diff --git a/html/_modules/index.html b/html/_modules/index.html
index f81e27d7cb4..2bef515e3ea 100644
--- a/html/_modules/index.html
+++ b/html/_modules/index.html
@@ -91,7 +91,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
·
PSI4
@@ -227,7 +227,7 @@ Navigation
·
- 1.4rc2.dev26
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PSI4
@@ -240,7 +240,7 @@ Navigation
diff --git a/html/_modules/psi4/driver/aliases.html b/html/_modules/psi4/driver/aliases.html
index 75c8e3baaf2..68ab9abab21 100644
--- a/html/_modules/psi4/driver/aliases.html
+++ b/html/_modules/psi4/driver/aliases.html
@@ -91,7 +91,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
·
PSI4
@@ -380,7 +380,7 @@ Navigation
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- 1.4rc2.dev26
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PSI4
@@ -394,7 +394,7 @@ Navigation
diff --git a/html/_modules/psi4/driver/diatomic.html b/html/_modules/psi4/driver/diatomic.html
index ed91f890e95..d2f236a5c4a 100644
--- a/html/_modules/psi4/driver/diatomic.html
+++ b/html/_modules/psi4/driver/diatomic.html
@@ -91,7 +91,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
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PSI4
@@ -476,7 +476,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
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PSI4
@@ -490,7 +490,7 @@ Navigation
diff --git a/html/_modules/psi4/driver/driver.html b/html/_modules/psi4/driver/driver.html
index 20ab6588c2d..850527f3671 100644
--- a/html/_modules/psi4/driver/driver.html
+++ b/html/_modules/psi4/driver/driver.html
@@ -91,7 +91,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
·
PSI4
@@ -2384,7 +2384,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
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PSI4
@@ -2398,7 +2398,7 @@ Navigation
diff --git a/html/_modules/psi4/driver/driver_cbs.html b/html/_modules/psi4/driver/driver_cbs.html
index f6bece2dbfe..e94d1e8381e 100644
--- a/html/_modules/psi4/driver/driver_cbs.html
+++ b/html/_modules/psi4/driver/driver_cbs.html
@@ -91,7 +91,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
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PSI4
@@ -2228,7 +2228,7 @@ Navigation
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- 1.4rc2.dev26
+ undefined
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PSI4
@@ -2242,7 +2242,7 @@ Navigation
diff --git a/html/_modules/psi4/driver/driver_nbody.html b/html/_modules/psi4/driver/driver_nbody.html
index c0e8d2fe07e..d3097e35749 100644
--- a/html/_modules/psi4/driver/driver_nbody.html
+++ b/html/_modules/psi4/driver/driver_nbody.html
@@ -91,7 +91,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
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PSI4
@@ -993,7 +993,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
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PSI4
@@ -1007,7 +1007,7 @@ Navigation
diff --git a/html/_modules/psi4/driver/inputparser.html b/html/_modules/psi4/driver/inputparser.html
index 355bd72a6eb..8e6fb88e903 100644
--- a/html/_modules/psi4/driver/inputparser.html
+++ b/html/_modules/psi4/driver/inputparser.html
@@ -91,7 +91,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
·
PSI4
@@ -975,7 +975,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
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PSI4
@@ -989,7 +989,7 @@ Navigation
diff --git a/html/_modules/psi4/driver/ipi_broker.html b/html/_modules/psi4/driver/ipi_broker.html
index 839f3779080..4c04a49e5c1 100644
--- a/html/_modules/psi4/driver/ipi_broker.html
+++ b/html/_modules/psi4/driver/ipi_broker.html
@@ -91,7 +91,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
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@@ -348,7 +348,7 @@ Navigation
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diff --git a/html/_modules/psi4/driver/mdi_engine.html b/html/_modules/psi4/driver/mdi_engine.html
index 1dc53e616b2..fe0c95b312d 100644
--- a/html/_modules/psi4/driver/mdi_engine.html
+++ b/html/_modules/psi4/driver/mdi_engine.html
@@ -91,7 +91,7 @@ Navigation
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- 1.4rc2.dev26
+ undefined
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PSI4
@@ -664,7 +664,7 @@ Navigation
diff --git a/html/_modules/psi4/driver/molutil.html b/html/_modules/psi4/driver/molutil.html
index ede13a825ea..cf8d5e20ca0 100644
--- a/html/_modules/psi4/driver/molutil.html
+++ b/html/_modules/psi4/driver/molutil.html
@@ -91,7 +91,7 @@ Navigation
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- 1.4rc2.dev26
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PSI4
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diff --git a/html/_modules/psi4/driver/p4util/exceptions.html b/html/_modules/psi4/driver/p4util/exceptions.html
index 332a16c322c..56c10621d69 100644
--- a/html/_modules/psi4/driver/p4util/exceptions.html
+++ b/html/_modules/psi4/driver/p4util/exceptions.html
@@ -91,7 +91,7 @@ Navigation
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PSI4
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diff --git a/html/_modules/psi4/driver/p4util/fchk.html b/html/_modules/psi4/driver/p4util/fchk.html
index 507afc1d8b8..5dade90db33 100644
--- a/html/_modules/psi4/driver/p4util/fchk.html
+++ b/html/_modules/psi4/driver/p4util/fchk.html
@@ -91,7 +91,7 @@ Navigation
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- 1.4rc2.dev26
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PSI4
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PSI4
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diff --git a/html/_modules/psi4/driver/p4util/fcidump.html b/html/_modules/psi4/driver/p4util/fcidump.html
index 7076cee3b99..f10dc5b7742 100644
--- a/html/_modules/psi4/driver/p4util/fcidump.html
+++ b/html/_modules/psi4/driver/p4util/fcidump.html
@@ -91,7 +91,7 @@ Navigation
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- 1.4rc2.dev26
+ undefined
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PSI4
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diff --git a/html/_modules/psi4/driver/p4util/numpy_helper.html b/html/_modules/psi4/driver/p4util/numpy_helper.html
index 0ff8af83f18..7bb4b9a0d09 100644
--- a/html/_modules/psi4/driver/p4util/numpy_helper.html
+++ b/html/_modules/psi4/driver/p4util/numpy_helper.html
@@ -91,7 +91,7 @@ Navigation
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- 1.4rc2.dev26
+ undefined
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PSI4
@@ -821,7 +821,7 @@ Navigation
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- 1.4rc2.dev26
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PSI4
@@ -835,7 +835,7 @@ Navigation
diff --git a/html/_modules/psi4/driver/p4util/python_helpers.html b/html/_modules/psi4/driver/p4util/python_helpers.html
index aab96a079cd..7192968c130 100644
--- a/html/_modules/psi4/driver/p4util/python_helpers.html
+++ b/html/_modules/psi4/driver/p4util/python_helpers.html
@@ -91,7 +91,7 @@ Navigation
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- 1.4rc2.dev26
+ undefined
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PSI4
@@ -1242,7 +1242,7 @@ Navigation
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PSI4
@@ -1256,7 +1256,7 @@ Navigation
diff --git a/html/_modules/psi4/driver/p4util/text.html b/html/_modules/psi4/driver/p4util/text.html
index e72a31bb297..a7555e8e5ed 100644
--- a/html/_modules/psi4/driver/p4util/text.html
+++ b/html/_modules/psi4/driver/p4util/text.html
@@ -91,7 +91,7 @@ Navigation
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- 1.4rc2.dev26
+ undefined
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PSI4
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- 1.4rc2.dev26
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PSI4
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diff --git a/html/_modules/psi4/driver/p4util/util.html b/html/_modules/psi4/driver/p4util/util.html
index 5e6bd099407..2f629c0de9a 100644
--- a/html/_modules/psi4/driver/p4util/util.html
+++ b/html/_modules/psi4/driver/p4util/util.html
@@ -91,7 +91,7 @@ Navigation
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- 1.4rc2.dev26
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PSI4
