Merge pull request #262 from wilhadams/qcschema_input

Add QCSchema Input `load_one` and `dump_one` functions

.pylintrc

@@ -50,7 +50,7 @@ confidence=
 # --enable=similarities". If you want to run only the classes checker, but have
 # no Warning level messages displayed, use"--disable=all --enable=classes
 # --disable=W"
-disable=print-statement,parameter-unpacking,unpacking-in-except,old-raise-syntax,backtick,long-suffix,old-ne-operator,old-octal-literal,import-star-module-level,raw-checker-failed,bad-inline-option,locally-disabled,locally-enabled,file-ignored,suppressed-message,useless-suppression,deprecated-pragma,apply-builtin,basestring-builtin,buffer-builtin,cmp-builtin,coerce-builtin,execfile-builtin,file-builtin,long-builtin,raw_input-builtin,reduce-builtin,standarderror-builtin,unicode-builtin,xrange-builtin,coerce-method,delslice-method,getslice-method,setslice-method,no-absolute-import,old-division,dict-iter-method,dict-view-method,next-method-called,metaclass-assignment,indexing-exception,raising-string,reload-builtin,oct-method,hex-method,nonzero-method,cmp-method,input-builtin,round-builtin,intern-builtin,unichr-builtin,map-builtin-not-iterating,zip-builtin-not-iterating,range-builtin-not-iterating,filter-builtin-not-iterating,using-cmp-argument,eq-without-hash,div-method,idiv-method,rdiv-method,exception-message-attribute,invalid-str-codec,sys-max-int,bad-python3-import,deprecated-string-function,deprecated-str-translate-call,too-many-arguments,too-many-locals,too-few-public-methods,fixme,invalid-name,duplicate-code,unsubscriptable-object,no-member
+disable=print-statement,parameter-unpacking,unpacking-in-except,old-raise-syntax,backtick,long-suffix,old-ne-operator,old-octal-literal,import-star-module-level,raw-checker-failed,bad-inline-option,locally-disabled,locally-enabled,file-ignored,suppressed-message,useless-suppression,deprecated-pragma,apply-builtin,basestring-builtin,buffer-builtin,cmp-builtin,coerce-builtin,execfile-builtin,file-builtin,long-builtin,raw_input-builtin,reduce-builtin,standarderror-builtin,unicode-builtin,xrange-builtin,coerce-method,delslice-method,getslice-method,setslice-method,no-absolute-import,old-division,dict-iter-method,dict-view-method,next-method-called,metaclass-assignment,indexing-exception,raising-string,reload-builtin,oct-method,hex-method,nonzero-method,cmp-method,input-builtin,round-builtin,intern-builtin,unichr-builtin,map-builtin-not-iterating,zip-builtin-not-iterating,range-builtin-not-iterating,filter-builtin-not-iterating,using-cmp-argument,eq-without-hash,div-method,idiv-method,rdiv-method,exception-message-attribute,invalid-str-codec,sys-max-int,bad-python3-import,deprecated-string-function,deprecated-str-translate-call,too-many-arguments,too-many-locals,too-few-public-methods,fixme,invalid-name,duplicate-code,unsubscriptable-object,no-member,too-many-lines
 
 # Enable the message, report, category or checker with the given id(s). You can
 # either give multiple identifier separated by comma (,) or put this option

iodata/test/data/H2O_CCSDprTpr_STO3G_output.json

@@ -0,0 +1,70 @@
+{
+  "molecule": {
+    "schema_name": "qcschema_molecule",
+    "schema_version": 2.0,
+    "symbols": [
+      "O",
+      "H",
+      "H"
+    ],
+    "geometry": [
+      0.0,
+      0.0,
+      -0.12947694,
+      0.0,
+      -1.49418734,
+      1.02744651,
+      0.0,
+      1.49418734,
+      1.02744651
+    ],
+    "molecular_charge": 0.0,
+    "molecular_multiplicity": 1,
+    "connectivity": [
+      [0, 1, 1],
+      [0, 2, 1]
+    ],
+    "fix_orientation": true,
+    "fix_symmetry": "c1",
+    "provenance": {
+      "creator": "HORTON3",
+      "routine": "Extracted from molpro_ccsd_prt_pr_water_energy_output.json"
+    },
+    "real": [true, true, true]
+  },
+  "driver": "energy",
+  "model": {
+    "method": "CCSD(T)",
+    "basis": "sto-3g"
+  },
+  "id": "1",
+  "schema_name": "qcschema_output",
+  "schema_version": 2.0,
+  "provenance": [
+    {
+    "creator": "QCElemental",
+    "version": "v0.2.6",
+    "routine": "qcelemental.models.results"
+    },
+    {
+      "creator": "HORTON3",
+      "routine": "Manual validation"
+    }
+  ],
+  "success": true,
+  "return_result": -75.0197177197499,
+  "properties": {
+    "nuclear_repulsion_energy": 8.80146205625184,
+    "scf_dipole_moment": [0.0, 0.0, 0.65662910269302],
+    "scf_total_energy": -74.9646625166939,
+    "ccsd_same_spin_correlation_energy": -0.0019035720854254133,
+    "ccsd_opposite_spin_correlation_energy": -0.0530757170419502,
+    "ccsd_correlation_energy": -0.0549792917918461,
+    "ccsd_total_energy": -75.0196418084857,
+    "ccsd_prt_pr_correlation_energy": -0.0550552030560323,
+    "ccsd_prt_pr_total_energy": -75.0197177197499,
+    "calcinfo_nalpha": 5,
+    "calcinfo_nbeta": 5,
+    "calcinfo_nbasis": 7
+  }
+}

