Updates to interface with CMA_benchmarker

CCQC · Feb 8, 2023 · 9db1a94 · 9db1a94
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diff --git a/__pycache__/__init__.cpython-35.pyc b/__pycache__/__init__.cpython-35.pyc
diff --git a/__pycache__/__init__.cpython-38.pyc b/__pycache__/__init__.cpython-38.pyc
diff --git a/__pycache__/__init__.cpython-39.pyc b/__pycache__/__init__.cpython-39.pyc
diff --git a/__pycache__/algorithm.cpython-35.pyc b/__pycache__/algorithm.cpython-35.pyc
diff --git a/__pycache__/algorithm.cpython-38.pyc b/__pycache__/algorithm.cpython-38.pyc
diff --git a/__pycache__/algorithm.cpython-39.pyc b/__pycache__/algorithm.cpython-39.pyc
diff --git a/__pycache__/cma.cpython-35.pyc b/__pycache__/cma.cpython-35.pyc
diff --git a/__pycache__/cma.cpython-38.pyc b/__pycache__/cma.cpython-38.pyc
diff --git a/__pycache__/cma.cpython-39.pyc b/__pycache__/cma.cpython-39.pyc
diff --git a/__pycache__/directory_tree.cpython-35.pyc b/__pycache__/directory_tree.cpython-35.pyc
diff --git a/__pycache__/directory_tree.cpython-38.pyc b/__pycache__/directory_tree.cpython-38.pyc
diff --git a/__pycache__/directory_tree.cpython-39.pyc b/__pycache__/directory_tree.cpython-39.pyc
diff --git a/__pycache__/f_convert.cpython-35.pyc b/__pycache__/f_convert.cpython-35.pyc
diff --git a/__pycache__/f_convert.cpython-38.pyc b/__pycache__/f_convert.cpython-38.pyc
diff --git a/__pycache__/f_convert.cpython-39.pyc b/__pycache__/f_convert.cpython-39.pyc
diff --git a/__pycache__/f_read.cpython-35.pyc b/__pycache__/f_read.cpython-35.pyc
diff --git a/__pycache__/f_read.cpython-38.pyc b/__pycache__/f_read.cpython-38.pyc
diff --git a/__pycache__/f_read.cpython-39.pyc b/__pycache__/f_read.cpython-39.pyc
diff --git a/__pycache__/force_constant.cpython-35.pyc b/__pycache__/force_constant.cpython-35.pyc
diff --git a/__pycache__/force_constant.cpython-38.pyc b/__pycache__/force_constant.cpython-38.pyc
diff --git a/__pycache__/force_constant.cpython-39.pyc b/__pycache__/force_constant.cpython-39.pyc
diff --git a/__pycache__/g_matrix.cpython-35.pyc b/__pycache__/g_matrix.cpython-35.pyc
diff --git a/__pycache__/g_matrix.cpython-38.pyc b/__pycache__/g_matrix.cpython-38.pyc
diff --git a/__pycache__/g_matrix.cpython-39.pyc b/__pycache__/g_matrix.cpython-39.pyc
diff --git a/__pycache__/gf_method.cpython-35.pyc b/__pycache__/gf_method.cpython-35.pyc
diff --git a/__pycache__/gf_method.cpython-38.pyc b/__pycache__/gf_method.cpython-38.pyc
diff --git a/__pycache__/gf_method.cpython-39.pyc b/__pycache__/gf_method.cpython-39.pyc
diff --git a/__pycache__/int2cart.cpython-35.pyc b/__pycache__/int2cart.cpython-35.pyc
diff --git a/__pycache__/int2cart.cpython-38.pyc b/__pycache__/int2cart.cpython-38.pyc
diff --git a/__pycache__/int2cart.cpython-39.pyc b/__pycache__/int2cart.cpython-39.pyc
diff --git a/__pycache__/masses.cpython-35.pyc b/__pycache__/masses.cpython-35.pyc
diff --git a/__pycache__/masses.cpython-38.pyc b/__pycache__/masses.cpython-38.pyc
diff --git a/__pycache__/masses.cpython-39.pyc b/__pycache__/masses.cpython-39.pyc
diff --git a/__pycache__/options.cpython-35.pyc b/__pycache__/options.cpython-35.pyc
diff --git a/__pycache__/options.cpython-38.pyc b/__pycache__/options.cpython-38.pyc
diff --git a/__pycache__/options.cpython-39.pyc b/__pycache__/options.cpython-39.pyc