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diff --git a/html/_modules/psi4/driver/pluginutil.html b/html/_modules/psi4/driver/pluginutil.html
index 14c07d12f72..60463d3f957 100644
--- a/html/_modules/psi4/driver/pluginutil.html
+++ b/html/_modules/psi4/driver/pluginutil.html
@@ -91,7 +91,7 @@ Navigation
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- 1.4rc2.dev26
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PSI4
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PSI4
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diff --git a/html/_modules/psi4/driver/procrouting/empirical_dispersion.html b/html/_modules/psi4/driver/procrouting/empirical_dispersion.html
index 97d3280df05..2cf7c03d033 100644
--- a/html/_modules/psi4/driver/procrouting/empirical_dispersion.html
+++ b/html/_modules/psi4/driver/procrouting/empirical_dispersion.html
@@ -91,7 +91,7 @@ Navigation
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PSI4
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PSI4
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diff --git a/html/_modules/psi4/driver/procrouting/interface_cfour.html b/html/_modules/psi4/driver/procrouting/interface_cfour.html
index 75c56b3fb0d..4a70d6fe74d 100644
--- a/html/_modules/psi4/driver/procrouting/interface_cfour.html
+++ b/html/_modules/psi4/driver/procrouting/interface_cfour.html
@@ -91,7 +91,7 @@ Navigation
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PSI4
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PSI4
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diff --git a/html/_modules/psi4/driver/procrouting/proc.html b/html/_modules/psi4/driver/procrouting/proc.html
index f214490ba00..9a5d99f95cf 100644
--- a/html/_modules/psi4/driver/procrouting/proc.html
+++ b/html/_modules/psi4/driver/procrouting/proc.html
@@ -91,7 +91,7 @@ Navigation
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PSI4
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diff --git a/html/_modules/psi4/driver/procrouting/proc_util.html b/html/_modules/psi4/driver/procrouting/proc_util.html
index 879e0cf9752..97ddfbafef8 100644
--- a/html/_modules/psi4/driver/procrouting/proc_util.html
+++ b/html/_modules/psi4/driver/procrouting/proc_util.html
@@ -91,7 +91,7 @@ Navigation
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PSI4
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PSI4
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diff --git a/html/_modules/psi4/driver/qcdb/molecule.html b/html/_modules/psi4/driver/qcdb/molecule.html
index fcd2bfaf6f9..fd01cc67d64 100644
--- a/html/_modules/psi4/driver/qcdb/molecule.html
+++ b/html/_modules/psi4/driver/qcdb/molecule.html
@@ -91,7 +91,7 @@ Navigation
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PSI4
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PSI4
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diff --git a/html/_modules/psi4/driver/qmmm.html b/html/_modules/psi4/driver/qmmm.html
index aef07e72062..af6074bd5a2 100644
--- a/html/_modules/psi4/driver/qmmm.html
+++ b/html/_modules/psi4/driver/qmmm.html
@@ -91,7 +91,7 @@ Navigation
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PSI4
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PSI4
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diff --git a/html/_modules/psi4/driver/util/filesystem.html b/html/_modules/psi4/driver/util/filesystem.html
index 6f9334cb7fe..28dbcfad8dd 100644
--- a/html/_modules/psi4/driver/util/filesystem.html
+++ b/html/_modules/psi4/driver/util/filesystem.html
@@ -91,7 +91,7 @@ Navigation
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PSI4
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PSI4
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diff --git a/html/_modules/psi4/driver/wrapper_database.html b/html/_modules/psi4/driver/wrapper_database.html
index 6ede7d5b000..55c7d8ded58 100644
--- a/html/_modules/psi4/driver/wrapper_database.html
+++ b/html/_modules/psi4/driver/wrapper_database.html
@@ -91,7 +91,7 @@ Navigation
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PSI4
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PSI4
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diff --git a/html/_modules/qcdb/interface_gcp.html b/html/_modules/qcdb/interface_gcp.html
index 4deacff2685..acfcd1b3c34 100644
--- a/html/_modules/qcdb/interface_gcp.html
+++ b/html/_modules/qcdb/interface_gcp.html
@@ -91,7 +91,7 @@ Navigation
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- 1.4rc2.dev26
+ undefined
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PSI4
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+ undefined
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PSI4
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diff --git a/html/_sources/autodoc_testsuite_json.rst.txt b/html/_sources/autodoc_testsuite_json.rst.txt
index f7c18a78f9d..282050d858c 100644
--- a/html/_sources/autodoc_testsuite_json.rst.txt
+++ b/html/_sources/autodoc_testsuite_json.rst.txt
@@ -8,11 +8,11 @@ JSON
======================================================= ============
Input File Description
======================================================= ============
-:srcsample:`json/schema-1-throws` test QC_JSON Schema noncontiguous mol
-:srcsample:`json/schema-1-orient` test QC_JSON Schema mol orientation
-:srcsample:`json/schema-1-properties` test QC_JSON Schema for properties
-:srcsample:`json/schema-1-gradient` test QC_JSON Schema for gradient
-:srcsample:`json/schema-1-energy` test QC_JSON Schema for energy
-:srcsample:`json/schema-1-ghost` test QC_JSON Schema with ghost atoms
+:srcsamplepy:`json/schema-1-throws` test QC_JSON Schema noncontiguous mol
+:srcsamplepy:`json/schema-1-orient` test QC_JSON Schema mol orientation
+:srcsamplepy:`json/schema-1-properties` test QC_JSON Schema for properties
+:srcsamplepy:`json/schema-1-gradient` test QC_JSON Schema for gradient
+:srcsamplepy:`json/schema-1-energy` test QC_JSON Schema for energy
+:srcsamplepy:`json/schema-1-ghost` test QC_JSON Schema with ghost atoms
======================================================= ============
diff --git a/html/_sources/autodoc_testsuite_psi4numpy.rst.txt b/html/_sources/autodoc_testsuite_psi4numpy.rst.txt
index c628acc1c08..fce7b938a9d 100644
--- a/html/_sources/autodoc_testsuite_psi4numpy.rst.txt
+++ b/html/_sources/autodoc_testsuite_psi4numpy.rst.txt
@@ -8,11 +8,11 @@ PSI4NUMPY
======================================================= ============
Input File Description
======================================================= ============
-:srcsample:`psi4numpy/cphf` Tests out the CG solver with CPHF Polarizabilities
-:srcsample:`psi4numpy/rhf-hessian` RHF Hessian code
-:srcsample:`psi4numpy/dfmp2` A simple Psi 4 input script to compute MP2 from a RHF reference
-:srcsample:`psi4numpy/rhf` A simple Psi 4 input script to compute a SCF reference using Psi4's libJK
-:srcsample:`psi4numpy/fci` coded full CI vs. detci
-:srcsample:`psi4numpy/rhf-gradient` rhf gradient code
+:srcsamplepy:`psi4numpy/cphf` Tests out the CG solver with CPHF Polarizabilities
+:srcsamplepy:`psi4numpy/rhf-hessian` RHF Hessian code
+:srcsamplepy:`psi4numpy/dfmp2` A simple Psi 4 input script to compute MP2 from a RHF reference
+:srcsamplepy:`psi4numpy/rhf` A simple Psi 4 input script to compute a SCF reference using Psi4's libJK
+:srcsamplepy:`psi4numpy/fci` coded full CI vs. detci
+:srcsamplepy:`psi4numpy/rhf-gradient` rhf gradient code
======================================================= ============
diff --git a/html/_sources/autodoc_testsuite_python.rst.txt b/html/_sources/autodoc_testsuite_python.rst.txt
index 749faae8c98..9f338a8bd61 100644
--- a/html/_sources/autodoc_testsuite_python.rst.txt
+++ b/html/_sources/autodoc_testsuite_python.rst.txt
@@ -8,15 +8,15 @@ PYTHON
======================================================= ============
Input File Description
======================================================= ============
-:srcsample:`python/mints9` A test of the basis specification. Various basis sets are specified outright and in blocks, both orbital and auxiliary. Constructs libmints BasisSet objects through the constructor that calls qcdb.BasisSet infrastructure. Checks that the resulting bases are of the right size and checks that symmetry of the Molecule observes the basis assignment to atoms.
