Attempt docs fix (psi4#2468)

* Attempt docs fix * Force GHA * auto-generated samples from docs build * Update CMakeLists.txt Co-authored-by: Lori A. Burns <[email protected]> * Update doc/sphinxman/source/notes_c.rst Co-authored-by: Lori A. Burns <[email protected]> * Update doc/sphinxman/source/notes_c.rst Co-authored-by: GitHub Action <[email protected]> Co-authored-by: Lori A. Burns <[email protected]>
JonathonMisiewicz · Mar 11, 2022 · 478584c · 478584c
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diff --git a/doc/sphinxman/source/notes_c.rst b/doc/sphinxman/source/notes_c.rst
@@ -60,20 +60,23 @@ Notes on Psivars
 ================
 
 .. note:: Starting in 1.6, there are three standard ways to access an excited state
-    property. We give examples below, but the method name and property name may change.
-    * ``method ROOT 0 -> ROOT m property`` to get root m.
-    * ``method ROOT 0 -> ROOT m property - h TRANSITION`` to get root m and
-      independently specify that the total transition symmetry is A2.
-    * ``method ROOT 0 (h) -> ROOT m (i) property`` to get the transition
-      between two roots, specifying the symmetry of both states and the index of the target
-      roots among states of their own symmetry.
-    For example, to target the second excited-state, which is also the lowest energy state
-    of its irrep, the first two calls will take m = 2, while the last takes m = 0.
-    Methods that use this interface are: TD-fctl.
-    Note that numberings are associated with the calculation much more strongly than 
-    with the molecular system. Changing the number of roots sought, the symmetry 
-    subspace or the symmetry apportionment or roots under which the computation is run, 
-    or the excited state method are all likely to scramble root numberings.
+   property. We give examples below, but the method name and property name may change.
+   * ``method ROOT 0 -> ROOT m property`` to get root m.
+
+   * ``method ROOT 0 -> ROOT m property - h TRANSITION`` to get root m and
+      independently specify that the total transition symmetry is h, e.g., A2.
+
+   * ``method ROOT 0 (h) -> ROOT m (i) property`` to get the transition
+     between two roots, specifying the symmetry of both states and the index of the target
+     roots among states of their own symmetry.
+
+   For example, to target the second excited-state, which is also the lowest energy state
+   of its irrep, the first two calls will take m = 2, while the last takes m = 0.
+   Methods that use this interface are: TD-fctl.
+   Note that numberings are associated with the calculation much more strongly than 
+   with the molecular system. Changing the number of roots sought, the symmetry 
+   subspace or the symmetry apportionment of roots under which the computation is run, 
+   or the excited state method are all likely to scramble root numberings.
 
 Alternate Implementations
 =========================

diff --git a/samples/adc1/input.dat b/samples/adc1/input.dat
@@ -12,6 +12,7 @@ set {
     basis 6-31G**
     guess core
     roots_per_irrep [20]
+    qc_module builtin
 }
 
 ref_energy = -76.22243196371332 

diff --git a/samples/adc1/test.in b/samples/adc1/test.in
@@ -12,6 +12,7 @@ set {
     basis 6-31G**
     guess core
     roots_per_irrep [20]
+    qc_module builtin
 }
 
 ref_energy = -76.22243196371332 

diff --git a/samples/adc2/input.dat b/samples/adc2/input.dat
@@ -15,6 +15,7 @@ set {
     basis aug-cc-pvdz
     guess core
     roots_per_irrep [2]
+    qc_module builtin
 }
 
 ref_energy = -152.52670794053822

diff --git a/samples/adc2/test.in b/samples/adc2/test.in
@@ -15,6 +15,7 @@ set {
     basis aug-cc-pvdz
     guess core
     roots_per_irrep [2]
+    qc_module builtin
 }
 
