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hmacdoperichardjgowers
hmacdope
authored and
richardjgowers
committed
remove Calc
1 parent 36a8b1d commit ab8ecb2

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6 files changed

+608
-608
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6 files changed

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‎distopia/pydistopia.pyx‎

Lines changed: 45 additions & 45 deletions
Original file line numberDiff line numberDiff line change
@@ -20,58 +20,58 @@ cdef extern from "distopia.h" namespace "distopia" nogil:
2020
int GetNFloatLanes();
2121
int GetNDoubleLanes();
2222

23-
void CalcDistancesNoBox[T](
23+
void DistancesNoBox[T](
2424
const T *coords0,
2525
const T *coords1,
2626
size_t n,
2727
T *output
2828
)
29-
void CalcDistancesOrtho[T](
29+
void DistancesOrtho[T](
3030
const T *coords0,
3131
const T *coords1,
3232
size_t n,
3333
const T *box,
3434
T *output
3535
)
36-
void CalcDistancesTriclinic[T](
36+
void DistancesTriclinic[T](
3737
const T *coords0,
3838
const T *coords1,
3939
size_t n,
4040
const T *box,
4141
T *output
4242
)
43-
void CalcAnglesNoBox[T](
43+
void AnglesNoBox[T](
4444
const T *coords0,
4545
const T *coords1,
4646
const T *coords2,
4747
size_t n,
4848
T *out
4949
)
50-
void CalcAnglesOrtho[T](
50+
void AnglesOrtho[T](
5151
const T *coords0,
5252
const T *coords1,
5353
const T *coords2,
5454
size_t n,
5555
const T *box,
5656
T *out
5757
)
58-
void CalcAnglesTriclinic[T](
58+
void AnglesTriclinic[T](
5959
const T *coords0,
6060
const T *coords1,
6161
const T *coords2,
6262
size_t n,
6363
const T *box,
6464
T *out
6565
)
66-
void CalcDihedralsNoBox[T](
66+
void DihedralsNoBox[T](
6767
const T *coords0,
6868
const T *coords1,
6969
const T *coords2,
7070
const T *coords3,
7171
size_t n,
7272
T *out
7373
)
74-
void CalcDihedralsOrtho[T](
74+
void DihedralsOrtho[T](
7575
const T *coords0,
7676
const T *coords1,
7777
const T *coords2,
@@ -80,7 +80,7 @@ cdef extern from "distopia.h" namespace "distopia" nogil:
8080
const T *box,
8181
T *out
8282
)
83-
void CalcDihedralsTriclinic[T](
83+
void DihedralsTriclinic[T](
8484
const T *coords0,
8585
const T *coords1,
8686
const T *coords2,
@@ -89,41 +89,41 @@ cdef extern from "distopia.h" namespace "distopia" nogil:
8989
const T *box,
9090
T *out
9191
)
92-
void CalcDistanceArrayNoBox[T](
92+
void DistanceArrayNoBox[T](
9393
const T *coords0,
9494
const T *coords1,
9595
size_t n0,
9696
size_t n1,
9797
T *out,
9898
)
99-
void CalcDistanceArrayOrtho[T](
99+
void DistanceArrayOrtho[T](
100100
const T *coords0,
101101
const T *coords1,
102102
size_t n0,
103103
size_t n1,
104104
const T *box,
105105
T *out,
106106
)
107-
void CalcDistanceArrayTriclinic[T](
107+
void DistanceArrayTriclinic[T](
108108
const T *coords0,
109109
const T *coords1,
110110
size_t n0,
111111
size_t n1,
112112
const T *box,
113113
T *out,
114114
)
115-
void CalcSelfDistanceArrayNoBox[T](
115+
void SelfDistanceArrayNoBox[T](
116116
const T *coords,
117117
size_t n,
118118
T *out,
119119
)
120-
void CalcSelfDistanceArrayOrtho[T](
120+
void SelfDistanceArrayOrtho[T](
121121
const T *coords,
122122
size_t n,
123123
const T *box,
124124
T *out,
125125
)
126-
void CalcSelfDistanceArrayTriclinic[T](
126+
void SelfDistanceArrayTriclinic[T](
127127
const T *coords,
128128
size_t n,
129129
const T *box,
@@ -171,7 +171,7 @@ def _check_shapes(*args):
171171
def calc_distances_no_box(floating[:, ::1] coords0,
172172
floating[:, ::1] coords1,
173173
results=None):
174-
"""Calculate pairwise distances between coords0 and coords1 with no periodic boundary conditions
174+
"""ulate pairwise distances between coords0 and coords1 with no periodic boundary conditions
175175
176176
Parameters
177177
----------
@@ -203,7 +203,7 @@ def calc_distances_no_box(floating[:, ::1] coords0,
203203