iodata/test/data/H2O_HF_STO3G_Gaussian_input.json

@@ -0,0 +1,36 @@
+{
+  "schema_name": "qcschema_input",
+  "schema_version": 2.0,
+  "molecule": {
+    "schema_name": "qcschema_molecule",
+    "schema_version": 2.0,
+    "symbols":  ["O", "H", "H"],
+    "geometry": [0.0, 0.0, -0.1295, 0.0, -1.4942, 1.0274, 0.0, 1.4942, 1.0274],
+    "molecular_charge": 0,
+    "molecular_multiplicity": 1,
+    "real": [true, true, true],
+    "provenance": [
+      {
+        "creator": "Gaussian 16",
+        "version": "ES64L-G16RevC.01"
+      }
+    ]
+  },
+  "driver": "energy",
+  "model": {
+    "method": "HF",
+    "basis": "STO-3G"
+  },
+  "keywords": {
+    "program": "Gaussian",
+    "verbose": "normal",
+    "run_type": "energy"
+  },
+  "provenance": [
+    {
+      "creator": "IOData",
+      "version": "X.X.X",
+      "routine": "iodata.dump_one.com"
+    }
+  ]
+}

iodata/test/data/LiCl_STO4G_Gaussian_input.json

@@ -0,0 +1,54 @@
+{
+  "schema_name": "qcschema_input",
+  "schema_version": 2.0,
+  "molecule": {
+    "schema_name": "qcschema_molecule",
+    "schema_version": 2.0,
+    "symbols":  ["Li", "Cl"],
+    "geometry": [0.000000, 0.000000, -1.631761, 0.000000, 0.000000, 0.287958],
+    "molecular_charge": 0,
+    "molecular_multiplicity": 1,
+    "real": [true, true],
+    "provenance": [
+      {
+        "creator": "Gaussian 16",
+        "version": "ES64L-G16RevC.01"
+      },
+      {
+        "creator": "HORTON3",
+        "routine": "Manual validation"
+      }
+    ]
+  },
+  "id": "LiCl_HF_STO4G",
+  "driver": "energy",
+  "model": {
+    "method": "HF",
+    "basis": "STO-4G"
+  },
+  "keywords": {
+    "program": "Gaussian",
+    "verbose": "normal",
+    "run_type": "freq",
+    "geom": "AllCheck",
+    "mem": "7GB",
+    "nprocshared": "2",
+    "oldchk": "LiCl_OPT.chk",
+    "chk": "LiCl_HF_STO4G.chk"
+  },
+  "protocols": {
+    "wavefunction": "none",
+    "stdout": false
+  },
+  "extras": {
+    "lewis_acid_group": "alkali_metals",
+    "lewis_base_group": "halides"
+  },
+  "provenance": [
+    {
+      "creator": "IOData",
+      "version": "X.X.X",
+      "routine": "iodata.dump_one.com"
+    }
+  ]
+}

