fix typos, add todos and edit examples

tjira · Apr 24, 2024 · 1e9db1f · 1e9db1f
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diff --git a/TODO.md b/TODO.md
@@ -1,5 +1,7 @@
 # TODO List
 
+- [ ] Split the model solver types into different objects in inputs
+- [ ] Make the method field for BAGEL actually work
 - [x] Add BAGEL interface with excited state dynamics
 - [x] Add Hermitian FFT for spectra calculation
 - [x] Add Mulliken analysis

diff --git a/docs/pages/configurationinteraction.md b/docs/pages/configurationinteraction.md
@@ -16,7 +16,7 @@ Configuration interaction (CI) is a post-Hartree-Fock, utilizing a linear variat
 Let's consider the restricted version of the Full Configuration Interaction (FCI) method, which considers all possible electronic configurations within a given basis set. The FCI wave function is expressed as a linear combination of Slater determinants, where each determinant represents a unique electron configuration. The FCI method provides the most accurate description of the electronic structure, but its computational cost grows exponentially with the number of electrons and basis functions, making it infeasible for large systems.
 
 ### The Transformation of Integrals to Molecular Spinorbital Basis
-To begin, we need to convert the coefficient matrix $\mathbf{C}$ into the basis of molecular spinorbitals (MS), as this matrix is essential for later transformations of the core Hamiltonian and the Coulomb integrals. Let the number of spatial basis functions be denoted as $n$. The coefficient matrix in the MS basis will then be of dimension $2n \times 2n$, to incorporate the electron spin. In this transformation, each column (orbital) is duplicated and vertically concatenated with itself. The corresponding segments are then zeroed out to respect the Pauli exclusion principle. This is done mathematically using the tiling matrix $\mathbf{P}_{n \times 2n}$, defined as
+To begin, we need to convert the coefficient matrix $\mathbf{C}$ into the basis of molecular spinorbitals (MS), as this matrix is essential for later transformations of the core Hamiltonian and the Coulomb integrals. Let the number of spatial basis functions be denoted as $n$. The coefficient matrix in the MS basis will then be of dimension $2n \times 2n$, to incorporate the electron spin. In this transformation, each column (orbital) is duplicated and the result is vertically concatenated with itself. The corresponding segments are then zeroed out to respect the Pauli exclusion principle. This is done mathematically using the tiling matrix $\mathbf{P}_{n \times 2n}$, defined as
 
 \begin{equation}
 \mathbf{P}=\begin{pmatrix}e_1&e_1&e_2&e_2&\dots&e_n&e_n\end{pmatrix}
@@ -83,7 +83,7 @@ The summations extend over all orbitals common between the two compared determin
 {:.warning}
 > To accurately calculate the differences between two Slater determinants, it's essential to sometimes permute the indices of one determinant for proper alignment before comparison. For instance, consider two determinants, $D_1=\\{1,2,3,4\\}$ and $D_2=\\{1,3,2,4\\}$. To properly compare $D_2$ with $D_1$, you need to permute the indices in $D_2$ to match $D_1$, resulting in $D_2$ being reorganized as $\\{1,2,3,4\\}$. In this case, the number of differences after proper alignment is 0.
 >
-> Moreover, it’s crucial to remember that each permutation of the orbitals alters the sign of the determinant. Therefore, when computing the matrix elements, this change must be accounted for by multiplying the result by $(−1)^p$, where $p$ is the number of permutations made to align the determinants. This factor is vital for ensuring the correct and sign of the matrix elements, which can significantly impact the results of quantum mechanical calculations.
+> Moreover, it’s crucial to remember that each permutation of the orbitals alters the sign of the determinant. Therefore, when computing the matrix elements, this change must be accounted for by multiplying the result by $(−1)^p$, where $p$ is the number of permutations made to align the determinants. This factor is vital for ensuring the correct sign of the matrix elements, which can significantly impact the results of quantum mechanical calculations.
 >
 > This requirement for alignment and sign adjustment adds complexity to the implementation, as each comparison between determinants not only involves checking for differences but also finding the minimal number of permutations needed for alignment.
 