204204
results_view = results
205205

206-
CalcDistancesNoBox(& coords0[0][0], & coords1[0][0], nvals, & results_view[0])
206+
DistancesNoBox(& coords0[0][0], & coords1[0][0], nvals, & results_view[0])
207207

208208
return np.array(results)
209209

@@ -214,7 +214,7 @@ def calc_distances_ortho(floating[:, ::1] coords0,
214214
floating[:, ::1] coords1,
215215
floating[::1] box,
216216
floating[::1] results=None):
217-
"""Calculate pairwise distances between coords0 and coords1 under orthorhombic boundary conditions
217+
"""ulate pairwise distances between coords0 and coords1 under orthorhombic boundary conditions
218218
219219
Parameters
220220
----------
@@ -250,7 +250,7 @@ def calc_distances_ortho(floating[:, ::1] coords0,
250250

251251
results_view = results
252252

253-
CalcDistancesOrtho(& coords0[0][0], & coords1[0][0], nvals, & box[0], & results_view[0])
253+
DistancesOrtho(& coords0[0][0], & coords1[0][0], nvals, & box[0], & results_view[0])
254254

255255
return np.array(results)
256256

@@ -261,7 +261,7 @@ def calc_distances_triclinic(floating[:, ::1] coords0,
261261
floating[:, ::1] coords1,
262262
floating[:, ::1] box,
263263
floating[::1] results=None):
264-
"""Calculate pairwise distances between coords0 and coords1 under triclinic boundary conditions
264+
"""ulate pairwise distances between coords0 and coords1 under triclinic boundary conditions
265265
266266
Parameters
267267
----------
@@ -296,7 +296,7 @@ def calc_distances_triclinic(floating[:, ::1] coords0,
296296

297297
results_view = results
298298

299-
CalcDistancesTriclinic(& coords0[0][0], & coords1[0][0], nvals, & box[0][0], & results_view[0])
299+
DistancesTriclinic(& coords0[0][0], & coords1[0][0], nvals, & box[0][0], & results_view[0])
300300

301301
return np.array(results)
302302

@@ -307,7 +307,7 @@ def calc_angles_no_box(
307307
floating[:, ::1] coords1,
308308
floating[:, ::1] coords2,
309309
floating[::1] results=None):
310-
"""Calculate angles between sets of coordinates with no periodic boundary conditions
310+
"""ulate angles between sets of coordinates with no periodic boundary conditions
311311
312312
Parameters
313313
----------
@@ -340,7 +340,7 @@ def calc_angles_no_box(
340340

341341
results_view = results
342342

343-
CalcAnglesNoBox(&coords0[0][0], &coords1[0][0], &coords2[0][0],
343+
AnglesNoBox(&coords0[0][0], &coords1[0][0], &coords2[0][0],
344344
nvals, &results_view[0])
345345

346346
return np.array(results)
@@ -354,7 +354,7 @@ def calc_angles_ortho(
354354
floating[::1] box,
355355
floating[::1] results=None):
356356

357-
"""Calculate angles between sets of coordinates under orthorhombic boundary conditions
357+
"""ulate angles between sets of coordinates under orthorhombic boundary conditions
358358
359359
Parameters
360360
----------
@@ -389,7 +389,7 @@ def calc_angles_ortho(
389389

390390
results_view = results
391391

392-
CalcAnglesOrtho(&coords0[0][0], &coords1[0][0], &coords2[0][0],
392+
AnglesOrtho(&coords0[0][0], &coords1[0][0], &coords2[0][0],
393393
nvals, &box[0], &results_view[0])
394394

