Merger updated to incorporate symmetry arguments

4_G3_99/01_methyl_allene/CCSD_T_DZ/zmat

@@ -0,0 +1,60 @@
+ZMAT begin
+2 4
+
+4 6
+
+6 8
+
+4 7
+
+8 9
+8 10
+
+2 3
+2 1
+2 5
+
+2 4 6
+
+7 4 6
+7 4 2
+
+9 8 10
+9 8 6
+10 8 6
+
+3 2 4
+1 2 4
+5 2 4
+1 2 5
+3 2 1
+3 2 5
+
+9 8 4 2 T
+10 8 4 2 T
+
+3 2 4 6 T
+1 2 4 6 T
+5 2 4 6 T
+
+7 4 6 2 O
+
+6 8 9 10 O
+
+2 4 6 8 Lx
+
+2 4 6 8 Ly
+ZMAT end
+
+cart begin
+H         -0.4063218930       -4.5452283214       -1.6653946656
+C         -0.7229462960       -3.3658602411        0.0000000000
+H         -2.6867737654       -2.7453582157        0.0000000000
+C          1.0473272954       -1.1300075516        0.0000000000
+H         -0.4063218930       -4.5452283214        1.6653946656
+C          0.3023666876        1.2388656707        0.0000000000
+H          3.0647744520       -1.5099939362        0.0000000000
+C         -0.4592199501        3.6035698432        0.0000000000
+H         -0.7800404816        4.6096431560       -1.7547533134
+H         -0.7800404816        4.6096431560        1.7547533134
+cart end

4_G3_99/01_methyl_allene/CCSD_T_TZ/Disps_CCSD_T_DZ/fc_cart.grad

@@ -0,0 +1,10 @@
+       -0.0014668600        0.0056712045        0.0079007955
+       -0.0026669359       -0.0034125894        0.0000000000
+        0.0095028831       -0.0027998940        0.0000000000
+        0.0003824371        0.0127330457        0.0000000000
+       -0.0014668600        0.0056712045       -0.0079007955
+        0.0001285568       -0.0004384410        0.0000000000
+       -0.0107091975        0.0023473332       -0.0000000000
+        0.0026757042       -0.0084962453        0.0000000000
+        0.0018103317       -0.0056382056        0.0089206090
+        0.0018103317       -0.0056382056       -0.0089206090

4_G3_99/01_methyl_allene/CCSD_T_TZ/Disps_CCSD_T_DZ/templateInit.dat

@@ -0,0 +1,14 @@
+*** Optimization of methyl_allene
+memory,1000,m
+gthresh,energy=1.0d-12,orbital=1.0d-10,oneint=1.0d-16,twoint=1.0d-16,optgrad=1.0d-6,compress=1.0d-13
+geomtyp=xyz
+
+
+
+bohr
+geometry = {
+}
+
+basis=VDZ
+{rhf;maxit,200}
+{ccsd(t);maxit,200}

4_G3_99/01_methyl_allene/CCSD_T_TZ/Disps_MP2_TZ/fc_cart.grad

@@ -0,0 +1,10 @@
+        0.0002190128       -0.0012472438       -0.0016095656
+       -0.0005472314       -0.0012358989        0.0000000000
+       -0.0019330702        0.0004486133        0.0000000000
+        0.0023691837       -0.0018749724        0.0000000000
+        0.0002190128       -0.0012472436        0.0016095656
+        0.0002599807       -0.0002143668        0.0000000000
+        0.0012967099       -0.0005961276       -0.0000000001
+       -0.0012024499        0.0037498892       -0.0000000000
+       -0.0003403583        0.0011082399       -0.0011653778
+       -0.0003403582        0.0011082396        0.0011653778

4_G3_99/01_methyl_allene/CCSD_T_TZ/Disps_MP2_TZ/templateInit.dat

@@ -0,0 +1,14 @@
+*** Optimization of methyl_allene
+memory,1000,m
+gthresh,energy=1.0d-12,orbital=1.0d-10,oneint=1.0d-16,twoint=1.0d-16,optgrad=1.0d-6,compress=1.0d-13
+geomtyp=xyz
+
+
+
+bohr
+geometry = {
+}
+
+basis=VTZ
+{rhf;maxit,200}
+{MP2}

4_G3_99/01_methyl_allene/CCSD_T_TZ/zmat

@@ -0,0 +1,60 @@
+ZMAT begin
+2 4
+
+4 6
+
+6 8
+
+4 7
+
+8 9
+8 10
+
+2 3
+2 1
+2 5
+
+2 4 6
+
+7 4 6
+7 4 2
+
+9 8 10
+9 8 6
+10 8 6
+
+3 2 4
+1 2 4
+5 2 4
+1 2 5
+3 2 1
+3 2 5
+
+9 8 4 2 T
+10 8 4 2 T
+
+3 2 4 6 T
+1 2 4 6 T
+5 2 4 6 T
+
+6 8 9 10 O
+
+7 4 6 2 O
+
+2 4 6 8 Lx
+
+2 4 6 8 Ly
+ZMAT end
+
+cart begin
+H         -0.4063218930       -4.5452283214       -1.6653946656
+C         -0.7229462960       -3.3658602411        0.0000000000
+H         -2.6867737654       -2.7453582157        0.0000000000
+C          1.0473272954       -1.1300075516        0.0000000000
+H         -0.4063218930       -4.5452283214        1.6653946656
+C          0.3023666876        1.2388656707        0.0000000000
+H          3.0647744520       -1.5099939362        0.0000000000
+C         -0.4592199501        3.6035698432        0.0000000000
+H         -0.7800404816        4.6096431560       -1.7547533134
+H         -0.7800404816        4.6096431560        1.7547533134
+cart end

