5 Commits 71eb4fa60f ... 15014666c6

Autor SHA1 Mensagem Data
  Kei Kebreau 15014666c6 Fix add_ligands.m to use CdSe clusters generated by generate_cdse.m. 5 anos atrás
  Kei Kebreau 2eda3714c4 Remove obsolete plane equation scripts. 5 anos atrás
  Kei Kebreau 5254c00bc8 Add new template molecules. 5 anos atrás
  Kei Kebreau 3e9b93b7e0 Relicense project to GPL version 3 or later where applicable. 5 anos atrás
  Kei Kebreau 5c3f61b5d6 Add cluster generation script. 5 anos atrás
10 arquivos alterados com 1025 adições e 536 exclusões
  1. 55 55
      Cd35Se20.xyz
  2. 0 21
      Cd35Se20_PlaneEquations.mac
  3. 91 91
      Cd56Se35.xyz
  4. 0 21
      Cd56Se35_PlaneEquations.mac
  5. 142 142
      Cd84Se56.xyz
  6. 0 26
      Cd84Se56_PlaneEquations.mac
  7. 671 5
      LICENSE
  8. 5 0
      README.md
  9. 61 175
      add_ligands.m
  10. 0 0
      calc_hydroxl_dist.m

+ 55 - 55
Cd35Se20.xyz

@@ -1,57 +1,57 @@
 55
 
-Cd         0.00000        0.00000        0.00000
-Se         1.51930        1.51930        1.51930
-Cd         0.00000        3.03850        3.03850
-Cd         3.03850        0.00000        3.03850
-Cd         3.03850        3.03850        0.00000
-Se         4.55780        4.55780        1.51930
-Se         4.55780        1.51930        4.55780
-Se         1.51930        4.55780        4.55780
-Cd         3.03850        3.03850        6.07700
-Cd         6.07700        3.03850        3.03850
-Cd         3.03850        6.07700        3.03850
-Cd         0.00000        6.07700        6.07700
-Cd         6.07700        0.00000        6.07700
-Cd         6.07700        6.07700        0.00000
-Se         4.55780        4.55780        7.59630
-Se         4.55780        7.59630        4.55780
-Se         7.59630        4.55780        4.55780
-Cd         6.07700        6.07700        6.07700
-Se         1.51930        7.59630        7.59630
-Se         7.59630        1.51930        7.59630
-Se         7.59630        7.59630        1.51930
-Cd         6.07700        3.03850        9.11550
-Cd         6.07700        9.11550        3.03850
-Cd         3.03850        6.07700        9.11550
-Cd         9.11550        6.07700        3.03850
-Cd         3.03850        9.11550        6.07700
-Cd         9.11550        3.03850        6.07700
-Cd         0.00000        9.11550        9.11550
-Cd         9.11550        0.00000        9.11550
-Cd         9.11550        9.11550        0.00000
-Se         7.59630        7.59630        7.59630
-Se         4.55780       10.63480        7.59630
-Se        10.63480        4.55780        7.59630
-Se         4.55780        7.59630       10.63480
-Se        10.63480        7.59630        4.55780
-Se         7.59630        4.55780       10.63480
-Se         7.59630       10.63480        4.55780
-Cd         6.07700        9.11550        9.11550
-Cd         9.11550        6.07700        9.11550
-Cd         9.11550        9.11550        6.07700
-Cd         6.07700        6.07700       12.15400
-Cd         6.07700       12.15400        6.07700
-Cd        12.15400        6.07700        6.07700
-Se        10.63480       10.63480        1.51930
-Se        10.63480        1.51930       10.63480
-Se         1.51930       10.63480       10.63480
-Cd        12.15400        9.11550        3.03850
-Cd         9.11550       12.15400        3.03850
-Cd        12.15400        3.03850        9.11550
-Cd         3.03850       12.15400        9.11550
-Cd         3.03850        9.11550       12.15400
-Cd         9.11550        3.03850       12.15400
-Cd         0.00000       12.15400       12.15400
-Cd        12.15400        0.00000       12.15400
-Cd        12.15400       12.15400        0.00000
+Cd 0.000000 12.154000 12.154000
+Cd 3.038500 9.115500 12.154000
+Cd 6.077000 6.077000 12.154000
+Cd 9.115500 3.038500 12.154000
+Cd 12.154000 0.000000 12.154000
+Cd 3.038500 12.154000 9.115500
+Cd 6.077000 9.115500 9.115500
+Cd 9.115500 6.077000 9.115500
+Cd 12.154000 3.038500 9.115500
+Cd 6.077000 12.154000 6.077000
+Cd 9.115500 9.115500 6.077000
+Cd 12.154000 6.077000 6.077000
+Cd 9.115500 12.154000 3.038500
+Cd 12.154000 9.115500 3.038500
+Cd 12.154000 12.154000 0.000000
+Cd 0.000000 9.115500 9.115500
+Cd 3.038500 6.077000 9.115500
+Cd 6.077000 3.038500 9.115500
+Cd 9.115500 0.000000 9.115500
+Cd 3.038500 9.115500 6.077000
+Cd 6.077000 6.077000 6.077000
+Cd 9.115500 3.038500 6.077000
+Cd 6.077000 9.115500 3.038500
+Cd 9.115500 6.077000 3.038500
+Cd 9.115500 9.115500 0.000000
+Cd 0.000000 6.077000 6.077000
+Cd 3.038500 3.038500 6.077000
+Cd 6.077000 0.000000 6.077000
+Cd 3.038500 6.077000 3.038500
+Cd 6.077000 3.038500 3.038500
+Cd 6.077000 6.077000 0.000000
+Cd 0.000000 3.038500 3.038500
+Cd 3.038500 0.000000 3.038500
+Cd 3.038500 3.038500 0.000000
+Cd 0.000000 0.000000 0.000000
+Se 1.519300 10.634800 10.634800
+Se 4.557800 7.596300 10.634800
+Se 7.596300 4.557800 10.634800
+Se 10.634800 1.519300 10.634800
+Se 4.557800 10.634800 7.596300
+Se 7.596300 7.596300 7.596300
+Se 10.634800 4.557800 7.596300
+Se 7.596300 10.634800 4.557800
+Se 10.634800 7.596300 4.557800
+Se 10.634800 10.634800 1.519300
+Se 1.519300 7.596300 7.596300
+Se 4.557800 4.557800 7.596300
+Se 7.596300 1.519300 7.596300
+Se 4.557800 7.596300 4.557800
+Se 7.596300 4.557800 4.557800
+Se 7.596300 7.596300 1.519300
+Se 1.519300 4.557800 4.557800
+Se 4.557800 1.519300 4.557800
+Se 4.557800 4.557800 1.519300
+Se 1.519300 1.519300 1.519300

