Merge pull request #714 from votca/updated_bench

Updated bench
votca · Jun 19, 2021 · be161bf · be161bf
2 parents 88224ed + 7e8f997
commit be161bf
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diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -38,6 +38,7 @@ Version 2022-dev
 -  add command line option for number of gpus (#711)
 -  reworked iqm statefile reading (#712)
 -  made membervariable format consistent (#713)
+-  updated benchmark (#714)
 -  reworked commandline options (#715)
 
 Version 2021.1 (released XX.03.21)

diff --git a/include/votca/xtp/qmpackage.h b/include/votca/xtp/qmpackage.h
@@ -49,8 +49,7 @@ class QMPackage {
   /// writes a coordinate file WITHOUT taking into account PBCs
   virtual bool WriteInputFile(const Orbitals& orbitals) = 0;
 
-  virtual bool Run() = 0;
-
+  bool Run();
   virtual bool ParseLogFile(Orbitals& orbitals) = 0;
 
   virtual bool ParseMOsFile(Orbitals& orbitals) = 0;
@@ -114,6 +113,7 @@ class QMPackage {
   tools::Property ParseCommonOptions(const tools::Property& options);
   std::string FindDefaultsFile() const;
 
+  virtual bool RunDFT() = 0;
   virtual void WriteChargeOption() = 0;
   std::vector<MinimalMMCharge> SplitMultipoles(const StaticSite& site) const;
   void ReorderOutput(Orbitals& orbitals) const;