4_G3_99/01_methyl_allene/MP2_TZ/zmat

@@ -0,0 +1,60 @@
+ZMAT begin
+2 4
+
+4 6
+
+6 8
+
+4 7
+
+8 9
+8 10
+
+2 3
+2 1
+2 5
+
+2 4 6
+
+7 4 6
+7 4 2
+
+9 8 10
+9 8 6
+10 8 6
+
+3 2 4
+1 2 4
+5 2 4
+1 2 5
+3 2 1
+3 2 5
+
+9 8 4 2 T
+10 8 4 2 T
+
+3 2 4 6 T
+1 2 4 6 T
+5 2 4 6 T
+
+6 8 9 10 O
+
+7 4 6 2 O
+
+2 4 6 8 Lx
+
+2 4 6 8 Ly
+ZMAT end
+
+cart begin
+H         -0.4063218930       -4.5452283214       -1.6653946656
+C         -0.7229462960       -3.3658602411        0.0000000000
+H         -2.6867737654       -2.7453582157        0.0000000000
+C          1.0473272954       -1.1300075516        0.0000000000
+H         -0.4063218930       -4.5452283214        1.6653946656
+C          0.3023666876        1.2388656707        0.0000000000
+H          3.0647744520       -1.5099939362        0.0000000000
+C         -0.4592199501        3.6035698432        0.0000000000
+H         -0.7800404816        4.6096431560       -1.7547533134
+H         -0.7800404816        4.6096431560        1.7547533134
+cart end

4_G3_99/01_methyl_allene/manual_projection.py

@@ -0,0 +1,108 @@
+import numpy as np
+from numpy.linalg import norm
+from scipy.linalg import block_diag
+
+
+class Projection(object):
+    """
+    This class is used to specify the manual projection matrix
+    for CMA. It is stored as an object and is only needed when
+    self.options.man_proj = True.
+    """
+
+    def __init__(self,  options):
+
+        self.options = options
+
+    def run(self):
+
+        # 0
+        str_c2c4 = np.eye(1)
+
+        # 1
+        str_c4c6 = np.eye(1)
+
+        # 2
+        str_c6c8 = np.eye(1)
+
+        # 3
+        str_c4h7 = np.eye(1)
+
+        # 4-5
+        str_ch2_c8 = normalize(np.array([
+            [1, 1],
+            [1, -1]
+        ]).T)
+
+        # 6-8
+        str_ch3_c2 = normalize(np.array([
+            [1, 1, 1],
+            [2, -1, -1],
+            [0, 1, -1]
+        ]).T)
+
+        # 9
+        ang_c2c4c6 = np.eye(1)
+
+        # 10
+        ang_ch_c4 = normalize(np.array([
+            [1, -1]
+        ]).T)
+
+        # 11-12
+        ang_ch2_c8 = normalize(np.array([
+            [2, -1, -1],
+            [0, 1, -1]
+        ]).T)
+
+        # 13-17
+        ang_ch3_c2 = normalize(np.array([
+            [1, 1, 1, -1, -1, -1],
+            [2, -1, -1, 0, 0, 0],
+            [0, 1, -1, 0, 0, 0],
+            [0, 0, 0, 2, -1, -1],
+            [0, 0, 0, 0, 1, -1]
+        ]).T)
+
+        # 18
+        rot_ch2_c8 = normalize(np.array([
+            [1, 1]
+        ]).T)
+
+        # 19
+        rot_ch3_c2 = normalize(np.array([
+            [1, 1, 1]
+        ]).T)
+
+        # 20
+        oop_c8 = np.eye(1)
+
+        # 21
+        oop_c4 = np.eye(1)
+
+        # 22
+        linx_c4 = np.eye(1)
+
+        # 23
+        liny_c4 = np.eye(1)
+
+        Proj = block_diag(str_c2c4, str_c4c6, str_c6c8, str_c4h7, str_ch2_c8, str_ch3_c2, ang_c2c4c6,
+                          ang_ch_c4, ang_ch2_c8, ang_ch3_c2, rot_ch2_c8, rot_ch3_c2, oop_c8, oop_c4, linx_c4, liny_c4)
+
+        self.Proj = Proj
+
+        self.sym_sort = np.array([
+            [0, 1, 2, 3, 4, 6, 7, 9, 10, 11, 13, 14, 16, 20, 22],
+            [5, 8, 12, 15, 17, 18, 19, 21, 23]
+        ], dtype=object)
+
+
+def normalize(mat):
+    return 1/norm(mat, axis=0)*mat
+
+
+if __name__ == "__main__":
+    np.set_printoptions(linewidth=400, precision=2, threshold=100000)
+    p = Projection([])
+    p.run()
+    print(p.Proj)