+ 0 - 21
Cd35Se20_PlaneEquations.mac

@@ -1,21 +0,0 @@
-load("vect")$
-A:[0,0,0]$
-B:[12.154,12.154,0]$
-C:[0,12.154,12.154]$
-D:[12.154,0,12.154]$
-AC:A-C$
-AD:A-D$
-BC:B-C$
-BD:B-D$
-express(AD ~ AC), numer$
-back_face:expand(%[1]*(x-A[1])+%[2]*(y-A[2])+%[3]*(z-A[3]) = 0)$
-express(BD ~ BC), numer$
-front_face:expand(%[1]*(x-B[1])+%[2]*(y-B[2])+%[3]*(z-B[3]) = 0)$
-express(AD ~ BD), numer$
-left_face:expand(%[1]*(x-B[1])+%[2]*(y-B[2])+%[3]*(z-B[3])=0)$
-express(AC ~ BC), numer$
-right_face:expand(%[1]*(x-B[1])+%[2]*(y-B[2])+%[3]*(z-B[3])=0)$
-back_face;
-front_face;
-left_face;
-right_face;

+ 91 - 91
Cd56Se35.xyz

@@ -1,93 +1,93 @@
 91
 
-Cd         0.00000        0.00000        0.00000
-Se         1.51930        1.51930        1.51930
-Cd         0.00000        3.03850        3.03850
-Cd         3.03850        0.00000        3.03850
-Cd         3.03850        3.03850        0.00000
-Se         4.55780        4.55780        1.51930
-Se         4.55780        1.51930        4.55780
-Se         1.51930        4.55780        4.55780
-Cd         3.03850        3.03850        6.07700
-Cd         6.07700        3.03850        3.03850
-Cd         3.03850        6.07700        3.03850
-Cd         0.00000        6.07700        6.07700
-Cd         6.07700        0.00000        6.07700
-Cd         6.07700        6.07700        0.00000
-Se         4.55780        4.55780        7.59630
-Se         4.55780        7.59630        4.55780
-Se         7.59630        4.55780        4.55780
-Cd         6.07700        6.07700        6.07700
-Se         1.51930        7.59630        7.59630
-Se         7.59630        1.51930        7.59630
-Se         7.59630        7.59630        1.51930
-Cd         6.07700        3.03850        9.11550
-Cd         6.07700        9.11550        3.03850
-Cd         3.03850        6.07700        9.11550
-Cd         9.11550        6.07700        3.03850
-Cd         3.03850        9.11550        6.07700
-Cd         9.11550        3.03850        6.07700
-Cd         0.00000        9.11550        9.11550
-Cd         9.11550        0.00000        9.11550
-Cd         9.11550        9.11550        0.00000
-Se         7.59630        7.59630        7.59630
-Se         4.55780       10.63480        7.59630
-Se        10.63480        4.55780        7.59630
-Se         4.55780        7.59630       10.63480
-Se        10.63480        7.59630        4.55780
-Se         7.59630        4.55780       10.63480
-Se         7.59630       10.63480        4.55780
-Cd         6.07700        9.11550        9.11550
-Cd         9.11550        6.07700        9.11550
-Cd         9.11550        9.11550        6.07700
-Cd         6.07700        6.07700       12.15400
-Cd         6.07700       12.15400        6.07700
-Cd        12.15400        6.07700        6.07700
-Se        10.63480       10.63480        1.51930
-Se        10.63480        1.51930       10.63480
-Se         1.51930       10.63480       10.63480
-Cd        12.15400        9.11550        3.03850
-Cd         9.11550       12.15400        3.03850
-Cd        12.15400        3.03850        9.11550
-Cd         3.03850       12.15400        9.11550
-Cd         3.03850        9.11550       12.15400
-Cd         9.11550        3.03850       12.15400
-Se        10.63480       10.63480        7.59630
-Se        10.63480        7.59630       10.63480
-Se         7.59630       10.63480       10.63480
-Cd         0.00000       12.15400       12.15400
-Cd        12.15400        0.00000       12.15400
-Cd        12.15400       12.15400        0.00000
-Se         7.59630        7.59630       13.67320
-Se         7.59630       13.67320        7.59630
-Se        13.67320        7.59630        7.59630
-Cd        12.15400        9.11550        9.11550
-Cd         9.11550       12.15400        9.11550
-Cd         9.11550        9.11550       12.15400
-Se         4.55780       10.63480       13.67320
-Se        10.63480        4.55780       13.67320
-Se         4.55780       13.67320       10.63480
-Se        10.63480       13.67320        4.55780