395395
return np.array(results)
@@ -402,7 +402,7 @@ def calc_angles_triclinic(
402402
floating[:, ::1] coords2,
403403
floating[:, ::1] box,
404404
floating[::1] results=None):
405-
"""Calculate angles between sets of coordinates under triclinic boundary conditions
405+
"""ulate angles between sets of coordinates under triclinic boundary conditions
406406
407407
Parameters
408408
----------
@@ -438,7 +438,7 @@ def calc_angles_triclinic(
438438

439439
results_view = results
440440

441-
CalcAnglesTriclinic(&coords0[0][0], &coords1[0][0], &coords2[0][0],
441+
AnglesTriclinic(&coords0[0][0], &coords1[0][0], &coords2[0][0],
442442
nvals, &box[0][0], &results_view[0])
443443

444444
return np.array(results)
@@ -451,7 +451,7 @@ def calc_dihedrals_no_box(
451451
floating[:, ::1] coords2,
452452
floating[:, ::1] coords3,
453453
floating[::1] results=None):
454-
"""Calculate dihedral angles between sets of coordinates with no periodic boundary conditions
454+
"""ulate dihedral angles between sets of coordinates with no periodic boundary conditions
455455
456456
Parameters
457457
----------
@@ -485,7 +485,7 @@ def calc_dihedrals_no_box(
485485

486486
results_view = results
487487

488-
CalcDihedralsNoBox(&coords0[0][0], &coords1[0][0], &coords2[0][0], &coords3[0][0],
488+
DihedralsNoBox(&coords0[0][0], &coords1[0][0], &coords2[0][0], &coords3[0][0],
489489
nvals, &results_view[0])
490490

491491
return np.array(results)
@@ -499,7 +499,7 @@ def calc_dihedrals_ortho(
499499
floating[:, ::1] coords3,
500500
floating[::1] box,
501501
floating[::1] results=None):
502-
"""Calculate dihedral angles between sets of coordinates under orthorhombic boundary conditions
502+
"""ulate dihedral angles between sets of coordinates under orthorhombic boundary conditions
503503
504504
Parameters
505505
----------
@@ -534,7 +534,7 @@ def calc_dihedrals_ortho(
534534

535535
results_view = results
536536

537-
CalcDihedralsOrtho(&coords0[0][0], &coords1[0][0], &coords2[0][0], &coords3[0][0],
537+
DihedralsOrtho(&coords0[0][0], &coords1[0][0], &coords2[0][0], &coords3[0][0],
538538
nvals, &box[0], &results_view[0])
539539

540540
return np.array(results)
@@ -549,7 +549,7 @@ def calc_dihedrals_triclinic(
549549
floating[:, ::1] coords3,
550550
floating[:, ::1] box,
551551
floating[::1] results=None):
552-
"""Calculate dihedral angles between sets of coordinates under triclinic boundary conditions
552+
"""ulate dihedral angles between sets of coordinates under triclinic boundary conditions
553553
554554
Parameters
555555
----------
@@ -585,7 +585,7 @@ def calc_dihedrals_triclinic(
585585

586586
results_view = results
587587

588-
CalcDihedralsTriclinic(&coords0[0][0], &coords1[0][0], &coords2[0][0], &coords3[0][0],
588+
DihedralsTriclinic(&coords0[0][0], &coords1[0][0], &coords2[0][0], &coords3[0][0],
589589
nvals, &box[0][0], &results_view[0])
590590

591591
return np.array(results)
@@ -597,7 +597,7 @@ def calc_distance_array_no_box(
597597
floating[:, ::1] coords0,
598598
floating[:, ::1] coords1,
599599
floating[:, ::1] results=None):
600-
"""Calculate pairwise distance matrix between coordinates with no periodic boundary conditions
600+
"""ulate pairwise distance matrix between coordinates with no periodic boundary conditions
601601
602602
Parameters
603603
----------
@@ -633,7 +633,7 @@ def calc_distance_array_no_box(
633633