-:srcsample:`python/curve` PsiAPI scanning a potential energy curve
-:srcsample:`python/cc54` CCSD dipole with user-specified basis set
-:srcsample:`python/mints13` test fragment decomposition + to/from_dict
-:srcsample:`python/energy` PsiAPI energy example
-:srcsample:`python/mints2` A test of the basis specification. A benzene atom is defined using a ZMatrix containing dummy atoms and various basis sets are assigned to different atoms. The symmetry of the molecule is automatically lowered to account for the different basis sets.
-:srcsample:`python/mints14` Check for correctness of ESP values. The ESP values are calculated using one or four threads The one thread values are checked against the four thread values. The one thread values are also checked against the reference values (1 thread values computed, when generating this test). Caution: The reference values are not obtained using an actual physical reference, but rather generated by Psi4 at one point in time.
-:srcsample:`python/cc-amps` API access to CCSD amplitudes
-:srcsample:`python/pubchem` PsiAPI pubchem access
-:srcsample:`python/3-index-transforms` examine JK packing forms
+:srcsamplepy:`python/mints9` A test of the basis specification. Various basis sets are specified outright and in blocks, both orbital and auxiliary. Constructs libmints BasisSet objects through the constructor that calls qcdb.BasisSet infrastructure. Checks that the resulting bases are of the right size and checks that symmetry of the Molecule observes the basis assignment to atoms.
+:srcsamplepy:`python/curve` PsiAPI scanning a potential energy curve
+:srcsamplepy:`python/cc54` CCSD dipole with user-specified basis set
+:srcsamplepy:`python/mints13` test fragment decomposition + to/from_dict
+:srcsamplepy:`python/energy` PsiAPI energy example
+:srcsamplepy:`python/mints2` A test of the basis specification. A benzene atom is defined using a ZMatrix containing dummy atoms and various basis sets are assigned to different atoms. The symmetry of the molecule is automatically lowered to account for the different basis sets.
+:srcsamplepy:`python/mints14` Check for correctness of ESP values. The ESP values are calculated using one or four threads The one thread values are checked against the four thread values. The one thread values are also checked against the reference values (1 thread values computed, when generating this test). Caution: The reference values are not obtained using an actual physical reference, but rather generated by Psi4 at one point in time.
+:srcsamplepy:`python/cc-amps` API access to CCSD amplitudes
+:srcsamplepy:`python/pubchem` PsiAPI pubchem access
+:srcsamplepy:`python/3-index-transforms` examine JK packing forms
======================================================= ============
diff --git a/html/_sources/basissets_tables.rst.txt b/html/_sources/basissets_tables.rst.txt
index 6d25e51678c..dc674751c84 100644
--- a/html/_sources/basissets_tables.rst.txt
+++ b/html/_sources/basissets_tables.rst.txt
@@ -57,7 +57,7 @@ approximations. JKFIT sets are appropriate for fitting :math:`(oo|`\ -type produ
such as encountered in SCF theory and the electrostatics/exchange terms of SAPT.
RI sets are appropriate for fitting :math:`(ov|`\ -type products, such as encountered in
MP2 and most SAPT terms. Citations for basis sets can be found in their
-definition files at :source:`share/basis` in the source. For basis set availability by
+definition files at :source:`psi4/share/psi4/basis` in the source. For basis set availability by
element and the default value for keyword |globals__puream|, consult
Appendix :ref:`apdx:basisElement`.
diff --git a/html/_sources/bibliography.rst.txt b/html/_sources/bibliography.rst.txt
index 2a1ad73ca87..6dc7ea6ad3c 100644
--- a/html/_sources/bibliography.rst.txt
+++ b/html/_sources/bibliography.rst.txt
@@ -110,7 +110,7 @@ Bibliography
Integrated Platform of Small Molecules and Biological Activities,
Chapter 12 in *Annual Reports in Computational Chemistry*, Volume
4 (American Chemical Society: Washington, DC, 2008).
- See `pubchem.ncbi.nlm.nih.gov `_.
+ See https://pubchem.ncbi.nlm.nih.gov/.
.. [Sherrill:1999:CI]
C. D. Sherrill and H. F. Schaefer,
diff --git a/html/_sources/build_planning.rst.txt b/html/_sources/build_planning.rst.txt
index dcdfa2edd34..47a61140709 100644
--- a/html/_sources/build_planning.rst.txt
+++ b/html/_sources/build_planning.rst.txt
@@ -201,9 +201,9 @@ that software for |PSIfour| and any notes and warnings pertaining to it.
* :ref:`Python interpreter and headers ` (3.6 or 3.7) https://www.python.org/
-* CMake (3.8+) http://www.cmake.org/download/
+* CMake (3.8+) https://cmake.org/download/
-* NumPy (needed at runtime *and* buildtime) http://www.numpy.org/
+* NumPy (needed at runtime *and* buildtime) https://numpy.org/
* System utilities: GNU make, GNU install, POSIX threads (Pthreads) library
@@ -214,9 +214,9 @@ build system will automatically download and build.
* :ref:`Libint ` |w---w| :ref:`[what is Libint?] ` `[Libint min version] `_
-* :ref:`Libxc ` |w---w| :ref:`[what is Libxc?] ` `[Libxc min version] `_
+* :ref:`Libxc ` |w---w| :ref:`[what is Libxc?] ` `[Libxc min version] `_
-* pybind11 |w---w| `[what is Pybind11?] `_ `[Pybind11 min version] `_
+* pybind11 |w---w| `[what is Pybind11?] `_ `[Pybind11 min version] `_
* QCElemental |w---w| `[what is QCElemental?] `_
@@ -224,7 +224,7 @@ build system will automatically download and build.
Additionally, there are runtime-only dependencies:
-* NumPy http://www.numpy.org/
+* NumPy https://numpy.org/
* networkx https://github.com/networkx/networkx (transitive dependency of QCElemental; optional for QCElemental but required for |PSIfour|)
@@ -253,14 +253,14 @@ are available pre-built from conda.