-Se        13.67320        4.55780       10.63480
-Se        13.67320       10.63480        4.55780
-Cd         6.07700       12.15400       12.15400
-Cd        12.15400        6.07700       12.15400
-Cd        12.15400       12.15400        6.07700
-Cd         6.07700        9.11550       15.19250
-Cd         6.07700       15.19250        9.11550
-Cd         9.11550        6.07700       15.19250
-Cd        15.19250        6.07700        9.11550
-Cd         9.11550       15.19250        6.07700
-Cd        15.19250        9.11550        6.07700
-Se         1.51930       13.67320       13.67320
-Se        13.67320        1.51930       13.67320
-Se        13.67320       13.67320        1.51930
-Cd        12.15400        3.03850       15.19250
-Cd        12.15400       15.19250        3.03850
-Cd         3.03850       12.15400       15.19250
-Cd        15.19250       12.15400        3.03850
-Cd         3.03850       15.19250       12.15400
-Cd        15.19250        3.03850       12.15400
-Cd         0.00000       15.19250       15.19250
-Cd        15.19250        0.00000       15.19250
-Cd        15.19250       15.19250        0.00000
+Cd 0.000000 15.192500 15.192500
+Cd 3.038500 12.154000 15.192500
+Cd 6.077000 9.115500 15.192500
+Cd 9.115500 6.077000 15.192500
+Cd 12.154000 3.038500 15.192500
+Cd 15.192500 0.000000 15.192500
+Cd 3.038500 15.192500 12.154000
+Cd 6.077000 12.154000 12.154000
+Cd 9.115500 9.115500 12.154000
+Cd 12.154000 6.077000 12.154000
+Cd 15.192500 3.038500 12.154000
+Cd 6.077000 15.192500 9.115500
+Cd 9.115500 12.154000 9.115500
+Cd 12.154000 9.115500 9.115500
+Cd 15.192500 6.077000 9.115500
+Cd 9.115500 15.192500 6.077000
+Cd 12.154000 12.154000 6.077000
+Cd 15.192500 9.115500 6.077000
+Cd 12.154000 15.192500 3.038500
+Cd 15.192500 12.154000 3.038500
+Cd 15.192500 15.192500 0.000000
+Cd 0.000000 12.154000 12.154000
+Cd 3.038500 9.115500 12.154000
+Cd 6.077000 6.077000 12.154000
+Cd 9.115500 3.038500 12.154000
+Cd 12.154000 0.000000 12.154000
+Cd 3.038500 12.154000 9.115500
+Cd 6.077000 9.115500 9.115500
+Cd 9.115500 6.077000 9.115500
+Cd 12.154000 3.038500 9.115500
+Cd 6.077000 12.154000 6.077000
+Cd 9.115500 9.115500 6.077000
+Cd 12.154000 6.077000 6.077000
+Cd 9.115500 12.154000 3.038500
+Cd 12.154000 9.115500 3.038500
+Cd 12.154000 12.154000 0.000000
+Cd 0.000000 9.115500 9.115500
+Cd 3.038500 6.077000 9.115500
+Cd 6.077000 3.038500 9.115500
+Cd 9.115500 0.000000 9.115500
+Cd 3.038500 9.115500 6.077000
+Cd 6.077000 6.077000 6.077000
+Cd 9.115500 3.038500 6.077000
+Cd 6.077000 9.115500 3.038500
+Cd 9.115500 6.077000 3.038500
+Cd 9.115500 9.115500 0.000000
+Cd 0.000000 6.077000 6.077000
+Cd 3.038500 3.038500 6.077000
+Cd 6.077000 0.000000 6.077000
+Cd 3.038500 6.077000 3.038500
+Cd 6.077000 3.038500 3.038500
+Cd 6.077000 6.077000 0.000000
+Cd 0.000000 3.038500 3.038500
+Cd 3.038500 0.000000 3.038500
+Cd 3.038500 3.038500 0.000000
+Cd 0.000000 0.000000 0.000000
+Se 1.519300 13.673300 13.673300
+Se 4.557800 10.634800 13.673300
+Se 7.596300 7.596300 13.673300
+Se 10.634800 4.557800 13.673300
+Se 13.673300 1.519300 13.673300
+Se 4.557800 13.673300 10.634800
+Se 7.596300 10.634800 10.634800
+Se 10.634800 7.596300 10.634800
+Se 13.673300 4.557800 10.634800
+Se 7.596300 13.673300 7.596300
+Se 10.634800 10.634800 7.596300
+Se 13.673300 7.596300 7.596300
+Se 10.634800 13.673300 4.557800
+Se 13.673300 10.634800 4.557800
+Se 13.673300 13.673300 1.519300
+Se 1.519300 10.634800 10.634800
+Se 4.557800 7.596300 10.634800
+Se 7.596300 4.557800 10.634800
+Se 10.634800 1.519300 10.634800
+Se 4.557800 10.634800 7.596300
+Se 7.596300 7.596300 7.596300
+Se 10.634800 4.557800 7.596300
+Se 7.596300 10.634800 4.557800
+Se 10.634800 7.596300 4.557800
+Se 10.634800 10.634800 1.519300
+Se 1.519300 7.596300 7.596300
+Se 4.557800 4.557800 7.596300
+Se 7.596300 1.519300 7.596300
+Se 4.557800 7.596300 4.557800
+Se 7.596300 4.557800 4.557800
+Se 7.596300 7.596300 1.519300
+Se 1.519300 4.557800 4.557800
+Se 4.557800 1.519300 4.557800
+Se 4.557800 4.557800 1.519300
+Se 1.519300 1.519300 1.519300