 ref_energy = -152.52670794053822

diff --git a/samples/adcc/formaldehyde-pe-adc1/input.dat b/samples/adcc/formaldehyde-pe-adc1/input.dat
@@ -0,0 +1,37 @@
+#! LR-PE-ADC(1)/sto-3g formaldehyde in presence of 6 water molecules
+#! cross-reference against PE-CIS from Psi4 itself
+
+molecule formaldehyde {
+    C 2.0092420208996 3.8300915804899 0.8199294419789
+    O 2.1078857690998 2.0406638776593 2.1812021228452
+    H 2.0682421748693 5.7438044586615 1.5798996515014
+    H 1.8588483602149 3.6361694243085 -1.2192956060942
+    symmetry c1
+    units au
+    no_reorient
+    no_com
+}
+
+set {
+    reference rhf
+    basis sto-3g
+    roots_per_irrep [5]
+    qc_module adcc
+    pe true
+    scf_type pk
+    tdscf_states 5
+    tdscf_tda true
+}
+
+set pe {
+ potfile fa_6w.pot
+}
+
+
+_, wfn = energy('td-hf', return_wfn=True)
+ref_energies = []
+for i in range(5):
+    ref_energies.append(wfn.variable(f'TD-HF ROOT 0 -> ROOT {i+1} EXCITATION ENERGY - A SYMMETRY'))
+
+_, wfn = properties('adc(1)', properties=["oscillator_strength", "dipole"], environment='linear_response', return_wfn=True)
+
diff --git a/samples/adcc/formaldehyde-pe-adc1/test.in b/samples/adcc/formaldehyde-pe-adc1/test.in
@@ -0,0 +1,39 @@
+#! LR-PE-ADC(1)/sto-3g formaldehyde in presence of 6 water molecules
+#! cross-reference against PE-CIS from Psi4 itself
+
+molecule formaldehyde {
+    C 2.0092420208996 3.8300915804899 0.8199294419789
+    O 2.1078857690998 2.0406638776593 2.1812021228452
+    H 2.0682421748693 5.7438044586615 1.5798996515014
+    H 1.8588483602149 3.6361694243085 -1.2192956060942
+    symmetry c1
+    units au
+    no_reorient
+    no_com
+}
+
+set {
+    reference rhf
+    basis sto-3g
+    roots_per_irrep [5]
+    qc_module adcc
+    pe true
+    scf_type pk
+    tdscf_states 5
+    tdscf_tda true
+}
+
+set pe {
+ potfile fa_6w.pot
+}
+
+
+_, wfn = energy('td-hf', return_wfn=True)
+ref_energies = []
+for i in range(5):
+    ref_energies.append(wfn.variable(f'TD-HF ROOT 0 -> ROOT {i+1} EXCITATION ENERGY - A SYMMETRY'))
+
+_, wfn = properties('adc(1)', properties=["oscillator_strength", "dipole"], environment='linear_response', return_wfn=True)
+
+compare_arrays(np.array([ref_energies]).T, wfn.variable("ADC(1) excitation energies").np,  #TEST
+               1e-5, "ADC(1) excitation energies")                                         #TEST
diff --git a/samples/adcc/formaldehyde-pe-adc2/fa_6w.pot b/samples/adcc/formaldehyde-pe-adc2/fa_6w.pot
diff --git a/samples/adcc/formaldehyde-pe-adc2/input.dat b/samples/adcc/formaldehyde-pe-adc2/input.dat
@@ -1,4 +1,5 @@
 #! PE-ADC(2)/cc-pvdz formaldehyde in presence of 6 water molecules
+#! including ptSS/ptLR corrections for excitation energies
 #! Reference data from Q-Chem calculation
 
 molecule formaldehyde {
@@ -25,7 +26,5 @@ set pe {
 }
 
 # Run computation of ADC(2) plus a few properties
-# environment="True" turns on ptSS/ptLR corrections
-_, wfn = properties('adc(2)', properties=["oscillator_strength", "dipole"],
-                    environment=True, return_wfn=True)
+_, wfn = properties('adc(2)', properties=["oscillator_strength", "dipole"], environment=True, return_wfn=True)
 
diff --git a/samples/adcc/formaldehyde-pe-adc2/test.in b/samples/adcc/formaldehyde-pe-adc2/test.in
@@ -1,4 +1,5 @@
 #! PE-ADC(2)/cc-pvdz formaldehyde in presence of 6 water molecules
+#! including ptSS/ptLR corrections for excitation energies
 #! Reference data from Q-Chem calculation
 
 molecule formaldehyde {
@@ -25,8 +26,7 @@ set pe {
 }
 
 # Run computation of ADC(2) plus a few properties
-# environment="True" turns ptSS/ptLR corrections on
-_, wfn = properties('adc(2)', properties=["oscillator_strength", "dipole"], environment="True", return_wfn=True)
+_, wfn = properties('adc(2)', properties=["oscillator_strength", "dipole"], environment=True, return_wfn=True)
 