diff --git a/share/benchmark/Geometries/Aromatic_hydrocarbons/Anthracene.xyz b/share/benchmark/Geometries/Aromatic_hydrocarbons/Anthracene.xyz
@@ -0,0 +1,26 @@
+24
+# converted from Conformer3D_CID_8418.json
+C    -1.225    0.706    0.0001
+C    -1.2251    -0.7061    0.0001
+C    1.2251    0.7061    0.0002
+C    1.2251    -0.7061    0.0001
+C    0    1.3937    0.0001
+C    0    -1.3938    0
+C    -2.4504    1.393    -0.0001
+C    -2.4505    -1.393    0
+C    2.4505    1.3929    0
+C    2.4505    -1.3929    0
+C    -3.6587    0.6956    -0.0001
+C    -3.6588    -0.6955    -0.0001
+C    3.6587    0.6956    -0.0002
+C    3.6587    -0.6956    -0.0002
+H    0    2.4838    0
+H    0    -2.4839    -0.0001
+H    -2.4742    2.4808    -0.0001
+H    -2.4744    -2.4809    0
+H    2.4742    2.4808    0
+H    2.4743    -2.4808    0
+H    -4.5989    1.2394    -0.0003
+H    -4.5991    -1.2391    -0.0002
+H    4.5989    1.2393    -0.0003
+H    4.5989    -1.2393    -0.0004
diff --git a/share/benchmark/Geometries/Aromatic_hydrocarbons/Benzene.xyz b/share/benchmark/Geometries/Aromatic_hydrocarbons/Benzene.xyz
@@ -0,0 +1,14 @@
+12
+# converted from Conformer3D_CID_241.json
+C    -1.2131    -0.6884    0
+C    -1.2028    0.7064    0.0001
+C    -0.0103    -1.3948    0
+C    0.0104    1.3948    -0.0001
+C    1.2028    -0.7063    0
+C    1.2131    0.6884    0
+H    -2.1577    -1.2244    0
+H    -2.1393    1.2564    0.0001
+H    -0.0184    -2.4809    -0.0001
+H    0.0184    2.4808    0
+H    2.1394    -1.2563    0.0001
+H    2.1577    1.2245    0
diff --git a/share/benchmark/Geometries/Aromatic_hydrocarbons/Decacene.xyz b/share/benchmark/Geometries/Aromatic_hydrocarbons/Decacene.xyz
@@ -0,0 +1,68 @@
+66
+# converted from Conformer3D_CID_54494119.json
+C    0    0.7042    -0.0024
+C    0    -0.704    -0.0028
+C    -2.4517    0.7041    -0.0039
+C    -2.4517    -0.704    -0.0034
+C    2.4518    0.7043    0.0002
+C    2.4518    -0.7039    -0.001
+C    -4.9035    0.7042    -0.004
+C    -4.9034    -0.704    -0.0023
+C    4.9036    0.7043    0.003
+C    4.9035    -0.7038    0.001
+C    1.2258    1.3911    -0.0008
+C    1.2258    -1.3909    -0.0024
+C    -1.2259    1.391    -0.0034
+C    -1.2258    -1.3909    -0.0033
+C    -3.6776    1.391    -0.0047
+C    -3.6775    -1.3908    -0.0026
+C    3.6776    1.3912    0.0025
+C    3.6776    -1.3908    -0.0008
+C    -7.3553    0.7043    -0.0025
+C    -7.3552    -0.7043    0
+C    7.3554    0.7044    0.0041
+C    7.3554    -0.7043    0.0014
+C    -6.1293    1.3911    -0.0046
+C    -6.1293    -1.3909    -0.0003
+C    6.1295    1.3911    0.005
+C    6.1294    -1.3909    0.0004
+C    -8.5807    1.3923    -0.0029
+C    -8.5805    -1.3924    0.0033
+C    8.5808    1.3923    0.0051
+C    8.5806    -1.3924    -0.0004
+C    -9.8063    0.7057    0.0001
+C    -9.8063    -0.7059    0.0037
+C    9.8063    0.7057    0.0029
+C    9.8061    -0.7059    -0.0001
+C    -11.0318    1.3926    -0.0003
+C    -11.0315    -1.3931    0.0076
+C    11.0317    1.3926    0.0031
+C    11.0313    -1.3932    -0.0028
+C    -12.24    0.6953    0.0035
+C    -12.2398    -0.6959    0.0079
+C    12.2398    0.6952    0
+C    12.2396    -0.696    -0.0029
+H    1.2258    2.4813    -0.0001
+H    1.2259    -2.481    -0.003
+H    -1.226    2.4812    -0.0034
+H    -1.2258    -2.481    -0.0031
+H    -3.6776    2.4812    -0.0055
+H    -3.6775    -2.481    -0.0016
+H    3.6776    2.4813    0.0037
+H    3.6777    -2.4809    -0.0021
+H    -6.1292    2.4813    -0.0062
+H    -6.1291    -2.4811    0.0014
+H    6.1294    2.4813    0.0067
+H    6.1291    -2.481    -0.0014
+H    -8.5805    2.4824    -0.0053
+H    -8.5802    -2.4825    0.0057
+H    8.5807    2.4825    0.0072
+H    8.5802    -2.4825    -0.0026
+H    -11.0555    2.4805    -0.0033
+H    -11.055    -2.4809    0.0107
+H    11.0554    2.4804    0.0054
+H    11.0547    -2.481    -0.0051
+H    -13.1802    1.2388    0.0033
+H    -13.18    -1.2397    0.011
+H    13.1801    1.2387    0.0001
+H    13.1797    -1.2399    -0.0052
diff --git a/share/benchmark/Geometries/Aromatic_hydrocarbons/Heptacene.xyz b/share/benchmark/Geometries/Aromatic_hydrocarbons/Heptacene.xyz
@@ -0,0 +1,50 @@
+48