+ 0 - 21
Cd56Se35_PlaneEquations.mac

@@ -1,21 +0,0 @@
-load("vect")$
-A:[0,0,0]$
-B:[15.1925,15.1925,0]$
-C:[0,15.1925,15.1925]$
-D:[15.1925,0,15.1925]$
-AC:A-C$
-AD:A-D$
-BC:B-C$
-BD:B-D$
-express(AD ~ AC), numer$
-back_face:expand(%[1]*(x-A[1])+%[2]*(y-A[2])+%[3]*(z-A[3]) = 0)$
-express(BD ~ BC), numer$
-front_face:expand(%[1]*(x-B[1])+%[2]*(y-B[2])+%[3]*(z-B[3]) = 0)$
-express(AD ~ BD), numer$
-left_face:expand(%[1]*(x-B[1])+%[2]*(y-B[2])+%[3]*(z-B[3])=0)$
-express(AC ~ BC), numer$
-right_face:expand(%[1]*(x-B[1])+%[2]*(y-B[2])+%[3]*(z-B[3])=0)$
-back_face;
-front_face;
-left_face;
-right_face;

+ 142 - 142
Cd84Se56.xyz

@@ -1,142 +1,142 @@
-140
-
-Cd      0.000000    0.000000    0.000000
-Se      1.519300    1.519300    1.519300
-Cd      0.000000    3.038500    3.038500
-Cd      3.038500    0.000000    3.038500
-Cd      3.038500    3.038500    0.000000
-Se      4.557800    4.557800    1.519300
-Se      4.557800    1.519300    4.557800
-Se      1.519300    4.557800    4.557800
-Cd      3.038500    3.038500    6.077000
-Cd      6.077000    3.038500    3.038500
-Cd      3.038500    6.077000    3.038500
-Cd      0.000000    6.077000    6.077000
-Cd      6.077000    0.000000    6.077000
-Cd      6.077000    6.077000    0.000000
-Se      4.557800    4.557800    7.596300
-Se      4.557800    7.596300    4.557800
-Se      7.596300    4.557800    4.557800
-Cd      6.077000    6.077000    6.077000
-Se      1.519300    7.596300    7.596300
-Se      7.596300    1.519300    7.596300
-Se      7.596300    7.596300    1.519300
-Cd      6.077000    3.038500    9.115500
-Cd      6.077000    9.115500    3.038500
-Cd      3.038500    6.077000    9.115500
-Cd      9.115500    6.077000    3.038500
-Cd      3.038500    9.115500    6.077000
-Cd      9.115500    3.038500    6.077000
-Cd      0.000000    9.115500    9.115500
-Cd      9.115500    0.000000    9.115500
-Cd      9.115500    9.115500    0.000000
-Se      7.596300    7.596300    7.596300
-Se      4.557800   10.634800    7.596300
-Se     10.634800    4.557800    7.596300
-Se      4.557800    7.596300   10.634800
-Se     10.634800    7.596300    4.557800
-Se      7.596300    4.557800   10.634800
-Se      7.596300   10.634800    4.557800
-Cd      6.077000    9.115500    9.115500
-Cd      9.115500    6.077000    9.115500
-Cd      9.115500    9.115500    6.077000
-Cd      6.077000    6.077000   12.154000
-Cd      6.077000   12.154000    6.077000
-Cd     12.154000    6.077000    6.077000
-Se     10.634800   10.634800    1.519300
-Se     10.634800    1.519300   10.634800
-Se      1.519300   10.634800   10.634800
-Cd     12.154000    9.115500    3.038500
-Cd      9.115500   12.154000    3.038500
-Cd     12.154000    3.038500    9.115500
-Cd      3.038500   12.154000    9.115500
-Cd      3.038500    9.115500   12.154000
-Cd      9.115500    3.038500   12.154000
-Se     10.634800   10.634800    7.596300
-Se     10.634800    7.596300   10.634800
-Se      7.596300   10.634800   10.634800
-Cd      0.000000   12.154000   12.154000
-Cd     12.154000    0.000000   12.154000
-Cd     12.154000   12.154000    0.000000
-Se      7.596300    7.596300   13.673200
-Se      7.596300   13.673200    7.596300
-Se     13.673200    7.596300    7.596300
-Cd     12.154000    9.115500    9.115500
-Cd      9.115500   12.154000    9.115500
-Cd      9.115500    9.115500   12.154000
-Se      4.557800   10.634800   13.673200
-Se     10.634800    4.557800   13.673200
-Se      4.557800   13.673200   10.634800
-Se     10.634800   13.673200    4.557800
-Se     13.673200    4.557800   10.634800
-Se     13.673200   10.634800    4.557800
-Cd      6.077000   12.154000   12.154000
-Cd     12.154000    6.077000   12.154000
-Cd     12.154000   12.154000    6.077000
-Cd      6.077000    9.115500   15.192500
-Cd      6.077000   15.192500    9.115500
-Cd      9.115500    6.077000   15.192500
-Cd     15.192500    6.077000    9.115500
-Cd      9.115500   15.192500    6.077000
-Cd     15.192500    9.115500    6.077000
-Se      1.519300   13.673200   13.673200
-Se     13.673200    1.519300   13.673200
-Se     13.673200   13.673200    1.519300
-Cd     12.154000    3.038500   15.192500
-Cd     12.154000   15.192500    3.038500
-Cd      3.038500   12.154000   15.192500
-Cd     15.192500   12.154000    3.038500
-Cd      3.038500   15.192500   12.154000
-Cd     15.192500    3.038500   12.154000
-Se     10.634800   10.634800   13.673200
-Se     10.634800   13.673200   10.634800
-Se     13.673200   10.634800   10.634800
-Se      7.596300   13.673200   13.673200
-Se     13.673200    7.596300   13.673200
-Se     13.673200   13.673200    7.596300
-Cd     12.154000   12.154000   12.154000
-Se     10.634800    7.596300   16.711800
-Se     16.711800    7.596300   10.634800
-Se      7.596300   10.634800   16.711800
-Se      7.596300   16.711800   10.634800
-Se     10.634800   16.711800    7.596300
-Se     16.711800   10.634800    7.596300
-Cd      0.000000   15.192500   15.192500
-Cd     15.192500    0.000000   15.192500