* |PSIfour| Testing
- * CTest http://www.cmake.org/download/
- * Perl (for some coupled-cluster CTest tests) http://perl.org
+ * CTest https://cmake.org/download/
+ * Perl (for some coupled-cluster CTest tests) https://www.perl.org/
* pytest (for installed testing) http://doc.pytest.org/en/latest/
-* |PSIfour| Documentation (available pre-built at http://www.psicode.org/psi4manual/master/index.html)
+* |PSIfour| Documentation (available pre-built at :psicode:`psi4manual/master/index.html`)
* Sphinx (1.5+) http://sphinx-doc.org
- * Perl (for some auto-documentation scripts) http://perl.org
+ * Perl (for some auto-documentation scripts) https://www.perl.org/
* nbsphinx (for converting Jupyter notebooks) http://nbsphinx.readthedocs.io/en/jupyter-theme/
* sphinx-psi-theme https://github.com/psi4/sphinx-psi-theme
* See `["message" lines] `_ for advice on obtaining docs dependencies
@@ -972,7 +972,7 @@ How to obtain C and C++ compilers for Mac without Fink, MacPorts, or Homebrew
The easiest compiler to obtain is ``clang`` which is a drop-in replacement
for ``gcc`` and ``g++``. Just install `XCode
-`_. Some old versions
+`_. Some old versions
of XCode can't handle some of the advanced C++ language features, but this
is a *software* not *hardware* limitation. Checks for version compliance
performed at build-time. Note that this "AppleClang" will not be compatible
@@ -1550,7 +1550,7 @@ CTest allows flexibly partitioned running of the test suite. In
the examples below, *testname* are regex of :source:`test names `,
and *testlabel* are regex of labels (*e.g.*, ``cc``, ``mints``,
``libefp`` defined `[here, for example]
-`_.
+`_.
* Run tests in parallel with ``-j`` flag. For maximum parallelism: :samp:`ctest -j\`getconf _NPROCESSORS_ONLN\`\ `
* Run full test suite: ``ctest``
diff --git a/html/_sources/cfour.rst.txt b/html/_sources/cfour.rst.txt
index 066eadc18b2..124a2893486 100644
--- a/html/_sources/cfour.rst.txt
+++ b/html/_sources/cfour.rst.txt
@@ -143,7 +143,7 @@ illustrated in the following example::
Here, the contents of the ``cfour {...}`` block are written directly to a
``ZMAT`` file. This is joined by a default ``GENBAS`` file
-(:source:`share/basis/GENBAS`). To preferentially use your own ``GENBAS``,
+(:source:`psi4/share/psi4/basis/GENBAS`). To preferentially use your own ``GENBAS``,
place it in :envvar:`PATH` or :envvar:`PSIPATH`. The line calling
:py:func:`~psi4.energy` with argument ``'cfour'`` invokes
:program:`xcfour`.
diff --git a/html/_sources/conda.rst.txt b/html/_sources/conda.rst.txt
index 9af4c02dde3..17cd3013a90 100644
--- a/html/_sources/conda.rst.txt
+++ b/html/_sources/conda.rst.txt
@@ -43,10 +43,10 @@ through `Anaconda (formerly Continuum Analytics
`_, the company that produces
`Anaconda Python `_ (a
full-fledged scientific python environment with package manager `conda
-`_) and, more particularly, `Miniconda
-`_ (a lightweight python
+`_) and, more particularly, `Miniconda
+`_ (a lightweight Python
distribution with same package manager `conda
-`_). Some nice features for us:
+`_). Some nice features for us:
* cross-platform
@@ -67,8 +67,7 @@ distribution with same package manager `conda
The |PSIfour| binary repository is at `Anaconda (formerly Binstar) `_.
For commands to get a default installation, go to :ref:`sec:psi4conda`
-or the `psicode downloads page `_
-(`pre-release downloads page `_).
+or the `psicode downloads page `_.
Users proficient with conda may prefer to consult :ref:`sec:condadetails`.
For more flexibility and a detailed explanation, go to
:ref:`sec:slowconda` and :ref:`sec:slowpsi4`.
@@ -434,7 +433,7 @@ Detailed Installation of Miniconda
Detailed Installation of |PSIfour|
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-5. Subscribe to |PSIfour|. Subscribe to our channel at http://anaconda.org/psi4 that contains the |PSIfour| package and several dependency packages. Make sure this shows up in your ``~/.condarc`` file.
+5. Subscribe to |PSIfour|. Subscribe to our channel at https://anaconda.org/psi4 that contains the |PSIfour| package and several dependency packages. Make sure this shows up in your ``~/.condarc`` file.
.. code-block:: bash
@@ -454,7 +453,7 @@ Detailed Installation of |PSIfour|
>>> which psi4
/path/to/miniconda/bin/psi4
-Or, you can install into a `conda environment `_ that places |PSIfour| and its dependencies (including python) into a sandbox unaffected by any other software installed in Ana/Miniconda. This is recommended for developers to avoid interference between multiple versions (including github/conda versions) or to test python versions, *etc.*. In practical terms, installing into a conda environment means you can turn |PSIfours| availability on/off by switching conda environments without turning on/off the whole Ana/Miniconda installation. Below, |PSIfour| is installed into an environment called ``p4env``. Then the environment is activated, removing the main Ana/Miniconda ``bin`` and adding ``envs/p4env/bin`` to :envvar:`PATH`. The ``conda activate`` command (conda >=4.4; December 2017) works in all shells, but if you're using old ``source activate`` that only works for ``bash``; adjust as needed for ``csh``/``tcsh``.
+Or, you can install into a `conda environment `_ that places |PSIfour| and its dependencies (including python) into a sandbox unaffected by any other software installed in Ana/Miniconda. This is recommended for developers to avoid interference between multiple versions (including github/conda versions) or to test python versions, *etc.*. In practical terms, installing into a conda environment means you can turn |PSIfours| availability on/off by switching conda environments without turning on/off the whole Ana/Miniconda installation. Below, |PSIfour| is installed into an environment called ``p4env``. Then the environment is activated, removing the main Ana/Miniconda ``bin`` and adding ``envs/p4env/bin`` to :envvar:`PATH`. The ``conda activate`` command (conda >=4.4; December 2017) works in all shells, but if you're using old ``source activate`` that only works for ``bash``; adjust as needed for ``csh``/``tcsh``.
.. code-block:: bash
diff --git a/html/_sources/documentation.rst.txt b/html/_sources/documentation.rst.txt
index 806c5a224fe..893436f1fc0 100644
--- a/html/_sources/documentation.rst.txt
+++ b/html/_sources/documentation.rst.txt
@@ -33,7 +33,7 @@
Updating the |PSIfour| Users' and Programmers' Manual
=====================================================
-|PSIfours| documentation is generated by `Sphinx `_
+|PSIfours| documentation is generated by `Sphinx `_
and lives in :source:`doc/sphinxman`. It is available online at
``_
for the latest development branch.
@@ -50,6 +50,7 @@ The sphinx executable should be in your path at CMake configure time for
documentation targets to be available.
* Binary: ``conda install sphinx``
+* Binary: ``conda env create -f devtools/conda-envs/docs-cf.yaml``
* Binary: ``pip install -U Sphinx``
* Source: https://pypi.org/project/Sphinx/
@@ -57,8 +58,8 @@ documentation targets to be available.
>>> which sphinx-build
//anaconda/bin/sphinx-build
- >>> sphinx-build --version # needs >= 1.4
- Sphinx (sphinx-build) 1.4.1
+ >>> sphinx-build --version # needs >= 3.5
+ Sphinx (sphinx-build) 3.5.3
>>> cmake
...
-- Documentation targets available: sphinxman (html), sphinxmini (quick html), sphinxpdf (LaTeX --> PDF)
@@ -75,9 +76,13 @@ documentation is a unified document covering information for both users
and programmers in separate sections. From the top-level object directory,
build the following target (note that a working version of the |PSIfour|
executable is a requirement for building the
-documentation).::
+documentation). Only GNU Makefiles, not Ninja, works for the docs:
+
+.. code-block:: console
>>> make sphinxman
+ # -OR-
+ >>> cmake --build . --target sphinxman
This will build a full set of documentation in the ``html`` directory that can be viewed offline through any browser. ::
@@ -108,11 +113,11 @@ this covers:
Some documentation is even extracted from |PSIfour| objects at runtime.