iodata/test/data/LiCl_STO4G_Gaussian_input_extra.json

@@ -0,0 +1,55 @@
+{
+  "schema_name": "qcschema_input",
+  "schema_version": 2.0,
+  "molecule": {
+    "schema_name": "qcschema_molecule",
+    "schema_version": 2.0,
+    "symbols":  ["Li", "Cl"],
+    "geometry": [0.000000, 0.000000, -1.631761, 0.000000, 0.000000, 0.287958],
+    "molecular_charge": 0,
+    "molecular_multiplicity": 1,
+    "real": [true, true],
+    "provenance": [
+      {
+        "creator": "Gaussian 16",
+        "version": "ES64L-G16RevC.01"
+      },
+      {
+        "creator": "HORTON3",
+        "routine": "Manual validation"
+      }
+    ]
+  },
+  "id": "LiCl_HF_STO4G",
+  "driver": "energy",
+  "model": {
+    "method": "HF",
+    "basis": "STO-4G"
+  },
+  "keywords": {
+    "program": "Gaussian",
+    "verbose": "normal",
+    "run_type": "freq",
+    "geom": "AllCheck",
+    "mem": "7GB",
+    "nprocshared": "2",
+    "oldchk": "LiCl_OPT.chk",
+    "chk": "LiCl_HF_STO4G.chk"
+  },
+  "protocols": {
+    "wavefunction": "none",
+    "stdout": false
+  },
+  "extras": {
+    "lewis_acid_group": "alkali_metals",
+    "lewis_base_group": "halides"
+  },
+  "provenance": [
+    {
+      "creator": "IOData",
+      "version": "X.X.X",
+      "routine": "iodata.dump_one.com"
+    }
+  ],
+  "another_field": true
+}

iodata/test/data/LiCl_STO4G_Gaussian_input_extra_molecule.json

@@ -0,0 +1,55 @@
+{
+  "schema_name": "qcschema_input",
+  "schema_version": 2.0,
+  "molecule": {
+    "schema_name": "qcschema_molecule",
+    "schema_version": 2.0,
+    "symbols":  ["Li", "Cl"],
+    "geometry": [0.000000, 0.000000, -1.631761, 0.000000, 0.000000, 0.287958],
+    "molecular_charge": 0,
+    "molecular_multiplicity": 1,
+    "real": [true, true],
+    "provenance": [
+      {
+        "creator": "Gaussian 16",
+        "version": "ES64L-G16RevC.01"
+      },
+      {
+        "creator": "HORTON3",
+        "routine": "Manual validation"
+      }
+    ],
+    "another_field": true
+  },
+  "id": "LiCl_HF_STO4G",
+  "driver": "energy",
+  "model": {
+    "method": "HF",
+    "basis": "STO-4G"
+  },
+  "keywords": {
+    "program": "Gaussian",
+    "verbose": "normal",
+    "run_type": "freq",
+    "geom": "AllCheck",
+    "mem": "7GB",
+    "nprocshared": "2",
+    "oldchk": "LiCl_OPT.chk",
+    "chk": "LiCl_HF_STO4G.chk"
+  },
+  "protocols": {
+    "wavefunction": "none",
+    "stdout": false
+  },
+  "extras": {
+    "lewis_acid_group": "alkali_metals",
+    "lewis_base_group": "halides"
+  },
+  "provenance": [
+    {
+      "creator": "IOData",
+      "version": "X.X.X",
+      "routine": "iodata.dump_one.com"
+    }
+  ]
+}

iodata/test/data/LiCl_STO4G_Gaussian_input_nested_extra.json

@@ -0,0 +1,62 @@
+{
+  "schema_name": "qcschema_input",
+  "schema_version": 2.0,
+  "molecule": {
+    "schema_name": "qcschema_molecule",
+    "schema_version": 2.0,
+    "symbols":  ["Li", "Cl"],
+    "geometry": [0.000000, 0.000000, -1.631761, 0.000000, 0.000000, 0.287958],
+    "molecular_charge": 0,
+    "molecular_multiplicity": 1,
+    "real": [true, true],
+    "provenance": [
+      {
+        "creator": "Gaussian 16",
+        "version": "ES64L-G16RevC.01"
+      },
+      {
+        "creator": "HORTON3",
+        "routine": "Manual validation"
+      }
+    ]
+  },
+  "id": "LiCl_HF_STO4G",
+  "driver": "energy",
+  "model": {
+    "method": "HF",
+    "basis": "STO-4G"
+  },
+  "keywords": {
+    "program": "Gaussian",
+    "verbose": "normal",
+    "run_type": "freq",
+    "geom": "AllCheck",
+    "mem": "7GB",
+    "nprocshared": "2",
+    "oldchk": "LiCl_OPT.chk",
+    "chk": "LiCl_HF_STO4G.chk"
+  },
+  "protocols": {
+    "wavefunction": "none",
+    "stdout": false
+  },
+  "extras": {
+    "lewis_acid_group": "alkali_metals",
+    "lewis_base_group": "halides"
+  },
+  "provenance": [
+    {
+      "creator": "IOData",
+      "version": "X.X.X",
+      "routine": "iodata.dump_one.com"
+    }
+  ],
+  "related_projects": {
+    "HSAB": {
+      "id": "HSAB_2019_LALB"
+    },
+    "4PB3": {
+      "id": "4PB3_2020_Group1"
+    }
+  }
+}