-Cd     15.192500   15.192500    0.000000
-Cd     12.154000    9.115500   15.192500
-Cd     12.154000   15.192500    9.115500
-Cd      9.115500   12.154000   15.192500
-Cd     15.192500   12.154000    9.115500
-Cd      9.115500   15.192500   12.154000
-Cd     15.192500    9.115500   12.154000
-Se      4.557800   16.711800   13.673200
-Se     16.711800    4.557800   13.673200
-Se      4.557800   13.673200   16.711800
-Se     16.711800   13.673200    4.557800
-Se     13.673200    4.557800   16.711800
-Se     13.673200   16.711800    4.557800
-Cd      6.077000   15.192500   15.192500
-Cd     15.192500    6.077000   15.192500
-Cd     18.231000    9.115500    9.115500
-Cd      9.115500   18.231000    9.115500
-Cd     15.192500   15.192500    6.077000
-Cd      9.115500    9.115500   18.231000
-Cd      6.077000   12.154000   18.231000
-Cd      6.077000   18.231000   12.154000
-Cd     12.154000    6.077000   18.231000
-Cd     12.154000   18.231000    6.077000
-Cd     18.231000    6.077000   12.154000
-Cd     18.231000   12.154000    6.077000
-Se     16.711800   16.711800    1.519300
-Se     16.711800    1.519300   16.711800
-Se      1.519300   16.711800   16.711800
-Cd     18.231000    3.038500   15.192500
-Cd     18.231000   15.192500    3.038500
-Cd      3.038500   18.231000   15.192500
-Cd     15.192500   18.231000    3.038500
-Cd      3.038500   15.192500   18.231000
-Cd     15.192500    3.038500   18.231000
-Cd     18.231000   18.231000    0.000000
-Cd      0.000000   18.231000   18.231000
-Cd     18.231000    0.000000   18.231000
+140
+
+Cd 0.000000 18.231000 18.231000
+Cd 3.038500 15.192500 18.231000
+Cd 6.077000 12.154000 18.231000
+Cd 9.115500 9.115500 18.231000
+Cd 12.154000 6.077000 18.231000
+Cd 15.192500 3.038500 18.231000
+Cd 18.231000 0.000000 18.231000
+Cd 3.038500 18.231000 15.192500
+Cd 6.077000 15.192500 15.192500
+Cd 9.115500 12.154000 15.192500
+Cd 12.154000 9.115500 15.192500
+Cd 15.192500 6.077000 15.192500
+Cd 18.231000 3.038500 15.192500
+Cd 6.077000 18.231000 12.154000
+Cd 9.115500 15.192500 12.154000
+Cd 12.154000 12.154000 12.154000
+Cd 15.192500 9.115500 12.154000
+Cd 18.231000 6.077000 12.154000
+Cd 9.115500 18.231000 9.115500
+Cd 12.154000 15.192500 9.115500
+Cd 15.192500 12.154000 9.115500
+Cd 18.231000 9.115500 9.115500
+Cd 12.154000 18.231000 6.077000
+Cd 15.192500 15.192500 6.077000
+Cd 18.231000 12.154000 6.077000
+Cd 15.192500 18.231000 3.038500
+Cd 18.231000 15.192500 3.038500
+Cd 18.231000 18.231000 0.000000
+Cd 0.000000 15.192500 15.192500
+Cd 3.038500 12.154000 15.192500
+Cd 6.077000 9.115500 15.192500
+Cd 9.115500 6.077000 15.192500
+Cd 12.154000 3.038500 15.192500
+Cd 15.192500 0.000000 15.192500
+Cd 3.038500 15.192500 12.154000
+Cd 6.077000 12.154000 12.154000
+Cd 9.115500 9.115500 12.154000
+Cd 12.154000 6.077000 12.154000
+Cd 15.192500 3.038500 12.154000
+Cd 6.077000 15.192500 9.115500
+Cd 9.115500 12.154000 9.115500
+Cd 12.154000 9.115500 9.115500
+Cd 15.192500 6.077000 9.115500
+Cd 9.115500 15.192500 6.077000
+Cd 12.154000 12.154000 6.077000
+Cd 15.192500 9.115500 6.077000
+Cd 12.154000 15.192500 3.038500
+Cd 15.192500 12.154000 3.038500
+Cd 15.192500 15.192500 0.000000
+Cd 0.000000 12.154000 12.154000
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+Cd 6.077000 6.077000 12.154000
+Cd 9.115500 3.038500 12.154000
+Cd 12.154000 0.000000 12.154000
+Cd 3.038500 12.154000 9.115500
+Cd 6.077000 9.115500 9.115500
+Cd 9.115500 6.077000 9.115500
+Cd 12.154000 3.038500 9.115500
+Cd 6.077000 12.154000 6.077000
+Cd 9.115500 9.115500 6.077000
+Cd 12.154000 6.077000 6.077000
+Cd 9.115500 12.154000 3.038500
+Cd 12.154000 9.115500 3.038500
+Cd 12.154000 12.154000 0.000000
+Cd 0.000000 9.115500 9.115500
+Cd 3.038500 6.077000 9.115500
+Cd 6.077000 3.038500 9.115500
+Cd 9.115500 0.000000 9.115500
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+Cd 6.077000 6.077000 6.077000
+Cd 9.115500 3.038500 6.077000
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+Se 13.673300 1.519300 13.673300
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+Se 10.634800 7.596300 10.634800
+Se 13.673300 4.557800 10.634800
+Se 7.596300 13.673300 7.596300
+Se 10.634800 10.634800 7.596300
+Se 13.673300 7.596300 7.596300
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+Se 13.673300 10.634800 4.557800
+Se 13.673300 13.673300 1.519300
+Se 1.519300 10.634800 10.634800
+Se 4.557800 7.596300 10.634800
+Se 7.596300 4.557800 10.634800
+Se 10.634800 1.519300 10.634800
+Se 4.557800 10.634800 7.596300
+Se 7.596300 7.596300 7.596300
+Se 10.634800 4.557800 7.596300
+Se 7.596300 10.634800 4.557800
+Se 10.634800 7.596300 4.557800
+Se 10.634800 10.634800 1.519300
+Se 1.519300 7.596300 7.596300
+Se 4.557800 4.557800 7.596300
+Se 7.596300 1.519300 7.596300
+Se 4.557800 7.596300 4.557800
+Se 7.596300 4.557800 4.557800
+Se 7.596300 7.596300 1.519300
+Se 1.519300 4.557800 4.557800
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+Se 4.557800 4.557800 1.519300
+Se 1.519300 1.519300 1.519300