diff --git a/example/input/ad1d.json b/example/input/ad1d.json
@@ -3,7 +3,8 @@
         "potential" : [["0.5*x^2"]],
         "variables" : ["x"],
         "limits" : [-16, 16],
-        "ngrid" : 1024
+        "ngrid" : 1024,
+        "mass" : 1
     },
     "solve" : {
         "dynamics" : {

diff --git a/example/input/bagel_dyn.json b/example/input/bagel_dyn.json
@@ -5,12 +5,12 @@
     },
     "bagel" : {
         "interface" : "../../interface/bagel-gradient.sh",
+        "method" : "CASSCF(4, 2)",
+        "nstate" : 3,
+        "state" : 2,
         "dynamics" : {
             "iters" : 100,
             "step" : 20
-        },
-        "method" : "CASSCF(4, 2)",
-        "nstate" : 3,
-        "state" : 2
+        }
     }
 }
diff --git a/example/input/bagel_dyn_thermo.json b/example/input/bagel_dyn_thermo.json
@@ -5,15 +5,15 @@
     },
     "bagel" : {
         "interface" : "../../interface/bagel-gradient-casscf.sh",
+        "method" : "CASSCF(4, 2)",
+        "nstate" : 3,
+        "state" : 1,
         "dynamics" : {
             "iters" : 100,
             "step" : 20,
             "berendsen" : {
                 "temp" : 298.15
             }
-        },
-        "method" : "CASSCF(4, 2)",
-        "nstate" : 3,
-        "state" : 1
+        }
     }
 }
diff --git a/example/input/qad1d_imag.json b/example/input/qad1d_imag.json
@@ -3,12 +3,15 @@
         "potential" : [["0.5*x^2"]],
         "variables" : ["x"],
         "limits" : [-16, 16],
-        "ngrid" : 1024
+        "ngrid" : 1024,
+        "mass" : 1
     },
     "solve" : {
-        "guess" : "exp(-(x-1)^2)",
         "real" : false,
         "nstate" : 3,
+        "guess" : "exp(-(x-1)^2)",
+        "step" : 0.1,
+        "iters" : 1000,
         "savewfn" : true
     }
 }
diff --git a/example/input/qad1d_real.json b/example/input/qad1d_real.json
@@ -3,11 +3,15 @@
         "potential" : [["0.5*x^2"]],
         "variables" : ["x"],
         "limits" : [-16, 16],
-        "ngrid" : 1024
+        "ngrid" : 1024,
+        "mass" : 1
     },
     "solve" : {
-        "guess" : "exp(-(x-1)^2)",
         "real" : true,
+        "nstate" : 1,
+        "guess" : "exp(-(x-1)^2)",
+        "step" : 0.1,
+        "iters" : 1000,
         "spectrum" : {},
         "savewfn" : true
     }

diff --git a/example/input/qad2d_imag.json b/example/input/qad2d_imag.json
@@ -3,12 +3,15 @@
         "potential" : [["0.5*(x^2+y^2)"]],
         "variables" : ["x", "y"],
         "limits" : [-16, 16],
-        "ngrid" : 256
+        "ngrid" : 256,
+        "mass" : 1
     },
     "solve" : {
-        "guess" : "exp(-(x^2+y^2))",
         "real" : false,
         "nstate" : 3,
+        "guess" : "exp(-(x^2+y^2))",
+        "step" : 0.1,
+        "iters" : 1000,
         "savewfn" : true
     }
 }
diff --git a/example/input/qad2d_real.json b/example/input/qad2d_real.json
@@ -3,11 +3,15 @@
         "potential" : [["0.5*(x^2+y^2)"]],
         "variables" : ["x", "y"],
         "limits" : [-16, 16],
-        "ngrid" : 256
+        "ngrid" : 256,
+        "mass" : 1
     },
     "solve" : {
-        "guess" : "exp(-(x^2+y^2))",
         "real" : true,
+        "nstate" : 1,
+        "guess" : "exp(-(x^2+y^2))",
+        "step" : 0.1,
+        "iters" : 1000,
         "spectrum" : {},
         "savewfn" : true
     }