-* psi4: docstrings for the psi4 built-in module constructed in :source:`psi4/src/psi4`
-* DFT: functional availability and characteristics as encoded in :source:`psi4/driver/procedures/dft_functional.py`
+* psi4: docstrings for the C++ submodule ``psi4.core`` and the Python submodule ``psi4.driver`` that comprise |PSIfour|. C++ docstrings from "core" and "export" files in :source:`psi4/src/`, and Py docstrings from :source:`psi4/driver/`.
+* DFT: functional availability and characteristics as encoded in :source:`psi4/driver/procrouting/dft`
* BasisFamily: fitting basis sets for each orbital basis as encoded in :source:`psi4/driver/qcdb/basislistdunning.py` and :source:`psi4/driver/qcdb/basislistother.py`
-Building all the documentation takes ~15 minutes. There is now good
+Building all the documentation takes ~10 minutes. There is now good
dependency structure built into the :source:`doc/sphinxman/CMakeLists.txt`
, so very long builds should be infrequent (unless you're touching
:source:`psi4/src/read_options.cc` or the driver. Note that not all dependencies are
@@ -120,7 +125,7 @@ encoded (PSI variables, for instance, depend on every .cc file in the
source tree), so for a definitive doc build, remove (in the object
directory) ``doc/sphinxman`` and start from scratch.
-Even ~15 minutes of build time can be annoying when developing
+Even ~10 minutes of build time can be annoying when developing
documentation and testing ``rst`` files. In that situation, use the target
below which builds only the written docs (not autodocs) in
``psi4/doc/sphinxman/source`` quickly, though with a lot of warnings for
@@ -136,10 +141,11 @@ documentation, source code is available from the sidebar. Here are a
few resources on Sphinx formatting.
* `reStructuredText `_
+* `links example `_
* `rendered test document `_
*vs.* `source test document `_
* `A third reStructuredText and Sphinx `_
-* `Sphinx Docs `_
+* `Sphinx Docs `_
.. * `Another reStructuredText `_
.. * `LaTeX that Sphinx can handle `_
diff --git a/html/_sources/fchk.rst.txt b/html/_sources/fchk.rst.txt
index 4d52fb33f34..1d00fb5aa0a 100644
--- a/html/_sources/fchk.rst.txt
+++ b/html/_sources/fchk.rst.txt
@@ -41,7 +41,7 @@ Interface to programs through FCHK files |w---w| :py:func:`~psi4.fchk()`
.. sectionauthor:: Andrew C. Simmonett
Many post-processing tools can read information from `Gaussian's formatted
-checkpoint (FCHK) files `_.
+checkpoint (FCHK) files `_.
To allow interoperability with such tools, |PSIfour| includes a utility to
generate FCHK files. Wavefunction information, such as orbitals, densities,
orbital energies and basis set information is currently supported, but geometry
diff --git a/html/_sources/introduction.rst.txt b/html/_sources/introduction.rst.txt
index c930c2849b5..c353ab97d7e 100644
--- a/html/_sources/introduction.rst.txt
+++ b/html/_sources/introduction.rst.txt
@@ -584,7 +584,7 @@ Architectures
Linux aka `Bash on Ubuntu on Windows
`_)
or as source code (git repository or zipped archive from
- `https://github.com/psi4/psi4 `_).
+ https://github.com/psi4/psi4.
Compilers
|PSIfour| has been successfully compiled using Intel, GCC, and Clang
compilers. :ref:`Compiler requirements ` are primarily
diff --git a/html/_sources/libefp.rst.txt b/html/_sources/libefp.rst.txt
index 29d4dc69982..a59ce0057b1 100644
--- a/html/_sources/libefp.rst.txt
+++ b/html/_sources/libefp.rst.txt
@@ -38,17 +38,17 @@ Interface to LIBEFP by I. Kaliman
.. codeauthor:: Andrew C. Simmonett, A. Eugene DePrince III, Rollin A. King, and Lori A. Burns
.. sectionauthor:: Lori A. Burns
-*Module:* :ref:`Keywords `, :ref:`PSI Variables `, :source:`LIBEFP `
+*Module:* :ref:`Keywords `, :ref:`PSI Variables `, :source:`LIBEFP `
.. image:: https://img.shields.io/badge/home-libefp-5077AB.svg
- :target: https://github.com/ilyak/libefp
+ :target: https://github.com/libefp2/libefp
.. raw:: html
.. image:: https://img.shields.io/badge/docs-latest-5077AB.svg
- :target: http://www.libefp.org/
+ :target: https://github.com/libefp2/libefp
|PSIfour| contains code to interface to the LIBEFP library developed
in L. Slipchenko's group by I. Kaliman. LIBEFP
diff --git a/html/_sources/libxc.rst.txt b/html/_sources/libxc.rst.txt
index 9d3067a1d96..c1b5070a94d 100644
--- a/html/_sources/libxc.rst.txt
+++ b/html/_sources/libxc.rst.txt
@@ -48,7 +48,7 @@ Interface to Libxc by M. A. L. Marques
.. image:: https://img.shields.io/badge/docs-latest-5077AB.svg
- :target: https://gitlab.com/libxc/libxc/wikis/Manual-4.0
+ :target: https://www.tddft.org/programs/libxc/manual/
|PSIfour|, relies upon the Libxc library for density functionals. Libxc
requires no
diff --git a/html/_sources/manage_addon.rst.txt b/html/_sources/manage_addon.rst.txt
index d85c57d801e..0bf92e17f9a 100644
--- a/html/_sources/manage_addon.rst.txt
+++ b/html/_sources/manage_addon.rst.txt
@@ -127,19 +127,19 @@ How to integrate an Add-On into build, testing, and docs
or simint with respect to libmints. Again, conditionalize as in
preceding bullet.
-* :source:`psi4/external/upstream/`
+* :source:`external/upstream/`
* Add a CMakeLists.txt that imitates another AddOn of similar
language and dependencies. Try to keep the format, messaging,
and variables passed as similar as possible so that differences
mean something. If BLAS/LAPACK or other common dependencies in
- :source:`psi4/common/` are needed, be sure to add them to the
+ :source:`external/common` are needed, be sure to add them to the
``DEPENDS`` argument.
* The usual practice to to get everything cohesive between
the CMake for the AddOn repository and |PSIfour| and then as a
last step, mint a tag in the former and add it to two places in
- :samp:`psi4/external/upstream/{addon_name}/CMakeLists.txt` and one
+ :samp:`external/upstream/{addon_name}/CMakeLists.txt` and one
place in :source:`psi4/CMakeLists.txt` so that only that version
and later are acceptable to |PSIfour| for detecting pre-built.
diff --git a/html/_sources/manage_release.rst.txt b/html/_sources/manage_release.rst.txt
index 350e00d9047..20bbc359b8a 100644
--- a/html/_sources/manage_release.rst.txt
+++ b/html/_sources/manage_release.rst.txt
@@ -135,8 +135,7 @@ Anticipate next release
-----------------------
* Bump version in ``codemeta.json``, https://github.com/psi4/psi4/blob/master/codemeta.json#L9
-* Add to branch list in ``.travis.yml``, https://github.com/psi4/psi4/blob/master/.travis.yml#L179
-* Add to branch list in ``azure-pipelines.yml``, https://github.com/psi4/psi4/blob/master/azure-pipelines.yml#L4
+* Add to branch list in ``azure-pipelines.yml``, :source:`azure-pipelines.yml`
Build Conda ecosystem stack
@@ -144,7 +143,7 @@ Build Conda ecosystem stack
By "ecosystem stack", mean packages that are upstream, downstream, required, and optional for a fully featured Psi4 build and which we can't get from "defaults" or "conda-forge" channels.