+ 0 - 26
Cd84Se56_PlaneEquations.mac

@@ -1,26 +0,0 @@
-A:[0,0,0];
-B:[18.231,18.231,0];
-C:[0,18.231,18.231];
-D:[18.231,0,18.231];
-load("vect");
-express((A-D) ~ (A-C));
-back_face:%o9[1]*(x-A[1])+%o9[2]*(y-A[2])+%o9[3]*(z-A[3]) = 0;
-back_face:expand(back_face);
-express((B-D) ~ (B-C));
-front_face:%[1]*(x-B[1])+%[2]*(y-B[2])+%[3]*(z-B[3]) = 0;
-front_face:expand(front_face);
-express((A-D) ~ (B-D));
-left_face:%[1]*(x-B[1])+%[2]*(y-B[2])+%[3]*(z-B[3]) = 0;
-left_face:expand(left_face);
-express((A-C) ~ (B-C));
-right_face:%[1]*(x-B[1])+%[2]*(y-B[2])+%[3]*(z-B[3]) = 0;
-right_face:expand(right_face);
-expand(float(solve(front_face,z)));
-expand(float(solve(left_face,z)));
-expand(float(solve(right_face,z)));
-expand(float(solve(back_face,z)));
-/*back_face:332.3693610000001*z-332.3693610000001*y-332.3693610000001*x = 0;
-front_face:(-332.3693610000001*z)-332.3693610000001*y-332.3693610000001*x+12118.851640782 = 0;
-left_face:(-332.3693610000001*z)-332.3693610000001*y+332.3693610000001*x = 0;
-right_face:332.3693610000001*z-332.3693610000001*y+332.3693610000001*x = 0;
-*/

+ 671 - 5
LICENSE

@@ -1,8 +1,674 @@
-Copyright (c) 2018, 2019 Kei Kebreau All rights reserved.
-Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+                    GNU GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
 
-1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
 
-2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+                            Preamble
 
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+  The GNU General Public License is a free, copyleft license for
+software and other kinds of works.
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+ 5 - 0
README.md

@@ -1,3 +1,8 @@
 # cdse-analysis-scripts
 
 Various Octave scripts for the analysis of cadmium selenide.
+
+## Licensing
+GNU GPL version 3 or later: add_ligands.m, calc_hydroxl_dist.m, generate_cdse.m, graph_potential.m and process_log.m.
+GNU LGPL version 3: tetrahedron_grid.m (credit to John Burkardt of the University of South Carolina).
+2-clause BSD license: normalizeVector3d.m and distancePointPlane.m (credit to MatGeom library).

