Release 3ob-3-1

Author: aradi

.github/workflows/release.yml

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+name: release
+
+on:
+  push:
+    tags:
+      - v[0-9]*.[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]*.[0-9]*')
+        SKF_VERSION=$(echo $GIT_TAG | sed -E 's/^v([0-9]+)\.([0-9])+\.([0-9]+)$/\1-\2/')
+        SKF_PATCH=$(echo $GIT_TAG | sed -E 's/^v([0-9]+)\.([0-9])+\.([0-9]+)$/\3/')
+        echo "SKF_VERSION=${SKF_VERSION}" >> ${GITHUB_ENV}
+        echo "SKF_PATCH=${SKF_PATCH}" >> ${GITHUB_ENV}
+        ARCHIVE_NAME="${SKF_NAME}-${SKF_VERSION}"
+        echo "ARCHIVE_NAME=${ARCHIVE_NAME}" >> ${GITHUB_ENV}
+        if [[ ${SKF_PATCH} -eq 0 ]]; then
+          echo "RELEASE_NAME=${ARCHIVE_NAME}" >> ${GITHUB_ENV}
+        else
+          echo "RELEASE_NAME=${ARCHIVE_NAME} (p${SKF_PATCH})" >> ${GITHUB_ENV}
+        fi
+
+    - name: Create archive
+      run: |
+        mkdir -p _build/${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.RELEASE_NAME }}
+        preserve_order: True
+        files: |
+          ${{ env.ARCHIVE_NAME }}.tar.xz
+          ${{ env.ARCHIVE_NAME }}-extras.tar.xz
+        body_path: RELEASE.md
+
+

CHANGELOG.md

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+# Changelog
+
+## 3ob-3-1
+
+First public release under CC-BY-SA license

LICENSE

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+======================================================================
+3ob-3-1
+======================================================================
+
+(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 Third-Order Parametrization for
+Organic and Biological Systems (3OB) has been specifically designed
+for Third Order Density Functional Tight Binding (DFTB3) and super-
+sedes the MIO parameter set. Main improvements over MIO are improved
+geometries for non-covalent bonds as e.g. the hydrogen bond in the
+water dimer, a great reduction of the consistent overbinding and an
+overall improved performance. Comprehensive benchmark tests for
+C-H-N-O can be found in [JCTC2013], for P-S-* in [JCTC2014],
+for Mg-Zn-* in [JCTC2015-1], and for Na-F-K-Ca-Cl-Br-I-* in
+[JCTC2015-2].
+
+----------------------------------------------------------------------
+
+The following parameter should be generally used for DFTB3/3OB
+calculations:
+
+zeta = 4.00 (gamma^h function exponent; DampXHExponent in DFTB+)
+
+----------------------------------------------------------------------
+
+List of all atomic Hubbard derivatives (atomic units):
+Br = -0.0573
+ C = -0.1492
+Ca = -0.0340
+Cl = -0.0697
+ F = -0.1623
+ H = -0.1857
+ I = -0.0433
+ K = -0.0339
+Mg = -0.02
+ N = -0.1535
+Na = -0.0454
+ O = -0.1575
+ P = -0.14
+ S = -0.11
+Zn = -0.03
+
+Maximum angular momenta for calculation input files:
+
+Br = "d"
+ C = "p"
+Ca = "p"
+Cl = "d"
+ F = "p"
+ H = "s"
+ I = "d"
+ K = "p"
+Mg = "p"
+ N = "p"
+Na = "p"
+ O = "p"
+ P = "d"
+ S = "d"
+Zn = "d"
+
+----------------------------------------------------------------------
+
+For the empirical halogend bond correction described in [JCTC2015-2]
+the following parameters are provided:
+
+DFTB3-D3(BJ) Parameters:
+a1 = 0.746
+a2 = 4.191
+s8 = 3.209
+
+General X-Correction parameters (AA and kcal/mol unit system):
+c1 = 7.761
+c2 = 0.050
+c3 = 4.518
+
+Element Pair Parameters (AA and kcal/mol unit system):
+O-Cl = 1.237
+O-Br = 1.099
+O-I  = 1.313
+N-Cl = 1.526
+N-Br = 1.349
+N-I  = 1.521
+
+
+Relevant Publications
+=====================
+
+[JCTC2013] J. Chem. Theory Comput., 2013, 9, 338-354.
+[JCTC2014] J. Chem. Theory Comput., 2014, 10, 1518–1537.
+[JCTC2015-1] J. Phys. Chem. B, 2015, 119, 1062–1082.
+[JCTC2015-2] J. Chem. Theory Comput., 2015, 11, 332–342.
+
+
+Required references
+===================
+O - N - C - H:		[JCTC2013]
+P,S-*:	    		[JCTC2014]
+Mg,Zn-*:		[JCTC2015-1]
+Na,F,K,Ca,Cl,Br,I-*:	[JCTC2015-2]