-* Main directions are in [cbcy](https://github.com/psi4/psi4meta/blob/master/conda-recipes/conda_build_config.yaml#L90-L103) and [poodle](https://github.com/psi4/psi4meta/blob/master/psinet-nightly/kitandkapoodle.py#L357-L411)
+* Main directions are in [cbcy](https://github.com/psi4/psi4meta/blob/master/conda-recipes/conda_build_config.yaml) and [poodle](https://github.com/psi4/psi4meta/blob/master/psinet-nightly/kitandkapoodle.py)
* A couple weeks before the first "rc" is planned, start going through L/LT in poodle, checking with upstream to see if new versions have been released. If good changes present, rebuild the packages, changing the version numbers in the respective recipes
* When L/LT all built and passed, edit the individual package version numbers in cbcy and increment to a new ``ltrtver`` with updated version numbers and/or build numbers (only if code changes)
* Build L/PSI4. If any trouble, edit psi4 code. Iterate until builds and passes. This stage is the only full ctest & pytest on Psi4+upstream
@@ -185,8 +184,8 @@ Tweak Conda for postrelease
Do final pass before release tag
--------------------------------
-* Check that ``external/`` repos and commits have been updated to match conda recipes sources. Also check versions with ``conda_build_config.yaml``
-* Check ``docs/sphinxman/source/introduction.rst`` for any compiler and Python minimum requirements to edit.
+* Check that :source:`external/` repos and commits have been updated to match conda recipes sources. Also check versions with ``conda_build_config.yaml``
+* Check :source:`docs/sphinxman/source/introduction.rst` for any compiler and Python minimum requirements to edit.
Tag (pre)release
diff --git a/html/_sources/molden.rst.txt b/html/_sources/molden.rst.txt
index dd3437cc02d..1a478a9a01b 100644
--- a/html/_sources/molden.rst.txt
+++ b/html/_sources/molden.rst.txt
@@ -44,8 +44,8 @@ Interface to Molden |w---w| :py:func:`~psi4.molden`
|PSIfour| contains an interface to the Molden program. Molden is a
visualization program for electronic structure developed by Gijs Schaftenaar
at the University of of Nijmegen, Netherlands. It is available at
-`http://www.cmbi.ru.nl/molden/ `_. Molden can
-plot atomic orbitals, densities, electrostatic potentials (ESP's), etc.
+https://www3.cmbi.umcn.nl/molden/ . Molden can
+plot atomic orbitals, densities, electrostatic potentials (ESPs), etc.
|PSIfour| can create a file containing
atomic coordinates, basis set, and SCF orbital coefficients in the
so-called Molden format. This file is
diff --git a/html/_sources/mrcc.rst.txt b/html/_sources/mrcc.rst.txt
index 9e72521a91d..d96af5a74d7 100644
--- a/html/_sources/mrcc.rst.txt
+++ b/html/_sources/mrcc.rst.txt
@@ -38,7 +38,7 @@ Interface to MRCC by M. K\ |a_acute|\ llay
.. sectionauthor:: Justin M. Turney
-*Module:* :ref:`Keywords `, :ref:`PSI Variables `, :source:`MRCC `, :ref:`Samples `
+*Module:* :ref:`Keywords `, :ref:`PSI Variables `, :source:`MRCC `
|PSIfour| contains code to interface to the MRCC program of M. K\ |a_acute|\ llay
and J. Gauss. The license and source code of the MRCC program must be
diff --git a/html/_sources/optionshandling.rst.txt b/html/_sources/optionshandling.rst.txt
index 1b02f18b771..be7750b8bf4 100644
--- a/html/_sources/optionshandling.rst.txt
+++ b/html/_sources/optionshandling.rst.txt
@@ -55,7 +55,7 @@ Declaring Options
Each module needs to make itself known to the Options object, via a
read_options function. For plugins, this routine is provided by the user
in the plugin code. For native |PSIfour| modules, the entries need to
-be appended to the read_options code in :source:`src/bin/psi4/read_options.cc`.
+be appended to the read_options code in :source:`psi4/src/read_options.cc`.
An example of such a routine is
.. code-block:: cpp
@@ -118,7 +118,7 @@ As is apparent from the examples above, comments can span multiple lines
see ``DOCC``), and can contain LaTeX notation (see ``AO_BASIS``). (To get
the LaTeX subscript command, use "@@" instead of "_".)
-See `Best Practices `_
+See :ref:`faq:readoptions`
for guidelines on naming options.
What is *has_changed* ?
diff --git a/html/_sources/pcmsolver.rst.txt b/html/_sources/pcmsolver.rst.txt
index ee7d9535fcf..ae068512122 100644
--- a/html/_sources/pcmsolver.rst.txt
+++ b/html/_sources/pcmsolver.rst.txt
@@ -38,7 +38,7 @@ Interface to PCMSolver by R. Di Remigio
.. codeauthor:: Roberto Di Remigio, T. Daniel Crawford, Andrew C. Simmonett
.. sectionauthor:: Roberto Di Remigio
-*Module:* :ref:`Keywords `, :ref:`PSI Variables `, :source:`PCMSolver `
+*Module:* :ref:`Keywords `, :ref:`PSI Variables `, :source:`PCMSolver `
.. image:: https://img.shields.io/badge/home-PCMSolver-5077AB.svg
:target: https://github.com/PCMSolver/pcmsolver
diff --git a/html/_sources/pep0001.rst.txt b/html/_sources/pep0001.rst.txt
index 8bebfb7f6a9..76ec5daf522 100644
--- a/html/_sources/pep0001.rst.txt
+++ b/html/_sources/pep0001.rst.txt
@@ -56,7 +56,7 @@ PEP1: Proposing PsiPEP for |PSIfour|
This document proposes using a (much more informal) version of Python's
PEP (Python Enhancement Proposal `PEP1
-`_) protocol to organize
+`_) protocol to organize
|PSIfour|. Presently, topics are brought up on e-mail threads (where
discussion is very temporally localized and not everyone is aware of it
unless cc'd), are brought up at workshops (where people may be absent, no
@@ -69,9 +69,9 @@ code).
Path of a PsiPEP
----------------
-* Someone creates a file ``psi4/doc/sphinxman/source/pepXXXX.rst`` modeled
+* Someone creates a file ``doc/sphinxman/source/pepXXXX.rst`` modeled
on :source:`doc/sphinxman/source/pep0000model.rst` and adds
- it to ``STATICDOC`` in :source:`doc/sphinxman/Makefile.in`. The file
+ it to ``STATICDOC`` in :source:`doc/sphinxman/CMakeLists.txt`. The file
should have header fields modeled on another PsiPEP and a discussion of
the proposed change or practice.
diff --git a/html/_sources/proc_py.rst.txt b/html/_sources/proc_py.rst.txt
index ae99b3f0863..92e03f36b17 100644
--- a/html/_sources/proc_py.rst.txt
+++ b/html/_sources/proc_py.rst.txt
@@ -150,7 +150,7 @@ keyword |globals__qc_module| and a set of type keywords analogous to
shared among modules rather than (or in addition to) being used internally
by the module). We're sticking with |globals__scf_type| and
|globals__mp2_type| defaulting to ``DF``, while everything higher defaults
-to ``CONV``. In :source:`share/python/driver.py`, a managed method calls a
+to ``CONV``. In :source:`psi4/driver/driver.py`, a managed method calls a
"select" function rather than a "run" function. ::
procedures = {
@@ -159,7 +159,7 @@ to ``CONV``. In :source:`share/python/driver.py`, a managed method calls a
'mp3' : select_mp3,
'dct' : run_dct,
-Then in :source:`share/python/proc.py`, the select function runs through
+Then in :source:`psi4/driver/procrouting/proc.py`, the select function runs through
reference (always outer loop) and type (inner loop) to specify the proc
function to call for any able, non-default module (*e.g.*, ``mtd_type ==
'DETCI'`` ) or able, default module (*e.g.*, ``mtd_typd == ['', 'FNOCC']`` ).
diff --git a/html/_sources/prog_help.rst.txt b/html/_sources/prog_help.rst.txt
index 91e8fc7a97e..5e24d88413d 100644
--- a/html/_sources/prog_help.rst.txt
+++ b/html/_sources/prog_help.rst.txt
@@ -37,7 +37,7 @@ Where to Get Help
Slack
-----
-|PSIfour| has an active `Slack channel `_
+|PSIfour| has an active `Slack channel `_
for developers, and a friendly community willing to answer your questions.