 energies_uncorrected = [0.15963251547743104, 0.3125861355885466, 0.36222631191059046,      #TEST
                         0.37972031238708653, 0.4118959244399415]                           #TEST

diff --git a/samples/aediis-1/input.dat b/samples/aediis-1/input.dat
@@ -0,0 +1,24 @@
+#! ADIIS test case, from 10.1063/1.3304922 
+
+molecule {
+2 1
+Cd       0.0000000000      0.0000000000      0.0000000000    
+N        0.0000000000      0.0000000000     -2.2600010635    
+N       -0.6854437203      0.0000000000     -4.3480354859    
+C        0.6760533303      0.0000000000     -4.3850694419    
+C        1.0852404753      0.0000000000     -3.0912317094    
+C       -1.0447523879      0.0000000000     -3.0602202054    
+H        1.2315299626      0.0000000000     -5.3007589304    
+H        2.0886410569      0.0000000000     -2.7110772355    
+H       -2.0687499916      0.0000000000     -2.7265149874    
+H       -1.3131700977      0.0000000000     -5.1747180497    
+}
+
+set guess core    # With this guess, un-accelerated DIIS will fail.
+set scf_type pk
+set basis 3-21G
+set scf_initial_accelerator adiis
+set maxiter 15
+energy = energy('scf')
+
+compare_values(-5663.1433914266744978, energy, 6, "SCF Energy")
diff --git a/samples/aediis-1/test.in b/samples/aediis-1/test.in
@@ -0,0 +1,24 @@
+#! ADIIS test case, from 10.1063/1.3304922 
+
+molecule {
+2 1
+Cd       0.0000000000      0.0000000000      0.0000000000    
+N        0.0000000000      0.0000000000     -2.2600010635    
+N       -0.6854437203      0.0000000000     -4.3480354859    
+C        0.6760533303      0.0000000000     -4.3850694419    
+C        1.0852404753      0.0000000000     -3.0912317094    
+C       -1.0447523879      0.0000000000     -3.0602202054    
+H        1.2315299626      0.0000000000     -5.3007589304    
+H        2.0886410569      0.0000000000     -2.7110772355    
+H       -2.0687499916      0.0000000000     -2.7265149874    
+H       -1.3131700977      0.0000000000     -5.1747180497    
+}
+
+set guess core    # With this guess, un-accelerated DIIS will fail.
+set scf_type pk
+set basis 3-21G
+set scf_initial_accelerator adiis
+set maxiter 15
+energy = energy('scf')
+
+compare_values(-5663.1433914266744978, energy, 6, "SCF Energy")
diff --git a/samples/aediis-2/input.dat b/samples/aediis-2/input.dat
@@ -0,0 +1,18 @@
+#! EDIIS test case from 10.1063/1.1470195
+
+molecule {
+U
+F   1 1.98
+F   1 1.98  2  109.4712
+F   1 1.98  2  109.4712  3  120.0000
+F   1 1.98  2  109.4712  3 -120.0000
+}
+
+set guess gwh    # With this guess, un-accelerated DIIS will fail
+set scf_type pk
+set basis lanl2dz
+set scf_initial_accelerator ediis
+set maxiter 28
+energy = energy('b3lyp')
+
+compare_values(-451.2300583940044021, energy, 6, "SCF Energy")
diff --git a/samples/aediis-2/test.in b/samples/aediis-2/test.in
@@ -0,0 +1,18 @@
+#! EDIIS test case from 10.1063/1.1470195
+
+molecule {
+U
+F   1 1.98
+F   1 1.98  2  109.4712
+F   1 1.98  2  109.4712  3  120.0000
+F   1 1.98  2  109.4712  3 -120.0000
+}
+
+set guess gwh    # With this guess, un-accelerated DIIS will fail
+set scf_type pk
+set basis lanl2dz
+set scf_initial_accelerator ediis
+set maxiter 28
+energy = energy('b3lyp')
+
+compare_values(-451.2300583940044021, energy, 6, "SCF Energy")
diff --git a/samples/cc11/input.dat b/samples/cc11/input.dat
@@ -1,6 +1,6 @@
 #! Frozen-core CCSD(ROHF)/cc-pVDZ on CN radical with disk-based AO algorithm
 
-molecule cn {
+molecule CN {
   0 2
   C
   N 1 R
@@ -18,3 +18,6 @@ set {
 }
 
 energy('ccsd')
+
+
+