diff --git a/__pycache__/reap.cpython-35.pyc b/__pycache__/reap.cpython-35.pyc
diff --git a/__pycache__/reap.cpython-38.pyc b/__pycache__/reap.cpython-38.pyc
diff --git a/__pycache__/reap.cpython-39.pyc b/__pycache__/reap.cpython-39.pyc
diff --git a/__pycache__/rmsd.cpython-38.pyc b/__pycache__/rmsd.cpython-38.pyc
diff --git a/__pycache__/rmsd.cpython-39.pyc b/__pycache__/rmsd.cpython-39.pyc
diff --git a/__pycache__/s_vectors.cpython-38.pyc b/__pycache__/s_vectors.cpython-38.pyc
diff --git a/__pycache__/s_vectors.cpython-39.pyc b/__pycache__/s_vectors.cpython-39.pyc
diff --git a/__pycache__/sapelo_template.cpython-38.pyc b/__pycache__/sapelo_template.cpython-38.pyc
diff --git a/__pycache__/sapelo_template.cpython-39.pyc b/__pycache__/sapelo_template.cpython-39.pyc
diff --git a/__pycache__/submit.cpython-38.pyc b/__pycache__/submit.cpython-38.pyc
diff --git a/__pycache__/submit.cpython-39.pyc b/__pycache__/submit.cpython-39.pyc
diff --git a/__pycache__/ted.cpython-38.pyc b/__pycache__/ted.cpython-38.pyc
diff --git a/__pycache__/ted.cpython-39.pyc b/__pycache__/ted.cpython-39.pyc
diff --git a/__pycache__/transf_disp.cpython-38.pyc b/__pycache__/transf_disp.cpython-38.pyc
diff --git a/__pycache__/transf_disp.cpython-39.pyc b/__pycache__/transf_disp.cpython-39.pyc
diff --git a/__pycache__/vulcan_template.cpython-38.pyc b/__pycache__/vulcan_template.cpython-38.pyc
diff --git a/__pycache__/vulcan_template.cpython-39.pyc b/__pycache__/vulcan_template.cpython-39.pyc
diff --git a/__pycache__/zmat.cpython-38.pyc b/__pycache__/zmat.cpython-38.pyc
diff --git a/__pycache__/zmat.cpython-39.pyc b/__pycache__/zmat.cpython-39.pyc
diff --git a/options.py b/options.py
@@ -1,7 +1,7 @@
 class Options(object):
     def __init__(self, **kwargs):
         self.benchmark_full = kwargs.pop("benchmark_full", False)
-        self.bond_tol = kwargs.pop("inter_tol", 3.778)
+        self.bond_threshold = kwargs.pop("bond_threshold", 1.2)
         self.calc = kwargs.pop("calc", True)
         self.cart_coords = kwargs.pop("cart_coords", "Bohr")
         self.calc_init = kwargs.pop("calc_init", True)
@@ -10,6 +10,7 @@ def __init__(self, **kwargs):
         self.clean_house = kwargs.pop("clean_house", True)
         self.cluster = kwargs.pop("cluster", "vulcan")
         self.coords = kwargs.pop("coords", "ZMAT")
+        self.covalent_radii = kwargs.pop("covalent_radii", False)
         self.deriv_level = kwargs.pop("deriv_level", 0)
         self.deriv_level_init = kwargs.pop("deriv_level_init", 0)
         self.dir_reap = kwargs.pop("dir_reap", True)
@@ -22,7 +23,6 @@ def __init__(self, **kwargs):
         self.gen_disps_init = kwargs.pop("gen_disps_init",True)
         self.geom_check = kwargs.pop("geom_check", False)
         self.gradient_regex = kwargs.pop("gradient_regex", "")
-        self.interatomic_distance = kwargs.pop("interatomic_distance", False)
         self.man_proj = kwargs.pop("man_proj", False)
         self.mode_coupling_check = kwargs.pop("mode_coupling_check", False)
         self.molly_regex_init = kwargs.pop("molly_regex_init", "")
@@ -43,4 +43,6 @@ def __init__(self, **kwargs):
         self.success_regex_init = kwargs.pop("success_regex_init", "")
         self.tight_disp = kwargs.pop("tight_disp", False)
         self.tol = kwargs.pop("tol", 1.0e-14)
+        self.topo_analysis = kwargs.pop("topo_analysis", False)