Reporting Bugs
diff --git a/html/_sources/prog_tour.rst.txt b/html/_sources/prog_tour.rst.txt
index 39a8cd43ebf..0492cc9b592 100644
--- a/html/_sources/prog_tour.rst.txt
+++ b/html/_sources/prog_tour.rst.txt
@@ -60,7 +60,7 @@ Wavefunction should be called::
set_variable("Variable Name", variable_value);
The new variable should also be documented in
-:source:`psi4/doc/sphinxman/source/glossary_psivariables.rst`. There are a
+:source:`doc/sphinxman/source/glossary_psivariables.rst`. There are a
number of different helpers to export various quantities from the wavefunction
to external formats such as FCHK and MOLDEN. Because the Wavefunction makes
its members available to the Python layer, any other similar export functions
diff --git a/html/_sources/psiapi.ipynb.txt b/html/_sources/psiapi.ipynb.txt
index ade1f38d519..a9063fecf55 100644
--- a/html/_sources/psiapi.ipynb.txt
+++ b/html/_sources/psiapi.ipynb.txt
@@ -141,7 +141,7 @@
"@DF-RHF Final Energy: -76.02663273486682\n",
"~~~\n",
"\n",
- "By default, the energy should be converged to about $1.0\\times 10^{-6}$, so agreement is only expected for about the first 6 digits after the decimal. If the computation does not complete, there is probably a problem with the compilation or installation of the program (see the installation instructions in the main Psi4 manual section [Compiling and Installing from Source](http://psicode.org/psi4manual/master/external.html#sec-installfile \"Go to Psi4 Manual\")).\n",
+ "By default, the energy should be converged to about $1.0\\times 10^{-6}$, so agreement is only expected for about the first 6 digits after the decimal. If the computation does not complete, there is probably a problem with the compilation or installation of the program (see the installation instructions in the main Psi4 manual section [Compiling and Installing from Source](https://psicode.org/psi4manual/master/build_planning.html \"Go to Psi4 Manual\")).\n",
"\n",
"This very simple input is sufficient to run the requested information. Notice we didn't tell the program some otherwise useful information like the charge of the molecule (0, it's neutral), the spin multiplicity (1 for a closed-shell molecule with all electrons paired), or the reference wavefunction to use (restricted Hartree-Fock, or RHF, is usually appropriate for a closed-shell molecule). The program correctly guessed all of these options for us. We can change the default behavior through additional keywords."
]
diff --git a/html/_sources/psithonmol.rst.txt b/html/_sources/psithonmol.rst.txt
index e3c3bedf26f..e2fafa59259 100644
--- a/html/_sources/psithonmol.rst.txt
+++ b/html/_sources/psithonmol.rst.txt
@@ -282,7 +282,7 @@ or ::
}
will generate a helium dimer with the second atom ghosted, *i.e.*, possessing
-basis functions but no electrons or nuclear charge. See :srcsample:`dfmp2_1`
+basis functions but no electrons or nuclear charge. See :srcsample:`dfmp2-1`
and :srcsample:`ghosts` for a demonstration of both mechanisms for specifying
ghost atoms.
@@ -311,7 +311,7 @@ molecule's point group symmetry. ::
}
The masses used by |PSIfour| can be found at
-:source:`psi4/include/psi4/masses.h`. See :srcsample:`freq-isotope` for about
+:source:`psi4/include/psi4/masses.h`. See :srcsample:`freq-isotope2` for about
the only use to which isotopologues can presently be put in |PSIfour|.
.. index::
diff --git a/html/_sources/quickadddatabase.rst.txt b/html/_sources/quickadddatabase.rst.txt
index b734f1f9885..46756bed5bc 100644
--- a/html/_sources/quickadddatabase.rst.txt
+++ b/html/_sources/quickadddatabase.rst.txt
@@ -76,11 +76,10 @@ below.
- The third and subsequent lines have four fields: the element symbol and the three cartesian coordinates in angstroms. The atom lines should not contain any dummy atoms (what's the use in cartesian form). For dimer systems, an algorithm is used to apportion the atoms into two fragments; thus the atoms need not be arranged with all fragmentA atoms before all fragmentB atoms. The algorithm will fail for very closely arranged fragments. For dimers, any charge and multiplicity from the second line will be applied to fragmentA (python); charge and multiplicity may need to be redistributed later in the editing step.
-* Run script :source:`share/scripts/ixyz2database.py`
+* Run script :source:`psi4/share/psi4/scripts/ixyz2database.py`
Move into the directory where all your xyz files are located. Run the
- script, probably as ``$PSIDATADIR/scripts/ixyz2database.py``. (If you
- run it in place, there won't be any path problems. It will ask a number of
+ script. It will ask a number of
questions about your intended database and generate a python file
named for your database. Uppercase is preferable for database names
(according to Sherrill lab convention). Note your choice for the route
@@ -90,7 +89,7 @@ below.
According to your responses in to questions in the ixyz2database.py script,
several bullets will be printed of edits you necessarily or optionally
- should make. Copy your new database into :source:`share/databases`.
+ should make. Copy your new database into :source:`psi4/share/psi4/databases`.
Alternately, append the directory containing your new database into
:envvar:`PSIPATH`.