README

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+# Parameter set 3ob-3-1
+
+Density Functional Tight Binding (DFTB) parameter set providing parameters for calculating biological and organic molecules using the DFTB3 model.
+
+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.**

RELEASE.md

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+# Values calculated with PBE using slateratom
+#
+SpinConstants {
+
+  H {  # 1 H: 1s1
+    # 1s
+    -0.07174  # 1s
+  }
+
+  C {  # 6 C: [1s2] 2s2 2p2
+    # 2s        2p
+    -0.03062  -0.02505  # 2s
+    -0.02505  -0.02265  # 2p
+  }
+  
+  N {  # 7 N: [1s2] 2s2 2p3
+    # 2s        2p
+    -0.03318  -0.02755  # 2s
+    -0.02755  -0.02545  # 2p
+  }
+
+  O {  # 8 O: [1s2] 2s2 3p4
+    # 2s        2p
+    -0.03524  -0.02956  # 2s
+    -0.02956  -0.02785  # 2p
+  }
+
+  F {  # 9 F: [1s2] 2s2 2p5
+    # 2s        2p
+    -0.03697  -0.03124  # 2s
+    -0.03124  -0.02990  # 2p
+
+  }
+
+  Na {  # 11 Na: [Ne] 3s1 3p0
+    # 3s        3p
+    -0.01528  -0.01528  # 3s
+    -0.01528  -0.01528  # 3p
+  }
+
+  Mg {  # 12 Mg: [Ne] 3s2 3p0
+    #  3s       3p
+    -0.01667  -0.01667  # 3p
+    -0.01667  -0.01667  # 3p
+  }
+
+  P {  # 15 P: [Ne] 3s2 3p3 3d0
+    # 3s        3p         3d  
+    -0.02062  -0.01609  -0.01609  # 3s
+    -0.01609  -0.01490  -0.01490  # 3p
+    -0.01609  -0.01490  -0.01490  # 3d
+  }
+
+  S {  # 16 S: [Ne] 3s2 3p4 3d0
+    # 3s        3p         3d  
+    -0.02137  -0.01699  -0.01699
+    -0.01699  -0.01549  -0.01549
+    -0.01699  -0.01549  -0.01549
+  }
+
+  Cl {  # 17 Cl: [Ne] 3s2 3p5 3d0
+    # 3s        3p         3d  
+    -0.02192  -0.01774   -0.01774  # 3s
+    -0.01774  -0.01606   -0.01606  # 3p
+    -0.01774  -0.01606   -0.01606  # 3d
+  }
+
+  K {  # 19 K: [Ar] 4s1 4p0
+    # 4s        4p
+    -0.01075  -0.01075  # 4s
+    -0.01075  -0.01075  # 4p
+  }
+
+  Ca {  # 20 Ca: [Ar] 4s2
+    # 3s        3p
+    -0.01196  -0.01196  # 3s
+    -0.01196  -0.01196  # 3p
+  }
+
+  Zn {  # 30 Zn: [Ar] 3d10 4s2 4p0
+    # 4s        4p        3d           
+    -0.01680  -0.01680  -0.00276  # 4s
+    -0.01680  -0.01680  -0.00276  # 4p
+    -0.00276  -0.00276  -0.01925  # 3d
+  }
+
+  Br {  # 35 Ca: [Ar 3d10]  4s2 4p5 4d0
+    # 4s        4p        4d
+    -0.01850  -0.01439  -0.01439  # 4s
+    -0.01439  -0.01377  -0.01377  # 4p
+    -0.01439  -0.01377  -0.01377  # 4d
+  }
+  
+  I {  # 53 I: [Kr 4d10] 5s2 5p2 5d0
+    # 5s        5p        5d
+    -0.01446  -0.01132  -0.01132  # 5s
+    -0.01132  -0.01144  -0.01144  # 5p
+    -0.01132  -0.01144  -0.01144  # 5d
+  }
+
+}