arbdmodel.py 31.1 KB
Newer Older
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
# -*- coding: utf-8 -*-
import abc
import numpy as np
from copy import copy, deepcopy
from inspect import ismethod

# from datetime import datetime
# from math import pi,sqrt,exp,floor
# from scipy.special import erf
# import scipy.optimize as opt
import os, sys, subprocess


## Abstract classes
class Transformable():
    def __init__(self, position, orientation=None):
        self.position = np.array(position)
        if orientation is not None:
            orientation = np.array(orientation)
        self.orientation = orientation

    def transform(self, R = ((1,0,0),(0,1,0),(0,0,1)),
                  center = (0,0,0), offset = (0,0,0)):

        R,center,offset = [np.array(x) for x in (R,center,offset)]

        self.position = R.dot(self.position-center)+center+offset
                
        if self.orientation is not None:
            ## TODO: what if self.orientation is taken from parent?!
            self.orientation = self.orientation.dot(R)
        ...        

    def collapsedPosition(self):
        # print("collapsedPosition called", type(self), self.name)
        if isinstance(self, Child):
            # print(self.parent, isinstance(self.parent,Transformable))
            if isinstance(self.parent, Transformable):
                return self.applyOrientation(self.position) + self.parent.collapsedPosition()
            
                # if self.parent.orientation is not None:
                #     return self.parent.collapsedOrientation().dot(self.position) + self.parent.collapsedPosition()
        return np.array(self.position) # return a copy
                
    def applyOrientation(self,obj):
        # print("applyOrientation called", self.name, obj)
        if isinstance(self, Child):
            # print( self.orientation, self.orientation is not None, None is not None )
            # if self.orientation is not None:
            #     # print("applyOrientation applying", self, self.name, self.orientation)
            #     obj = self.orientation.dot(obj)
            if isinstance(self.parent, Transformable):
                if self.parent.orientation is not None:
                    obj = self.parent.orientation.dot(obj)
                obj = self.parent.applyOrientation(obj)
        # print("applyOrientation returning", self.name, obj)
        return obj

class Parent():
    def __init__(self, children=[]):
        self.children = []
        for x in children:
            self.add(x)
        # self.children = children

        self.bonds = []
        self.angles = []
        self.dihedrals = []
cmaffeo2's avatar
cmaffeo2 committed
69
        self.impropers = []
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
        self.exclusions = []

        ## TODO: self.cacheInvalid = True # What will be in the cache?


    def add(self,x):
        ## TODO: check the parent-child tree to make sure there are no cycles
        if not isinstance(x,Child):
            raise Exception('Attempted to add an object to a group that does not inherit from the "Child" type')

        if x.parent is not None and x.parent is not self:
            raise Exception("Child {} already belongs to some group".format(x))
        x.parent = self
        self.children.append(x)

85
86
87
88
89
90
91
92
    def clear_all(self, keep_children=False):
        if keep_children == False:
            for x in self.children:
                x.parent = None
            self.children = []
        self.bonds = []
        self.angles = []
        self.dihedrals = []
cmaffeo2's avatar
cmaffeo2 committed
93
        self.impropers = []
94
95
        self.exclusions = []

96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
    def remove(self,x):
        if x in self.children:
            self.children.remove(x)
            x.parent = None

    def add_bond(self, i,j, bond, exclude=False):
        ## TODO: how to handle duplicating and cloning bonds
        beads = [b for b in self]
        for b in (i,j): assert(b in beads)
        self.bonds.append( (i,j, bond, exclude) )

    def add_angle(self, i,j,k, angle):
        beads = [b for b in self]
        for b in (i,j,k): assert(b in beads)
        self.angles.append( (i,j,k, angle) )

    def add_dihedral(self, i,j,k,l, dihedral):
        beads = [b for b in self]
        for b in (i,j,k,l): assert(b in beads)
        self.dihedrals.append( (i,j,k,l, dihedral) )

cmaffeo2's avatar
cmaffeo2 committed
117
118
119
120
121
    def add_improper(self, i,j,k,l, dihedral):
        beads = [b for b in self]
        for b in (i,j,k,l): assert(b in beads)
        self.impropers.append( (i,j,k,l, dihedral) )

122
123
    def add_exclusion(self, i,j):
        ## TODO: how to handle duplicating and cloning bonds
124
125
126
        ## TODO: perform following check elsewhere
        # beads = [b for b in self]
        # for b in (i,j): assert(b in beads)
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
        self.exclusions.append( (i,j) )

    def get_bonds(self):
        ret = self.bonds
        for c in self.children:
            if isinstance(c,Parent): ret.extend( c.get_bonds() )
        return ret

    def get_angles(self):
        ret = self.angles
        for c in self.children:
            if isinstance(c,Parent): ret.extend( c.get_angles() )
        return ret

    def get_dihedrals(self):
        ret = self.dihedrals
        for c in self.children:
            if isinstance(c,Parent): ret.extend( c.get_dihedrals() )
        return ret

cmaffeo2's avatar
cmaffeo2 committed
147
148
149
150
151
152
    def get_impropers(self):
        ret = self.impropers
        for c in self.children:
            if isinstance(c,Parent): ret.extend( c.get_impropers() )
        return ret