+        self.topo_max_it = kwargs.pop("topo_max_it", 20)
         self.units = kwargs.pop("units", "HartreeBohr")
diff --git a/reap.py b/reap.py
@@ -97,8 +97,8 @@ def run(self):
                     direc, success_regex, energy_regex
                 )
                 # print(energy)
-                rel = ref_en - energy
-                print("Relative plus  " + "{:4d}".format(i) + " " + "{:4d}".format(j) + ": " + "{:10.9f}".format(rel))
+                rel = energy - ref_en
+                print("Relative plus  " + "{:4d}".format(direc) + "{:4d}".format(i) + " " + "{:4d}".format(j) + ": " + "{: 10.9f}".format(rel))
                 rel_en_p[i, j] = rel
                 relative_energies.append([(i, j), "plus", rel, direc])
                 absolute_energies.append([(i, j), "plus", energy, direc])
@@ -115,9 +115,9 @@ def run(self):
                     direc + 1, success_regex, energy_regex
                 )
                 # print(energy)
-                rel = ref_en - energy
+                rel = energy - ref_en
                 # print("Relative minus " + str(i) + " " + str(j) + ": " + "{:10.6f}".format(rel))
-                print("Relative minus " + "{:4d}".format(i) + " " + "{:4d}".format(j) + ": " + "{:10.9f}".format(rel))
+                print("Relative minus " + "{:4d}".format(direc + 1) + "{:4d}".format(i) + " " + "{:4d}".format(j) + ": " + "{: 10.9f}".format(rel))
                 rel_en_m[i, j] = rel
                 relative_energies.append([(i, j), "minus", rel, direc + 1])
                 absolute_energies.append([(i, j), "minus", energy, direc + 1])

diff --git a/s_vectors.py b/s_vectors.py
@@ -430,7 +430,7 @@ def run(self, carts, B_proj, proj=None, second_order=False):
                 axis=0,
             )
         # raise RuntimeError
-        tol = 1e-8
+        tol = 1e-4
         # Now we acquire a linearly independant set of internal coordinates from the diagonalized
         # BB^T Matrix
         if not self.options.man_proj:

diff --git a/tests/__pycache__/suite_execute.cpython-39.pyc b/tests/__pycache__/suite_execute.cpython-39.pyc
diff --git a/tests/__pycache__/test_directory_tree.cpython-39-pytest-7.2.0.pyc b/tests/__pycache__/test_directory_tree.cpython-39-pytest-7.2.0.pyc
diff --git a/tests/__pycache__/test_f_convert.cpython-39-pytest-7.2.0.pyc b/tests/__pycache__/test_f_convert.cpython-39-pytest-7.2.0.pyc
diff --git a/tests/__pycache__/test_f_read.cpython-39-pytest-7.2.0.pyc b/tests/__pycache__/test_f_read.cpython-39-pytest-7.2.0.pyc
diff --git a/tests/__pycache__/test_g_matrix.cpython-39-pytest-7.2.0.pyc b/tests/__pycache__/test_g_matrix.cpython-39-pytest-7.2.0.pyc
diff --git a/tests/__pycache__/test_gf_method.cpython-39-pytest-7.2.0.pyc b/tests/__pycache__/test_gf_method.cpython-39-pytest-7.2.0.pyc
diff --git a/tests/__pycache__/test_reap.cpython-39-pytest-7.2.0.pyc b/tests/__pycache__/test_reap.cpython-39-pytest-7.2.0.pyc
diff --git a/tests/__pycache__/test_s_vectors.cpython-39-pytest-7.2.0.pyc b/tests/__pycache__/test_s_vectors.cpython-39-pytest-7.2.0.pyc
diff --git a/tests/__pycache__/test_transf_disp.cpython-39-pytest-7.2.0.pyc b/tests/__pycache__/test_transf_disp.cpython-39-pytest-7.2.0.pyc
diff --git a/tests/__pycache__/test_zmat.cpython-39-pytest-7.2.0.pyc b/tests/__pycache__/test_zmat.cpython-39-pytest-7.2.0.pyc