Skip to content

Commit 66475bd

Browse files
tjduignatjduigna
authored
Merge pull request #79 from tjduigna/master
Bug fixes to orbital viewing
2 parents 735b901 + d28be5d commit 66475bd

8 files changed

Lines changed: 207 additions & 157 deletions

File tree

‎exatomic/__init__.py‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -18,7 +18,7 @@
1818
1919
.. _atomic: https://en.wikipedia.org/wiki/Atomic_units
2020
"""
21-
__exatomic_version__ = (0, 3, 0)
21+
__exatomic_version__ = (0, 3, 1)
2222
__version__ = '.'.join((str(v) for v in __exatomic_version__))
2323

2424

@@ -27,7 +27,7 @@
2727
from exatomic import error
2828

2929
# User API
30-
from exatomic.container import Universe
30+
from exatomic.container import Universe, basis_function_contributions
3131
from exatomic.editor import Editor
3232
from exatomic.filetypes import XYZ, Cube
3333

‎exatomic/_nbextension/ao.js‎

Lines changed: 9 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -1,24 +1,22 @@
11
// Copyright (c) 2015-2016, Exa Analytics Development Team
2-
// Distributed under the terms of the Apache License 2.0
3-
/*"""
4-
================
5-
ao.js
6-
================
7-
*/
8-
'use strict';
2+
// Distributed under the terms of the Apache License 2.0
3+
/*"""
4+
================
5+
ao.js
6+
================
7+
*/
8+
'use strict';
99

1010

1111
require.config({
1212
shim: {
13-
'nbextensions/exa/field': {
14-
exports: 'field'
15-
},
13+
"nbextensions/exa/field": {exports: 'field'}
1614
},
1715
});
1816

1917

2018
define([
21-
'nbextensions/exa/field'
19+
"nbextensions/exa/field"
2220
], function(field) {
2321
class AO extends field.ScalarField {
2422
/*"""

‎exatomic/_nbextension/gaussian.js‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -2,11 +2,11 @@
22
// Distributed under the terms of the Apache License 2.0
33
/*"""
44
=====================
5-
gaussian.js
6-
=====================
7-
*/
8-
'use strict';
9-
5+
gaussian.js
6+
=====================
7+
*/
8+
'use strict';
9+
1010

1111
require.config({
1212
shim: {

‎exatomic/_nbextension/gtf.js‎

Lines changed: 15 additions & 75 deletions
Original file line numberDiff line numberDiff line change
@@ -7,19 +7,18 @@ gtf.js
77
*/
88
'use strict';
99

10-
1110
require.config({
1211
shim: {
13-
'nbextensions/exa/field': {
14-
exports: 'field'
15-
},
12+
"nbextensions/exa/num": {exports: 'num'},
13+
"nbextensions/exa/field": {exports: 'field'}
1614
},
1715
});
1816

1917

2018
define([
21-
'nbextensions/exa/field'
22-
], function(field) {
19+
"nbextensions/exa/num",
20+
"nbextensions/exa/field"
21+
], function(num, field) {
2322
class GTF extends field.ScalarField {
2423
/*"""
2524
*/
@@ -35,83 +34,38 @@ define([
3534
var y2 = y*y;
3635
var z2 = z*z;
3736
var r2 = x2 + y2 + z2;
38-
return 5 * Math.exp(-r2);
39-
},
40-
/*
41-
'2s': function(x, y, z) {
42-
var x2 = x*x;
43-
var y2 = y*y;
44-
var z2 = z*z;
45-
var r2 = x2 + y2 + z2;
46-
return Math.exp(-r2);
37+
return num.normalize_gaussian(25000, 0) * Math.exp(-r2);
4738
},
48-
*/
4939
'px': function(x, y, z) {
5040
var x2 = x*x;
5141
var y2 = y*y;
5242
var z2 = z*z;
5343
var r2 = x2 + y2 + z2;
54-
return 5 * x * Math.exp(-r2);
44+
return num.normalize_gaussian(25000, 1) * x * Math.exp(-r2);
5545
},
5646

5747
'py': function(x, y, z) {
5848
var x2 = x*x;
5949
var y2 = y*y;
6050
var z2 = z*z;
6151
var r2 = x2 + y2 + z2;
62-
return 5 * y * Math.exp(-r2);
52+
return num.normalize_gaussian(25000, 1) * y * Math.exp(-r2);
6353
},
6454