+ 61 - 175
add_ligands.m

@@ -1,140 +1,50 @@
 #!/usr/bin/env octave
 
-% Copyright 2018 Kei Kebreau
+% Copyright (C) 2019 Kei Kebreau
 %
-% Redistribution and use in source and binary forms, with or without
-% modification, are permitted provided that the following conditions are met:
+% This program is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
 %
-% 1. Redistributions of source code must retain the above copyright notice,
-% this list of conditions and the following disclaimer.
+% This program is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+% GNU General Public License for more details.
 %
-% 2. Redistributions in binary form must reproduce the above copyright notice,
-% this list of conditions and the following disclaimer in the documentation
-% and/or other materials provided with the distribution.
-%
-% THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-% AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-% IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-% ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
-% LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
-% CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
-% SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
-% INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
-% CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
-% ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
-% POSSIBILITY OF SUCH DAMAGE.
+% You should have received a copy of the GNU General Public License
+% along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 clear -g;
 global PROJECTION_DISTANCE = 2.2;
 global HYDROXL_ATOM = 'O';
 % It's probably not good practice to compare floating-point values like this.
-global EPSILON = 10**-3;
-
-try
-  pkg load quaternion;
-catch
-  error('Could not load Octave Forge package "quaternion"');
-end
-
-% Arguments: Location of atom.
-%
-% Returns: String containing b, f, l, r, and/or n, representing the atom's
-%          presence on the back, front, left, right, and/or no faces.
-function return_str = which_faces (location)
-  global ORIGINAL_NUM_ATOMS;
-  global EPSILON;
-  x = location.x;
-  y = location.y;
-  z = location.z;
-  return_str = '';
-  % Equations generated by the Maxima (*.mac) files in the same repository as
-  % this file.
-  if ORIGINAL_NUM_ATOMS == 140
-    SCALE_FACTOR = 332.369361;
-    back_eq = abs(SCALE_FACTOR * (-x - y + z));
-    front_eq = abs(SCALE_FACTOR * (x + y + z) - 12118.851640782);
-    left_eq = abs(SCALE_FACTOR * (x - y - z));
-    right_eq = abs(SCALE_FACTOR * (x - y + z));
-  elseif ORIGINAL_NUM_ATOMS == 91
-    SCALE_FACTOR = 230.81205625;
-    back_eq = abs(SCALE_FACTOR * (-x - y + z));
-    front_eq = abs(SCALE_FACTOR * (x + y + z) - 7013.224329156251);
-    left_eq = abs(SCALE_FACTOR * (x - y - z));
-    right_eq = abs(SCALE_FACTOR * (x - y + z));
-  elseif ORIGINAL_NUM_ATOMS == 55
-    SCALE_FACTOR = 147.719716;
-    back_eq = abs(SCALE_FACTOR * (-x - y + z));
-    front_eq = abs(SCALE_FACTOR * (x + y + z) - 3590.770856528);
-    left_eq = abs(SCALE_FACTOR * (x - y - z));
-    right_eq = abs(SCALE_FACTOR * (x - y + z));
-  else
-    SCALE_FACTOR = 83.09234025000002;
-    back_eq = abs(SCALE_FACTOR * (-x - y + z) - 631.1901896240628);
-    front_eq = abs(SCALE_FACTOR * (x + y + z) - 631.1901896240628);
-    left_eq = abs(SCALE_FACTOR * (x - y - z) - 126.2380379248125);
-    right_eq = abs(SCALE_FACTOR * (x - y + z) + 126.2380379248125);
-  endif
-
-  if back_eq < EPSILON
-    return_str = [return_str 'b'];
-  endif
-  if front_eq < EPSILON
-    return_str = [return_str 'f'];
-  endif
-  if left_eq < EPSILON
-    return_str = [return_str 'l'];
-  endif
-  if right_eq < EPSILON
-    return_str = [return_str 'r'];
-  endif
-  if strcmp(return_str, '')
-    return_str = 'n';
-  endif
-endfunction
-
-% Arguments: Location of atom.
-%
-% Returns: New location projected from back face.
-function new_location = project_back(location)
-  global PROJECTION_DISTANCE;
-  x = location.x - (PROJECTION_DISTANCE / sqrt(3));
-  y = location.y - (PROJECTION_DISTANCE / sqrt(3));
-  z = location.z + (PROJECTION_DISTANCE / sqrt(3));
-  new_location = quaternion(x, y, z);
-endfunction
+global TOLERANCE = 1e-6;
 
-% Arguments: Location of atom.
+% Arguments: 1x3 location of atom and the planes it may be on.
 %
-% Returns: New location projected from front face.
-function new_location = project_front(location)
-  global PROJECTION_DISTANCE;
-  x = location.x + (PROJECTION_DISTANCE / sqrt(3));
-  y = location.y + (PROJECTION_DISTANCE / sqrt(3));
-  z = location.z + (PROJECTION_DISTANCE / sqrt(3));
-  new_location = quaternion(x, y, z);
-endfunction
-
-% Arguments: Location of atom.
-%
-% Returns: New location projected from left face.
-function new_location = project_left(location)
-  global PROJECTION_DISTANCE;
-  x = location.x + (PROJECTION_DISTANCE / sqrt(3));
-  y = location.y - (PROJECTION_DISTANCE / sqrt(3));
-  z = location.z - (PROJECTION_DISTANCE / sqrt(3));
-  new_location = quaternion(x, y, z);
-endfunction
+% Returns: Indices of the planes where the atom is located.
+function indices = which_planes (location, planes)
+  global TOLERANCE;
+  indices = [];
+  for plane = 1:size(planes)(1)
+    if abs(distancePointPlane(location, planes(plane, :))) < TOLERANCE
+      indices(end + 1) = plane;
+    end
+  end
+end
 
-% Arguments: Location of atom.
+% Arguments: Location of atom, the normals to planes, and the index of the plane
+% to project from.
 %
-% Returns: New location projected from right face.
-function new_location = project_right(location)
+% Returns: New location projected from the given plane.
+function new_location = project(location, plane_normals, plane_index)
   global PROJECTION_DISTANCE;
-  x = location.x - (PROJECTION_DISTANCE / sqrt(3));
-  y = location.y + (PROJECTION_DISTANCE / sqrt(3));
-  z = location.z - (PROJECTION_DISTANCE / sqrt(3));
-  new_location = quaternion(x, y, z);
-endfunction
+  new_location = zeros(1, 3);
+  new_location(1) = location(1) + sign(plane_normals(plane_index, 1)) * PROJECTION_DISTANCE / sqrt(3);
+  new_location(2) = location(2) + sign(plane_normals(plane_index, 2)) * PROJECTION_DISTANCE / sqrt(3);
+  new_location(3) = location(3) + sign(plane_normals(plane_index, 3)) * PROJECTION_DISTANCE / sqrt(3);
+end
 