153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
    def get_exclusions(self):
        ret = self.exclusions
        for c in self.children:
            if isinstance(c,Parent): ret.extend( c.get_exclusions() )
        return ret

    def __iter__(self):
        ## TODO: decide if this is the nicest way to do it!
        """Depth-first iteration through tree"""
        for x in self.children:
            if isinstance(x,Parent):
                if isinstance(x,Clone) and not isinstance(x.get_original_recursively(),Parent):
                    yield x
                else:
                    for y in x:
                        yield y
            else:
                yield x    

    def __len__(self):
        l = 0
        for x in self.children:
            if isinstance(x,Parent):
                l += len(x)
            else:
                l += 1
        return l
        
    def __getitem__(self, i):
        return self.children[i]
    
    def __setitem__(self, i, val):
        x = self.children[i]
        x.parent = None
        val.parent = self
        self.children[i] = val
        
class Child():
    def __init__(self, parent=None):
        self.parent = parent
193
194
195
        if parent is not None:
            assert( isinstance(parent, Parent) )
            parent.children.append(self)
196
197
198
199
200
201

    def __getattr__(self, name):
        """
        Try to get attribute from the parent
        """
        # if self.parent is not None:
202
        if "parent" not in self.__dict__ or self.__dict__["parent"] is None or name is "children":
203
            raise AttributeError("'{}' object has no attribute '{}'".format(type(self).__name__, name))
cmaffeo2's avatar
cmaffeo2 committed
204
205
206
207
208
209
210
211
212
213

        ## TODO: determine if there is a way to avoid __getattr__ if a method is being looked up  
        try:
            ret = getattr(self.parent,name)
        except:
            raise AttributeError("'{}' object has no attribute '{}'".format(type(self).__name__, name))
        if ismethod(ret):
            raise AttributeError("'{}' object has no method '{}'".format(type(self).__name__, name))
        return ret 

214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
            
    # def __getstate__(self):
    #     print("Child getstate called", self)
    #     print(self.__dict__)
    #     return (self.__dict__,)

    # def __setstate__(self, state):
    #     self.__dict__, = state

class Clone(Transformable, Parent, Child):
    def __init__(self, original, parent=None,
                 position = None,
                 orientation = None):
        if position is None and original.position is not None:
            position = np.array( original.position )
        if orientation is None and original.orientation is not None:
            orientation = np.array( original.orientation )
        if parent is None:
            parent = original.parent
        self.original = original
        Child.__init__(self, parent)        
        Transformable.__init__(self, position, orientation)        

        ## TODO: keep own bond_list, etc, update when needed original changes

        if "children" in original.__dict__ and len(original.children) > 0:
            self.children = [Clone(c, parent = self) for c in original.children]
        else:
            self.children = []

    def get_original_recursively(self):
        if isinstance(self.original, Clone):
            return self.original.get_original_recursively()
        else:
            return self.original

    def __getattr__(self, name):
        """
        Try to get attribute from the original without descending the tree heirarchy, then look up parent

        TODO: handle PointParticle lookups into ParticleType
        """
        # print("Clone getattr",name)
        if name in self.original.__dict__:
            return self.original.__dict__[name]
        else:
            if "parent" not in self.__dict__ or self.__dict__["parent"] is None:
                raise AttributeError("'{}' object has no attribute '{}'".format(type(self).__name__, name))
            return getattr(self.parent, name)
        

## Particle classes
class ParticleType():
    """Class that hold common attributes that particles can point to"""

    excludedAttributes = ("idx","type_",
                          "position",
271
                          "children",
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
                          "parent", "excludedAttributes",
    )

    def __init__(self, name, charge=0, **kargs):
        # parent = None
        # if "parent" in kargs: parent = kargs["parent"]
        # Child.__init__(self, parent)

        self.name        = name
        self.charge = charge
        for key in ParticleType.excludedAttributes:
            assert( key not in kargs )

        for key,val in kargs.items():
            self.__dict__[key] = val

    def __hash_key(self):
        l = [self.name,self.charge]
        for keyval in sorted(self.__dict__.items()):
            l.extend(keyval)
        return tuple(l)

    def __hash__(self):
        return hash(self.__hash_key())
    
    def _equal_check(a,b):
        if a.name == b.name:
            if a.__hash_key() != b.__hash_key():
300
                raise Exception("Two different ParticleTypes have same 'name' attribute")
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320

    def __eq__(a,b):
        a._equal_check(b)
        return a.name == b.name
    def __lt__(a,b):
        a._equal_check(b)
        return a.name < b.name
    def __le__(a,b):
        a._equal_check(b)
        return a.name <= b.name
    def __gt__(a,b):
        a._equal_check(b)
        return a.name > b.name
    def __ge__(a,b):
        a._equal_check(b)
        return a.name >= b.name
    

class PointParticle(Transformable, Child):
    def __init__(self, type_, position, name="A", segname="A", **kwargs):
321
322
323
324
        parent = None
        if 'parent' in kwargs:
            parent = kwargs['parent']
        Child.__init__(self, parent=parent)
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
        Transformable.__init__(self,position)

        self.type_    = type_                
        self.idx     = None
        self.segname = segname
        self.name = name
        self.counter = 0

        for key,val in kwargs.items():
            self.__dict__[key] = val
        

    def __getattr__(self, name):
        """
        First try to get attribute from the parent, then type_
        
        Note that this data structure seems to be fragile, can result in stack overflow
        
        """
        # return Child.__getattr__(self,name)
        try:
            return Child.__getattr__(self,name)
        except Exception as e:
            if 'type_' in self.__dict__:
                return getattr(self.type_, name)
            else:
                raise AttributeError("'{}' object has no attribute '{}'".format(type(self).__name__, name))


class Group(Transformable, Parent, