Merge pull request #4 from nlk36701/Mitchell

Reap fixes

Author: nlk36701

Merger.py

@@ -204,9 +204,8 @@ def run(self, opts, Proj, energy_regex=None, success_regex=None, cma1_coord=None
                     options,
                     eigs_init,
                     indices,
-                    options.gradient_regex,
                     options.energy_regex_init,
-                    None,
+                    options.gradient_regex,
                     options.success_regex_init,
                     deriv_level = self.options.deriv_level
                 )
@@ -444,6 +443,12 @@ def run(self, opts, Proj, energy_regex=None, success_regex=None, cma1_coord=None
         print(G)
         G = np.dot(np.dot(eig_inv, G), eig_inv.T)
         # G[np.abs(G) < options.tol] = 0
+        # print("Nat F:")
+        # F[np.abs(F) < 1.0e-5] = 0 
+        # print(F)
+        # Conversion to aJ/Ang
+        # F *= 4.3597447222071
+        # F /= 0.529177210903
         F = np.dot(np.dot(TED_obj.proj.T,F),TED_obj.proj)
         if len(sym_sort) > 1:
             F = F[flat_sym_sort]

exec_cma_database.py

@@ -25,8 +25,8 @@
 
 # High and low levels of theory
 # Available: "CCSD_T_TZ", "CCSD_T_DZ", "B3LYP_6-31G_2df,p_"
-h_theory = ["CCSD_T_aTZ"]
-# h_theory = ["CCSD_T_TZ"]
+# h_theory = ["CCSD_T_aTZ"]
+h_theory = ["CCSD_T_TZ"]
 # l_theory = ["MP2_haTZ"]
 # l_theory = ["MP2_haDZ"]
 # l_theory = ["MP2_aTZ"]
@@ -37,8 +37,8 @@
 # l_theory = ["CCSD_T_haDZ"]
 # l_theory = ["CCSD_T_aDZ"]
 # l_theory = ["CCSD_haTZ"]
-l_theory = ["CCSD_T_TZ"]
-# l_theory = ["CCSD_T_DZ"]
+# l_theory = ["CCSD_T_TZ"]
+l_theory = ["CCSD_T_DZ"]
 # l_theory = [
 # # "CCSD_aTZ",
 # # "CCSD_haTZ",
@@ -75,6 +75,7 @@
 # "MP2_TZ"]
 
 # cma1_energy_regexes = ["CCSD\s*t?o?t?a?l? energy\s+(\-\d+\.\d+)"]
+cma1_gradient_regex = []
 # cma1_gradient_regex = ["\s*virial=\S\S+\.\d+E\S\d+\S\>\s+"]
 # cma1_energy_regexes = ["\(T\)\s*t?o?t?a?l? energy\s+(\-\d+\.\d+)","Grab this energy (\-\d+\.\d+)"]
 # cma1_energy_regexes = ["\(T\)\s*t?o?t?a?l? energy\s+(\-\d+\.\d+)",[r"Total Gradient",r"tstop"]]
@@ -111,7 +112,7 @@
 # paths = ['/1*','/2*']
 # job_list = ["4.31"]
 # job_list = ["1.104"]
-job_list = ["3.4"]
+job_list = ["0.1"]
 
 # Various output control statements
 n = 0                    # Number of CMA2 corrections (n = 0 -> CMA0)
@@ -128,8 +129,8 @@
 # compute_all = True       # run calculations for all or a select few
 off_diag_bands = False   # (CMA2/3 ONLY) If set to true, "n" off-diag bands selected, if false, "n" largest fc will be selected
 deriv_level = 0         # (CMA1) if 0, compute initial hessian by singlepoints. If 1, compute initial hessian with findif of gradients
-second_order = True    # If True, read in cartesian gradient and force constant info to be converted to internal coordinates.
-# second_order = False    # If False, generate displacements to manually compute the CMA-0A internal coord force constants.
+# second_order = True    # If True, read in cartesian gradient and force constant info to be converted to internal coordinates.
+second_order = False    # If False, generate displacements to manually compute the CMA-0A internal coord force constants.
 
 
 # =====================