diff --git a/example/input/rcid.json b/example/input/rcid.json
@@ -5,6 +5,8 @@
     },
     "rhf" : {},
     "rci" : {
-        "excitations" : [2]
+        "excitations" : [2],
+        "nstate" : 3,
+        "state" : 1
     }
 }
diff --git a/example/input/rcid_dyn.json b/example/input/rcid_dyn.json
@@ -6,6 +6,8 @@
     "rhf" : {},
     "rci" : {
         "excitations" : [2],
+        "nstate" : 3,
+        "state" : 1,
         "dynamics" : {
             "iters" : 100,
             "step" : 20

diff --git a/example/input/rcid_dyn_thermo.json b/example/input/rcid_dyn_thermo.json
@@ -6,6 +6,8 @@
     "rhf" : {},
     "rci" : {
         "excitations" : [2],
+        "nstate" : 3,
+        "state" : 1,
         "dynamics" : {
             "iters" : 100,
             "step" : 20,

diff --git a/example/input/rcid_grad.json b/example/input/rcid_grad.json
@@ -6,6 +6,8 @@
     "rhf" : {},
     "rci" : {
         "excitations" : [2],
+        "nstate" : 3,
+        "state" : 1,
         "gradient" : {
             "step" : 1e-5
         }

diff --git a/example/input/rcid_hess.json b/example/input/rcid_hess.json
@@ -6,6 +6,8 @@
     "rhf" : {},
     "rci" : {
         "excitations" : [2],
+        "nstate" : 3,
+        "state" : 1,
         "hessian" : {
             "step" : 1e-5
         }

diff --git a/example/input/rcis.json b/example/input/rcis.json
@@ -6,5 +6,7 @@
     "rhf" : {},
     "rci" : {
         "excitations" : [1]
+        "nstate" : 3,
+        "state" : 1
     }
 }
diff --git a/example/input/rcis_dyn.json b/example/input/rcis_dyn.json
@@ -6,6 +6,8 @@
     "rhf" : {},
     "rci" : {
         "excitations" : [1],
+        "nstate" : 3,
+        "state" : 1,
         "dynamics" : {
             "iters" : 100,
             "step" : 20

diff --git a/example/input/rcis_dyn_thermo.json b/example/input/rcis_dyn_thermo.json
@@ -6,6 +6,8 @@
     "rhf" : {},
     "rci" : {
         "excitations" : [1],
+        "nstate" : 3,
+        "state" : 1,
         "dynamics" : {
             "iters" : 100,
             "step" : 20,

diff --git a/example/input/rcis_grad.json b/example/input/rcis_grad.json
@@ -6,6 +6,8 @@
     "rhf" : {},
     "rci" : {
         "excitations" : [1],
+        "nstate" : 3,
+        "state" : 1,
         "gradient" : {
             "step" : 1e-5
         }

diff --git a/example/input/rcis_hess.json b/example/input/rcis_hess.json
@@ -6,6 +6,8 @@
     "rhf" : {},
     "rci" : {
         "excitations" : [1],
+        "nstate" : 3,
+        "state" : 1,
         "hessian" : {
             "step" : 1e-5
         }

diff --git a/example/input/rcisd.json b/example/input/rcisd.json
@@ -6,5 +6,7 @@
     "rhf" : {},
     "rci" : {
         "excitations" : [1, 2]
+        "nstate" : 3,
+        "state" : 1
     }
 }
diff --git a/example/input/rcisd_dyn.json b/example/input/rcisd_dyn.json
@@ -6,6 +6,8 @@
     "rhf" : {},
     "rci" : {
         "excitations" : [1, 2],
+        "nstate" : 3,
+        "state" : 1,
         "dynamics" : {
             "iters" : 100,
             "step" : 20