6555
'pz': function(x, y, z) {
6656
var x2 = x*x;
6757
var y2 = y*y;
6858
var z2 = z*z;
6959
var r2 = x2 + y2 + z2;
70-
return 5 * z * Math.exp(-r2);
71-
},
72-
73-
/*
74-
'3s': function(x, y, z) {
75-
var x2 = x*x;
76-
var y2 = y*y;
77-
var z2 = z*z;
78-
var r2 = x2 + y2 + z2;
79-
return Math.exp(-r2);
80-
},
81-
'3px': function(x, y, z) {
82-
var x2 = x*x;
83-
var y2 = y*y;
84-
var z2 = z*z;
85-
var r2 = x2 + y2 + z2;
86-
var r = Math.sqrt(r2);
87-
return x * Math.exp(-r2);
88-
},
89-
90-
'3py': function(x, y, z) {
91-
var x2 = x*x;
92-
var y2 = y*y;
93-
var z2 = z*z;
94-
var r2 = x2 + y2 + z2;
95-
var r = Math.sqrt(r2);
96-
return y * r * Math.exp(-r2);
60+
return num.normalize_gaussian(25000, 1) * z * Math.exp(-r2);
9761
},
9862

99-
'3pz': function(x, y, z) {
100-
var x2 = x*x;
101-
var y2 = y*y;
102-
var z2 = z*z;
103-
var r2 = x2 + y2 + z2;
104-
var r = Math.sqrt(r2);
105-
return z * r * Math.exp(-r2);
106-
},
107-
*/
10863
'd200': function(x, y, z) {
10964
var x2 = x*x;
11065
var y2 = y*y;
11166
var z2 = z*z;
11267
var r2 = x2 + y2 + z2;
113-
var r = Math.sqrt(r2);
114-
return 20 * x2 * Math.exp(-r2);
68+
return num.normalize_gaussian(25000, 2) * x2 * Math.exp(-r2);
11569
},
11670

11771
'd110': function(x, y, z) {
@@ -120,16 +74,15 @@ define([
12074
var z2 = z*z;
12175
var r2 = x2 + y2 + z2;
12276
var r = Math.sqrt(r2);
123-
return 20 * x * y * Math.exp(-r2);
77+
return num.normalize_gaussian(25000, 2) * x * y * Math.exp(-r2);
12478
},
12579

12680
'd101': function(x, y, z) {
12781
var x2 = x*x;
12882
var y2 = y*y;
12983
var z2 = z*z;
13084
var r2 = x2 + y2 + z2;
131-
var r = Math.sqrt(r2);
132-
return 20 * x * z * Math.exp(-r2);
85+
return num.normalize_gaussian(25000, 2) * x * z * Math.exp(-r2);
13386
},
13487

13588

@@ -138,37 +91,24 @@ define([
13891
var y2 = y*y;
13992
var z2 = z*z;
14093
var r2 = x2 + y2 + z2;
141-
var r = Math.sqrt(r2);
142-
return 20 * y2 * Math.exp(-r2);
94+
return num.normalize_gaussian(25000, 2) * y2 * Math.exp(-r2);
14395
},
14496

14597
'd011': function(x, y, z) {
14698
var x2 = x*x;
14799
var y2 = y*y;
148100
var z2 = z*z;
149101
var r2 = x2 + y2 + z2;
150-
var r = Math.sqrt(r2);
151-
return 20 * y * z * Math.exp(-r2);
102+
return num.normalize_gaussian(25000, 2) * y * z * Math.exp(-r2);
152103
},
153104

154105
'd002': function(x, y, z) {
155106
var x2 = x*x;
156107
var y2 = y*y;
157108
var z2 = z*z;
158109
var r2 = x2 + y2 + z2;
159-
var r = Math.sqrt(r2);
160-
return 20 * z2 * Math.exp(-r2);
110+
return num.normalize_gaussian(25000, 2) * z2 * Math.exp(-r2);
161111
},
162-
/*
163-
'3dx2-y2': function(x, y, z) {
164-
var x2 = x*x;
165-
var y2 = y*y;
166-
var z2 = z*z;
167-
var r2 = x2 + y2 + z2;
168-
var r = Math.sqrt(r2);
169-
return (x2 - y2) * Math.exp(-r2);
170-
},
171-
*/
172112

173113
};
174114

0 commit comments

Comments
 (0)