634634
results_view = results
635635

636-
CalcDistanceArrayNoBox(&coords0[0][0], &coords1[0][0],
636+
DistanceArrayNoBox(&coords0[0][0], &coords1[0][0],
637637
nvals0, nvals1,
638638
&results_view[0][0])
639639

@@ -646,7 +646,7 @@ def calc_distance_array_ortho(
646646
floating[:, ::1] coords1,
647647
floating[::1] box,
648648
floating[:, ::1] results=None):
649-
"""Calculate pairwise distance matrix between coordinates under orthorhombic boundary conditions
649+
"""ulate pairwise distance matrix between coordinates under orthorhombic boundary conditions
650650
651651
Parameters
652652
----------
@@ -681,7 +681,7 @@ def calc_distance_array_ortho(
681681

682682
results_view = results
683683

684-
CalcDistanceArrayOrtho(&coords0[0][0], &coords1[0][0],
684+
DistanceArrayOrtho(&coords0[0][0], &coords1[0][0],
685685
nvals0, nvals1,
686686
&box[0],
687687
&results_view[0][0])
@@ -696,7 +696,7 @@ def calc_distance_array_triclinic(
696696
floating[:, ::1] coords1,
697697
floating[:, ::1] box,
698698
floating[:, ::1] results=None):
699-
"""Calculate pairwise distance matrix between coordinates under triclinic boundary conditions
699+
"""ulate pairwise distance matrix between coordinates under triclinic boundary conditions
700700
701701
Parameters
702702
----------
@@ -733,7 +733,7 @@ def calc_distance_array_triclinic(
733733

734734
results_view = results
735735

736-
CalcDistanceArrayTriclinic(&coords0[0][0], &coords1[0][0],
736+
DistanceArrayTriclinic(&coords0[0][0], &coords1[0][0],
737737
nvals0, nvals1,
738738
&box[0][0],
739739
&results_view[0][0])
@@ -748,7 +748,7 @@ def calc_distance_array_triclinic(
748748
def calc_self_distance_array_no_box(
749749
floating[:, ::1] coords0,
750750
floating[::1] results=None):
751-
"""Calculate self-pairwise distance matrix between coordinates with no periodic boundary conditions
751+
"""ulate self-pairwise distance matrix between coordinates with no periodic boundary conditions
752752
753753
Parameters
754754
----------
@@ -786,7 +786,7 @@ def calc_self_distance_array_no_box(
786786

787787
results_view = results
788788

789-
CalcSelfDistanceArrayNoBox(&coords0[0][0],
789+
SelfDistanceArrayNoBox(&coords0[0][0],
790790
nvals0,
791791
&results_view[0])
792792

@@ -801,7 +801,7 @@ def calc_self_distance_array_ortho(
801801
floating[:, ::1] coords0,
802802
floating[::1] box,
803803
floating[::1] results=None):
804-
"""Calculate self-pairwise distance matrix between coordinates under orthorhombic periodic boundary conditions
804+
"""ulate self-pairwise distance matrix between coordinates under orthorhombic periodic boundary conditions
805805
806806
Parameters
807807
----------
@@ -842,7 +842,7 @@ def calc_self_distance_array_ortho(
842842

843843
results_view = results
844844

845-
CalcSelfDistanceArrayOrtho(&coords0[0][0],
845+
SelfDistanceArrayOrtho(&coords0[0][0],
846846
nvals0,
847847
&box[0],
848848
&results_view[0])
@@ -856,7 +856,7 @@ def calc_self_distance_array_triclinic(
856856
floating[:, ::1] coords0,
857857
floating[:, ::1] box,
858858
floating[::1] results=None):
859-
"""Calculate self-pairwise distance matrix between coordinates under triclinic boundary conditions
859+
"""ulate self-pairwise distance matrix between coordinates under triclinic boundary conditions
860860
861861
Parameters
862862
----------
@@ -897,7 +897,7 @@ def calc_self_distance_array_triclinic(
897897

898898
results_view = results
899899

900-
CalcSelfDistanceArrayTriclinic(&coords0[0][0],
900+
SelfDistanceArrayTriclinic(&coords0[0][0],
901901
nvals0,
902902
&box[0][0],
903903
&results_view[0])

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