diff --git a/example/input/rcisd_dyn_thermo.json b/example/input/rcisd_dyn_thermo.json
@@ -6,6 +6,8 @@
     "rhf" : {},
     "rci" : {
         "excitations" : [1, 2],
+        "nstate" : 3,
+        "state" : 1,
         "dynamics" : {
             "iters" : 100,
             "step" : 20,

diff --git a/example/input/rcisd_grad.json b/example/input/rcisd_grad.json
@@ -6,6 +6,8 @@
     "rhf" : {},
     "rci" : {
         "excitations" : [1, 2],
+        "nstate" : 3,
+        "state" : 1,
         "gradient" : {
             "step" : 1e-5
         }

diff --git a/example/input/rcisd_hess.json b/example/input/rcisd_hess.json
@@ -6,6 +6,8 @@
     "rhf" : {},
     "rci" : {
         "excitations" : [1, 2],
+        "nstate" : 3,
+        "state" : 1,
         "hessian" : {
             "step" : 1e-5
         }

diff --git a/example/input/rfci.json b/example/input/rfci.json
@@ -4,5 +4,9 @@
         "basis" : "sto-3g"
     },
     "rhf" : {},
-    "rci" : {}
+    "rci" : {
+        "excitations" : [],
+        "nstate" : 3,
+        "state" : 1
+    }
 }
diff --git a/example/input/rfci_dyn.json b/example/input/rfci_dyn.json
@@ -5,6 +5,9 @@
     },
     "rhf" : {},
     "rci" : {
+        "excitations" : [],
+        "nstate" : 3,
+        "state" : 1,
         "dynamics" : {
             "iters" : 100,
             "step" : 20

diff --git a/example/input/rfci_dyn_thermo.json b/example/input/rfci_dyn_thermo.json
@@ -5,6 +5,9 @@
     },
     "rhf" : {},
     "rci" : {
+        "excitations" : [],
+        "nstate" : 3,
+        "state" : 1,
         "dynamics" : {
             "iters" : 100,
             "step" : 20,

diff --git a/example/input/rfci_grad.json b/example/input/rfci_grad.json
@@ -5,6 +5,9 @@
     },
     "rhf" : {},
     "rci" : {
+        "excitations" : [],
+        "nstate" : 3,
+        "state" : 1,
         "gradient" : {
             "step" : 1e-5
         }

diff --git a/example/input/rfci_hess.json b/example/input/rfci_hess.json
@@ -5,6 +5,9 @@
     },
     "rhf" : {},
     "rci" : {
+        "excitations" : [],
+        "nstate" : 3,
+        "state" : 1,
         "hessian" : {
             "step" : 1e-5
         }

diff --git a/example/input/rmp2.json b/example/input/rmp2.json
@@ -4,5 +4,7 @@
         "basis" : "sto-3g"
     },
     "rhf" : {},
-    "rmp" : {}
+    "rmp" : {
+        "order" : 2
+    }
 }
diff --git a/example/input/rmp2_dyn.json b/example/input/rmp2_dyn.json
@@ -5,6 +5,7 @@
     },
     "rhf" : {},
     "rmp" : {
+        "order" : 2,
         "dynamics" : {
             "iters" : 100,
             "step" : 20

diff --git a/example/input/rmp2_dyn_thermo.json b/example/input/rmp2_dyn_thermo.json
@@ -5,6 +5,7 @@
     },
     "rhf" : {},
     "rmp" : {
+        "order" : 2,
         "dynamics" : {
             "iters" : 100,
             "step" : 20,

diff --git a/example/input/rmp2_grad.json b/example/input/rmp2_grad.json
@@ -5,6 +5,7 @@
     },
     "rhf" : {},
     "rmp" : {
+        "order" : 2,
         "gradient" : {
             "step" : 1e-5
         }

diff --git a/example/input/rmp2_hess.json b/example/input/rmp2_hess.json
@@ -5,6 +5,7 @@
     },
     "rhf" : {},
     "rmp" : {
+        "order" : 2,
         "hessian" : {
             "step" : 1e-5
         }