diff --git a/html/_sources/thermo.rst.txt b/html/_sources/thermo.rst.txt
index f167c557103..240a9a9c76d 100644
--- a/html/_sources/thermo.rst.txt
+++ b/html/_sources/thermo.rst.txt
@@ -39,7 +39,7 @@ Vibrational and Thermochemical Analysis
.. codeauthor:: Rollin A. King and Lori A. Burns
.. sectionauthor:: Lori A. Burns
-*Module:* :ref:`Keywords `, :ref:`PSI Variables `, :source:`THERMO `
+*Module:* :ref:`Keywords `, :ref:`PSI Variables `, :source:`THERMO `
.. caution:: It is important to know that |PSIfour|, like any other
diff --git a/html/_static/documentation_options.js b/html/_static/documentation_options.js
index 36022f9938e..8e8f50c0181 100644
--- a/html/_static/documentation_options.js
+++ b/html/_static/documentation_options.js
@@ -1,6 +1,6 @@
var DOCUMENTATION_OPTIONS = {
URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
- VERSION: 'f5b7cf9',
+ VERSION: '2768887',
LANGUAGE: 'None',
COLLAPSE_INDEX: false,
BUILDER: 'html',
diff --git a/html/adc.html b/html/adc.html
index a69b4f4c1dc..d832fdcac59 100644
--- a/html/adc.html
+++ b/html/adc.html
@@ -102,7 +102,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
·
PSI4
@@ -685,7 +685,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
·
PSI4
@@ -699,7 +699,7 @@ Navigation
diff --git a/html/adcc.html b/html/adcc.html
index 40fbdb3b254..08de8635d58 100644
--- a/html/adcc.html
+++ b/html/adcc.html
@@ -102,7 +102,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
·
PSI4
@@ -405,7 +405,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
·
PSI4
@@ -419,7 +419,7 @@ Navigation
diff --git a/html/add_tests.html b/html/add_tests.html
index 7f6d9db58fa..1907b19dc6e 100644
--- a/html/add_tests.html
+++ b/html/add_tests.html
@@ -102,7 +102,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
·
PSI4
@@ -316,7 +316,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
·
PSI4
@@ -329,7 +329,7 @@ Navigation
diff --git a/html/api/psi4.core.AOShellCombinationsIterator.html b/html/api/psi4.core.AOShellCombinationsIterator.html
index f2cd8b089ce..d239889b5ff 100644
--- a/html/api/psi4.core.AOShellCombinationsIterator.html
+++ b/html/api/psi4.core.AOShellCombinationsIterator.html
@@ -102,7 +102,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
·
PSI4
@@ -309,7 +309,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
·
PSI4
@@ -323,7 +323,7 @@ Navigation
diff --git a/html/api/psi4.core.AngularMomentumInt.html b/html/api/psi4.core.AngularMomentumInt.html
index d7f77ea04d8..0f33625329d 100644
--- a/html/api/psi4.core.AngularMomentumInt.html
+++ b/html/api/psi4.core.AngularMomentumInt.html
@@ -102,7 +102,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
·
PSI4
@@ -292,7 +292,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
·
PSI4
@@ -306,7 +306,7 @@ Navigation
diff --git a/html/api/psi4.core.BSVec.html b/html/api/psi4.core.BSVec.html
index 60edc03da0f..60da006c224 100644
--- a/html/api/psi4.core.BSVec.html
+++ b/html/api/psi4.core.BSVec.html
@@ -102,7 +102,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
·
PSI4
@@ -315,7 +315,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
·
PSI4
@@ -329,7 +329,7 @@ Navigation
diff --git a/html/api/psi4.core.BasisExtents.html b/html/api/psi4.core.BasisExtents.html
index d488526b9ee..eec5073c661 100644
--- a/html/api/psi4.core.BasisExtents.html
+++ b/html/api/psi4.core.BasisExtents.html
@@ -102,7 +102,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
·
PSI4
@@ -282,7 +282,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
·
PSI4
@@ -296,7 +296,7 @@ Navigation
diff --git a/html/api/psi4.core.BasisFunctions.html b/html/api/psi4.core.BasisFunctions.html
index 97d2aa3f3e2..af084717ce5 100644
--- a/html/api/psi4.core.BasisFunctions.html
+++ b/html/api/psi4.core.BasisFunctions.html
@@ -102,7 +102,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
·
PSI4
@@ -291,7 +291,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
·
PSI4
@@ -305,7 +305,7 @@ Navigation
diff --git a/html/api/psi4.core.BasisSet.html b/html/api/psi4.core.BasisSet.html
index 5d0b669b085..0b860c65f84 100644
--- a/html/api/psi4.core.BasisSet.html
+++ b/html/api/psi4.core.BasisSet.html
@@ -102,7 +102,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
·
PSI4
@@ -558,7 +558,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
·
PSI4
@@ -572,7 +572,7 @@ Navigation
diff --git a/html/api/psi4.core.BlockOPoints.html b/html/api/psi4.core.BlockOPoints.html
index ede1c27bbd9..0a4c3da8d98 100644
--- a/html/api/psi4.core.BlockOPoints.html
+++ b/html/api/psi4.core.BlockOPoints.html
@@ -102,7 +102,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
·
PSI4
@@ -314,7 +314,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
·
PSI4
@@ -328,7 +328,7 @@ Navigation
diff --git a/html/api/psi4.core.BoysLocalizer.html b/html/api/psi4.core.BoysLocalizer.html
index 2a1e33dfbdf..06e820b79c9 100644
--- a/html/api/psi4.core.BoysLocalizer.html
+++ b/html/api/psi4.core.BoysLocalizer.html
@@ -102,7 +102,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
·
PSI4
@@ -292,7 +292,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
·
PSI4
@@ -306,7 +306,7 @@ Navigation
diff --git a/html/api/psi4.core.CCWavefunction.html b/html/api/psi4.core.CCWavefunction.html
index 1a070e2ccdc..77be4a50ecb 100644
--- a/html/api/psi4.core.CCWavefunction.html
+++ b/html/api/psi4.core.CCWavefunction.html
@@ -102,7 +102,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
·
PSI4
@@ -1278,7 +1278,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
·
PSI4
@@ -1292,7 +1292,7 @@ Navigation
diff --git a/html/api/psi4.core.CIVector.html b/html/api/psi4.core.CIVector.html
index 322252ea32c..c41e5ba45cb 100644
--- a/html/api/psi4.core.CIVector.html
+++ b/html/api/psi4.core.CIVector.html
@@ -102,7 +102,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
·
PSI4
@@ -400,7 +400,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
·
PSI4
@@ -414,7 +414,7 @@ Navigation
diff --git a/html/api/psi4.core.CIWavefunction.html b/html/api/psi4.core.CIWavefunction.html
index 94c622b28fb..4fb3485b148 100644
--- a/html/api/psi4.core.CIWavefunction.html
+++ b/html/api/psi4.core.CIWavefunction.html
@@ -102,7 +102,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
·
PSI4
@@ -1538,7 +1538,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
·
PSI4
@@ -1552,7 +1552,7 @@ Navigation
diff --git a/html/api/psi4.core.CUHF.html b/html/api/psi4.core.CUHF.html
index 4f0d42ce41e..29c19eec9cf 100644
--- a/html/api/psi4.core.CUHF.html
+++ b/html/api/psi4.core.CUHF.html
@@ -102,7 +102,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
·
PSI4
@@ -1874,7 +1874,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
·
PSI4
@@ -1888,7 +1888,7 @@ Navigation
diff --git a/html/api/psi4.core.CdSalc.html b/html/api/psi4.core.CdSalc.html
index ad11cb2ae85..4c3a9c49576 100644
--- a/html/api/psi4.core.CdSalc.html
+++ b/html/api/psi4.core.CdSalc.html
@@ -102,7 +102,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
·
PSI4
@@ -264,7 +264,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
·
PSI4
@@ -278,7 +278,7 @@ Navigation
diff --git a/html/api/psi4.core.CdSalcList.html b/html/api/psi4.core.CdSalcList.html
index 7724c343c2f..e3ffcb24031 100644
--- a/html/api/psi4.core.CdSalcList.html
+++ b/html/api/psi4.core.CdSalcList.html
@@ -102,7 +102,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
·
PSI4
@@ -300,7 +300,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
·
PSI4
@@ -314,7 +314,7 @@ Navigation
diff --git a/html/api/psi4.core.CharacterTable.html b/html/api/psi4.core.CharacterTable.html
index 5edc29ebcb2..61b5458dd9f 100644
--- a/html/api/psi4.core.CharacterTable.html
+++ b/html/api/psi4.core.CharacterTable.html
@@ -102,7 +102,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
·
PSI4
@@ -264,7 +264,7 @@ Navigation
·
- 1.4rc2.dev26
+ undefined
·
PSI4
@@ -278,7 +278,7 @@ Navigation
diff --git a/html/api/psi4.core.CorrelationFactor.html b/html/api/psi4.core.CorrelationFactor.html
index 5bcbd010d01..d7599c00e54 100644
--- a/html/api/psi4.core.CorrelationFactor.html
+++ b/html/api/psi4.core.CorrelationFactor.html
@@ -102,7 +102,7 @@ Navigation