+# converted from Conformer3D_CID_5460712.json
+C    1.2259    -0.704    -0.001
+C    1.2259    0.7042    -0.0013
+C    -1.2259    -0.704    -0.0006
+C    -1.2259    0.7042    -0.0009
+C    3.6777    -0.7043    -0.0009
+C    3.6777    0.7043    -0.001
+C    -3.6777    -0.7045    0
+C    -3.6778    0.7042    -0.0004
+C    0    -1.3909    -0.0008
+C    0.0001    1.391    -0.0012
+C    2.4517    -1.391    -0.0009
+C    2.4517    1.3911    -0.0015
+C    -2.4516    -1.3911    -0.0002
+C    -2.4518    1.391    -0.0004
+C    4.903    -1.3924    -0.0009
+C    4.9031    1.3924    0
+C    -4.903    -1.3924    0.0005
+C    -4.9031    1.3923    -0.0003
+C    6.1286    -0.7059    -0.0001
+C    6.1287    0.7059    0.0008
+C    -6.1287    -0.7058    0.0006
+C    -6.1287    0.7058    0.0001
+C    7.354    -1.393    0.0001
+C    7.354    1.3928    0.0022
+C    -7.354    -1.3929    0.0015
+C    -7.354    1.393    0.0003
+C    8.5622    -0.6956    0.0013
+C    8.5623    0.6956    0.0026
+C    -8.5623    -0.6956    0.0015
+C    -8.5622    0.6956    0.0009
+H    0    -2.481    -0.0006
+H    0    2.4812    -0.0012
+H    2.4515    -2.4812    -0.0007
+H    2.4517    2.4813    -0.0014
+H    -2.4513    -2.4812    0
+H    -2.4517    2.4812    -0.0004
+H    4.9028    -2.4825    -0.0012
+H    4.9028    2.4826    0.0004
+H    -4.9028    -2.4826    0.0009
+H    -4.9027    2.4823    -0.0005
+H    7.3776    -2.4808    -0.0007
+H    7.3776    2.4807    0.003
+H    -7.3776    -2.4808    0.002
+H    -7.3776    2.4808    0
+H    9.5024    -1.2393    0.0015
+H    9.5024    1.2392    0.0037
+H    -9.5025    -1.2392    0.002
+H    -9.5024    1.2393    0.0009
diff --git a/share/benchmark/Geometries/Aromatic_hydrocarbons/Hexacene.xyz b/share/benchmark/Geometries/Aromatic_hydrocarbons/Hexacene.xyz
@@ -0,0 +1,44 @@
+42
+# converted from Conformer3D_CID_123044.json
+C    0.0001    -0.7041    0.0002
+C    0    0.7041    0.0001
+C    2.4518    -0.7043    -0.0006
+C    2.4518    0.7043    -0.0003
+C    -2.4518    -0.7044    0.0007
+C    -2.4519    0.7043    0.0002
+C    -1.2259    -1.391    0.0008
+C    -1.2259    1.391    0.0001
+C    1.2258    -1.391    -0.0004
+C    1.2258    1.391    -0.0002
+C    3.6772    -1.3923    -0.001
+C    3.6773    1.3924    0
+C    -3.6772    -1.3924    0.0009
+C    -3.6772    1.3923    -0.0004
+C    4.9028    -0.7058    -0.0007
+C    4.9028    0.7058    0
+C    -4.9028    -0.7059    0.0004
+C    -4.9028    0.7058    -0.0003
+C    6.1281    -1.3929    -0.0012
+C    6.1281    1.3929    0.0011
+C    -6.1281    -1.3929    0.0006
+C    -6.1281    1.3929    -0.001
+C    7.3364    -0.6957    -0.0002
+C    7.3363    0.6956    0.0015
+C    -7.3364    -0.6955    0
+C    -7.3364    0.6957    -0.0007
+H    -1.2257    -2.4812    0.0011
+H    -1.2257    2.4812    -0.0002
+H    1.2257    -2.4812    -0.0004
+H    1.2256    2.4811    -0.0001
+H    3.6769    -2.4824    -0.0014
+H    3.677    2.4825    0.0005
+H    -3.6769    -2.4825    0.0015
+H    -3.6769    2.4825    -0.0008
+H    6.1516    -2.4807    -0.002
+H    6.1518    2.4808    0.0019
+H    -6.1517    -2.4808    0.0013
+H    -6.1516    2.4808    -0.0015
+H    8.2765    -1.2393    -0.0003
+H    8.2765    1.2393    0.0026
+H    -8.2766    -1.2392    0.0002
+H    -8.2766    1.2394    -0.0011
diff --git a/share/benchmark/Geometries/Aromatic_hydrocarbons/Naphthalene.xyz b/share/benchmark/Geometries/Aromatic_hydrocarbons/Naphthalene.xyz
@@ -0,0 +1,20 @@
+18
+# converted from Conformer3D_CID_931.json
+C    0    -0.7076    0
+C    0    0.7076    0.0001
+C    1.225    -1.3944    0.0001
+C    1.225    1.3944    0
+C    -1.225    -1.3943    0
+C    -1.225    1.3943    0
+C    2.4327    -0.6958    0
+C    2.4327    0.6959    -0.0001
+C    -2.4327    -0.6958    -0.0001
+C    -2.4327    0.6958    0
+H    1.2489    -2.4822    0.0001
+H    1.2489    2.4821    -0.0001
+H    -1.2489    -2.4822    -0.0001
+H    -1.249    2.4821    0.0001
+H    3.3733    -1.239    -0.0001
+H    3.3732    1.2391    -0.0001
+H    -3.3733    -1.239    -0.0001
+H    -3.3732    1.239    0
diff --git a/share/benchmark/Geometries/Aromatic_hydrocarbons/Nonacene.xyz b/share/benchmark/Geometries/Aromatic_hydrocarbons/Nonacene.xyz
