chg      -4 -1 0 1   ../../../geom_bnl0.3/h3cno2_-4_-1.eig    
+  ../../../geom_bnl0.3/hno2.xyz          0 1 0   ../../../geom_bnl0.3/hno2.chg        -4 -1 0 1   ../../../geom_bnl0.3/hno2_-4_-1.eig      
+  ../../../geom_bnl0.3/hcooch3.xyz       0 1 0   ../../../geom_bnl0.3/hcooch3.chg     -4 -1 0 1   ../../../geom_bnl0.3/hcooch3_-4_-1.eig   
+  ../../../geom_bnl0.3/hooh.xyz          0 1 0   ../../../geom_bnl0.3/hooh.chg        -4 -1 0 1   ../../../geom_bnl0.3/hooh_-4_-1.eig      
+  ../../../geom_bnl0.3/co2.xyz           0 1 0   ../../../geom_bnl0.3/co2.chg         -4 -1 0 1   ../../../geom_bnl0.3/co2_-4_-1.eig       
+  ../../../geom_bnl0.3/h2co.xyz          0 1 0   ../../../geom_bnl0.3/h2co.chg        -4 -1 0 1   ../../../geom_bnl0.3/h2co_-4_-1.eig      
+  ../../../geom_bnl0.3/h3ccooh.xyz       0 1 0   ../../../geom_bnl0.3/h3ccooh.chg     -4 -1 0 1   ../../../geom_bnl0.3/h3ccooh_-4_-1.eig   
+  ../../../geom_bnl0.3/hno3.xyz          0 1 0   ../../../geom_bnl0.3/hno3.chg        -4 -1 0 1   ../../../geom_bnl0.3/hno3_-4_-1.eig      
+  ../../../geom_bnl0.3/n2o.xyz           0 1 0   ../../../geom_bnl0.3/n2o.chg         -4 -1 0 1   ../../../geom_bnl0.3/n2o_-4_-1.eig       
+  ../../../geom_bnl0.3/h3cooh.xyz        0 1 0   ../../../geom_bnl0.3/h3cooh.chg      -4 -1 0 1   ../../../geom_bnl0.3/h3cooh_-4_-1.eig       
+$end