 % Let user select input file.
 [input_file, file_path] = uigetfile({'*.xyz*', 'Supported file formats'});
@@ -144,67 +54,43 @@ raw_data = fileread([file_path input_file]);
 
 cd_regexp = ['Cd' repmat('\s+([+-]?[0-9]*\.?[0-9]+)', [1,3])];
 cd_locations = regexp(raw_data, cd_regexp, 'tokens');
+% Convert cd_locations from a nested cell array of strings to rows of XYZ coordinates.
+cd_locations = reshape(cellfun(@str2num, cell2mat(cd_locations)), 3, [])';
 num_atoms = str2num(regexp(raw_data, '^(\d+)', 'tokens', 'once'){1});
-global ORIGINAL_NUM_ATOMS = num_atoms;
 max_hydroxl = num_atoms - length(cd_locations);
 
-tic;
-
 new_atom_count = 0;
 new_atoms = '';
-loc_arr = cell(1, length(cd_locations));
-for num = 1:length(cd_locations)
-  vectors = cellfun(@str2num, cd_locations{:,num});
-  loc_arr{:,num} = quaternion(vectors(1), vectors(2), vectors(3));
-endfor
 
-for elem = loc_arr
-  elem = elem{:};
-  faces = which_faces(elem);
+% Find vertices and faces of the minimum convex hull and their planes.
+faces = convhull(cd_locations);
+vertices = cd_locations(unique(faces), :);
+planes = zeros(length(faces), 9);
+plane_normals = zeros(length(faces), 3);
+for plane = 1:size(planes)(1)
+  planes(plane, :) = createPlane(vertices([1 2 3 4]([1 2 3 4] ~= plane), :));
+  plane_normals(plane, :) = planeNormal(planes(plane, :));
+end
+
+% Orient the normals of these planes away from the center of the tetrahedron.
+plane_normals(1, :) = plane_normals(1, :) * -1;
+plane_normals(3, :) = plane_normals(3, :) * -1;
+
+for row = 1:length(cd_locations)
+  cd_atom = cd_locations(row, :);
+  cd_faces = which_planes(cd_atom, planes);
   
-  % After the coordinates, letters representing the face that the new atom is on
-  % will be placed for further processing by the hydroxl distance calculation
+  % After the coordinates, indices representing the planes that the new atom is
+  % on will be placed for further processing by the hydroxl distance calculation
   % script! This should not interfere with proper processing of the resulting
   % .xyz files.
-  if strfind(faces, 'b')
-    new_atom_location = project_back(elem);
-    new_atoms{new_atom_count + 1} = sprintf('N %s',
-                                            sprintf('%f ', [new_atom_location.x,
-                                                            new_atom_location.y,
-                                                            new_atom_location.z]));
-    num_atoms = num_atoms + 1;
-    new_atom_count = new_atom_count + 1;
-  endif
-  if strfind(faces, 'f')
-    new_atom_location = project_front(elem);
+  for cd_face = 1:length(cd_faces)
+    new_atom_location = project(cd_atom, plane_normals, cd_faces(cd_face));
     new_atoms{new_atom_count + 1} = sprintf('N %s',
-                                            sprintf('%f ', [new_atom_location.x,
-                                                            new_atom_location.y,
-                                                            new_atom_location.z]));
-    num_atoms = num_atoms + 1;
+                                            sprintf('%f ', new_atom_location));
     new_atom_count = new_atom_count + 1;
-  endif
-  if strfind(faces, 'l')
-    new_atom_location = project_left(elem);
-    new_atoms{new_atom_count + 1} = sprintf('N %s',
-                                            sprintf('%f ', [new_atom_location.x,
-                                                            new_atom_location.y,
-                                                            new_atom_location.z]));
-    num_atoms = num_atoms + 1;
-    new_atom_count = new_atom_count + 1;
-  endif
-  if strfind(faces, 'r')
-    new_atom_location = project_right(elem);
-    new_atoms{new_atom_count + 1} = sprintf('N %s',
-                                            sprintf('%f ', [new_atom_location.x,
-                                                            new_atom_location.y,
-                                                            new_atom_location.z]));
-    num_atoms = num_atoms + 1;
-    new_atom_count = new_atom_count + 1;
-  endif
-endfor
-
-runtime = toc;
+  end
+end
 
 output_dir = uigetdir('.', 'Select output directory for output xyz files');
 % Let the user input how many output files they want.
@@ -222,15 +108,15 @@ for cluster = 1:num_clusters
   rand_mutations = randperm(new_atom_count)(1:max_hydroxl);
   for r = rand_mutations
     new_atoms{r} = strrep(new_atoms{r}, 'N', HYDROXL_ATOM);
-  endfor
+  end
   xyz_name = sprintf(xyz_format_str, output_dir, filesep, file_name, cluster);
   xyz_id = fopen(xyz_name, 'w');
-  fdisp(xyz_id, sprintf('%d\n', num_atoms));
+  fdisp(xyz_id, sprintf('%d\n', num_atoms + new_atom_count));
   fdisp(xyz_id, regexp(raw_data, '(Cd.*)\n', 'tokens', 'once'){1});
   fdisp(xyz_id, strjoin(new_atoms, '\n'));
   fclose(xyz_id);
   waitbar(cluster / num_clusters, loading_bar);
-endfor
+end
 
 close(loading_bar);
 clear -g;

+ 0 - 0
calc_hydroxl_dist.m


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