Copy cioverlap.pyx and tdnac.c files for orbital based calculation

copy cioverlap.pyx to cioverlap_orb.pyx
copy tdnac.c to tdnac_orb.c

Author: JaeHyeokLee98

src/qm/cioverlap/cioverlap_orb.pyx

@@ -0,0 +1,137 @@
+# cython: language_level=3
+from cpython.mem cimport PyMem_Malloc, PyMem_Free
+
+cdef extern from "tdnac.c":
+    void TD_NAC(int istep, int nst, int nbasis, int norb, int nocc, int nvirt, double dt, \
+        int *orb_ini, int *orb_final, double **nacme, double **ao_overlap, \
+        double **mo_coef_old, double **mo_coef_new, double ***ci_coef_old, double ***ci_coef_new)
+
+def wf_overlap(qm, molecule, istep_py, dt_py):
+    cdef:
+        int *orb_ini
+        int *orb_final
+        double **nacme
+        double **ao_overlap
+        double **mo_coef_old
+        double **mo_coef_new
+        double ***ci_coef_old
+        double ***ci_coef_new
+
+        int istep, ist, nst, ibasis, jbasis, iorb, jorb, nbasis, norb, nocc, nvirt
+        double dt
+
+    # Assign size variables
+    dt = dt_py
+    istep = istep_py
+    nst = molecule.nst
+    nbasis = qm.nbasis
+    norb = qm.norb
+    nocc = qm.nocc
+    nvirt = qm.nvirt
+
+    # Allocate NACME variables
+    orb_ini = <int*> PyMem_Malloc(1 * sizeof(int))
+    orb_final = <int*> PyMem_Malloc(1 * sizeof(int))
+
+    nacme = <double**> PyMem_Malloc(nst * sizeof(double*))
+
+    ao_overlap = <double**> PyMem_Malloc(nbasis * sizeof(double*))
+    mo_coef_old = <double**> PyMem_Malloc(norb * sizeof(double*))
+    mo_coef_new = <double**> PyMem_Malloc(norb * sizeof(double*))
+
+    for ist in range(nst):
+        nacme[ist] = <double*> PyMem_Malloc(nst * sizeof(double))
+
+    for ibasis in range(nbasis):
+        ao_overlap[ibasis] = <double*> PyMem_Malloc(nbasis * sizeof(double))
+
+    for iorb in range(norb):
+        mo_coef_old[iorb] = <double*> PyMem_Malloc(nbasis * sizeof(double))
+        mo_coef_new[iorb] = <double*> PyMem_Malloc(nbasis * sizeof(double))
+
+    ci_coef_old = <double***> PyMem_Malloc(nst * sizeof(double**))
+    ci_coef_new = <double***> PyMem_Malloc(nst * sizeof(double**))
+
+    for ist in range(nst):
+        ci_coef_old[ist] = <double**> PyMem_Malloc(nocc * sizeof(double*))
+        ci_coef_new[ist] = <double**> PyMem_Malloc(nocc * sizeof(double*))
+
+    for ist in range(nst):
+        for iorb in range(nocc):
+            ci_coef_old[ist][iorb] = <double*> PyMem_Malloc(nvirt * sizeof(double))
+            ci_coef_new[ist][iorb] = <double*> PyMem_Malloc(nvirt * sizeof(double))
+
+    # Assign NACME variables from python to C
+    orb_ini[0] = qm.orb_ini[0]
+    orb_final[0] = qm.orb_final[0]
+
+    for ist in range(nst):
+        for jst in range(nst):
+            nacme[ist][jst] = 0.
+
+    for ibasis in range(nbasis):
+        for jbasis in range(nbasis):
+            ao_overlap[ibasis][jbasis] = qm.ao_overlap[ibasis, jbasis]
+    
+    for iorb in range(norb):
+        for ibasis in range(nbasis):
+            mo_coef_old[iorb][ibasis] = qm.mo_coef_old[iorb, ibasis]
+            mo_coef_new[iorb][ibasis] = qm.mo_coef_new[iorb, ibasis]
+
+    for ist in range(nst):
+        for iorb in range(nocc):
+            for jorb in range(nvirt):
+                ci_coef_old[ist][iorb][jorb] = qm.ci_coef_old[ist, iorb, jorb]
+                ci_coef_new[ist][iorb][jorb] = qm.ci_coef_new[ist, iorb, jorb]
+
+    # Calculate TDNAC term for CIoverlap
+    TD_NAC(istep, nst, nbasis, norb, nocc, nvirt, dt, orb_ini, orb_final, nacme, \
+        ao_overlap, mo_coef_old, mo_coef_new, ci_coef_old, ci_coef_new)
+
+    # Assign NACME variables from C to python
+    for ist in range(nst):
+        for jst in range(nst):
+             molecule.nacme[ist, jst] = nacme[ist][jst]
+
+    for iorb in range(norb):
+        for ibasis in range(nbasis):
+            qm.mo_coef_old[iorb, ibasis] = mo_coef_new[iorb][ibasis]
+
+    for ist in range(nst):
+        for iorb in range(nocc):
+            for jorb in range(nvirt):
+                qm.ci_coef_old[ist, iorb, jorb] = ci_coef_new[ist][iorb][jorb]
+
+    # Deallocate NACME variables
+    PyMem_Free(orb_ini)
+    PyMem_Free(orb_final)
+
+    for ist in range(nst):
+        PyMem_Free(nacme[ist])
+
+    PyMem_Free(nacme)
+
+    for ibasis in range(nbasis):
+        PyMem_Free(ao_overlap[ibasis])
+
+    for iorb in range(norb):
+        PyMem_Free(mo_coef_old[iorb])
+        PyMem_Free(mo_coef_new[iorb])
+
+    PyMem_Free(ao_overlap)
+    PyMem_Free(mo_coef_old)
+    PyMem_Free(mo_coef_new)
+
+    for ist in range(nst):
+        for iorb in range(nocc):
+            PyMem_Free(ci_coef_old[ist][iorb])
+            PyMem_Free(ci_coef_new[ist][iorb])
+
+    for ist in range(nst):
+        PyMem_Free(ci_coef_old[ist])
+        PyMem_Free(ci_coef_new[ist])
+
+    PyMem_Free(ci_coef_old)
+    PyMem_Free(ci_coef_new)
+
+