@@ -0,0 +1,62 @@
+60
+# converted from Conformer3D_CID_6857587.json
+C    -1.2259    0.705    0.0063
+C    -1.2258    -0.7033    0.0073
+C    1.226    0.7048    0.005
+C    1.2258    -0.7035    0.0054
+C    -3.6776    0.705    0.0052
+C    -3.6776    -0.7032    0.0064
+C    3.6777    0.7044    0.0025
+C    3.6775    -0.7038    0.0023
+C    0.0001    1.3918    0.0056
+C    -0.0001    -1.3902    0.007
+C    -2.4518    1.3918    0.0055
+C    -2.4517    -1.39    0.0077
+C    2.4519    1.3915    0.0039
+C    2.4515    -1.3905    0.004
+C    -6.1295    0.7048    0.0015
+C    -6.1292    -0.7039    0.0025
+C    6.1295    0.7041    -0.0006
+C    6.1293    -0.7045    -0.0017
+C    -4.9037    1.3917    0.0032
+C    -4.9032    -1.3903    0.0053
+C    4.9037    1.3911    0.0014
+C    4.9032    -1.3909    0.0001
+C    -7.3552    1.3923    -0.0015
+C    -7.3542    -1.3924    0.0001
+C    7.355    1.392    -0.0013
+C    7.3546    -1.3927    -0.0043
+C    -8.5807    0.7053    -0.0044
+C    -8.58    -0.7063    -0.0036
+C    8.5804    0.7052    -0.0034
+C    8.5803    -0.7063    -0.0051
+C    -9.8064    1.3918    -0.0083
+C    -9.8051    -1.3941    -0.0072
+C    9.8058    1.3922    -0.0036
+C    9.8056    -1.3937    -0.0074
+C    -11.0143    0.6938    -0.0117
+C    -11.0137    -0.6974    -0.0112
+C    11.014    0.6948    -0.0056
+C    11.0138    -0.6965    -0.0075
+H    0.0001    2.4819    0.005
+H    -0.0001    -2.4804    0.0073
+H    -2.4519    2.482    0.0046
+H    -2.4518    -2.4802    0.0083
+H    2.4521    2.4817    0.0039
+H    2.4513    -2.4806    0.0039
+H    -4.9037    2.4819    0.0023
+H    -4.9028    -2.4805    0.0059
+H    4.9038    2.4813    0.002
+H    4.9029    -2.4811    -0.0005
+H    -7.3554    2.4825    -0.0022
+H    -7.3536    -2.4825    0.0005
+H    7.3549    2.4821    -0.0001
+H    7.3542    -2.4828    -0.0054
+H    -9.8305    2.4795    -0.0089
+H    -9.8281    -2.4819    -0.0069
+H    9.8296    2.48    -0.0022
+H    9.829    -2.4815    -0.0089
+H    -11.9548    1.237    -0.0148
+H    -11.9535    -1.2416    -0.0138
+H    11.9542    1.2384    -0.0058
+H    11.954    -1.2402    -0.0091
diff --git a/share/benchmark/Geometries/Aromatic_hydrocarbons/Octacene.xyz b/share/benchmark/Geometries/Aromatic_hydrocarbons/Octacene.xyz
@@ -0,0 +1,56 @@
+54
+# converted from Conformer3D_CID_5460708.json
+C    -0.0001    0.7043    -0.0026
+C    0    -0.7039    -0.0027
+C    2.4518    0.7043    -0.0011
+C    2.4517    -0.7039    -0.0021
+C    -2.4518    0.7043    -0.0031
+C    -2.4517    -0.7039    -0.0023
+C    -1.2259    1.3912    -0.0032
+C    -1.2259    -1.3907    -0.0025
+C    1.226    1.3912    -0.0017
+C    1.2258    -1.3907    -0.0028
+C    4.9038    0.7045    0.0012
+C    4.9036    -0.7043    -0.0005
+C    -4.9037    0.7045    -0.0021
+C    -4.9036    -0.7043    -0.0005
+C    3.6778    1.3912    0.0006
+C    3.6776    -1.3909    -0.002
+C    -3.6777    1.3911    -0.0034
+C    -3.6776    -1.3908    -0.0009
+C    6.1293    1.3923    0.0032
+C    6.1289    -1.3924    -0.0008
+C    -6.1292    1.3923    -0.0018
+C    -6.1289    -1.3923    0.002
+C    7.3548    0.7057    0.0029
+C    7.3545    -0.706    0.0007
+C    -7.3547    0.7057    0.0003
+C    -7.3546    -0.706    0.0026
+C    8.5802    1.3926    0.0044
+C    8.5798    -1.3932    -0.0001
+C    -8.5802    1.3926    0.0004
+C    -8.5798    -1.3931    0.0055
+C    9.7883    0.6953    0.0032
+C    9.7882    -0.696    0.0011
+C    -9.7883    0.6952    0.0028
+C    -9.7882    -0.696    0.0054
+H    -1.2259    2.4814    -0.0034
+H    -1.2259    -2.4809    -0.0021
+H    1.226    2.4814    -0.0013
+H    1.2257    -2.4809    -0.0031
+H    3.6777    2.4814    0.0017
+H    3.6773    -2.481    -0.0029
+H    -3.6776    2.4813    -0.0042
+H    -3.6773    -2.481    0.0001
+H    6.1291    2.4824    0.0047
+H    6.1285    -2.4825    -0.0023
+H    -6.129    2.4825    -0.0032
+H    -6.1285    -2.4824    0.0037
+H    8.6039    2.4804    0.006
+H    8.6033    -2.4811    -0.0019
+H    -8.6039    2.4804    -0.0014
+H    -8.6033    -2.481    0.0075
+H    10.7285    1.2388    0.0041
+H    10.7283    -1.2398    0.0004
+H    -10.7285    1.2388    0.0028
+H    -10.7284    -1.2398    0.0074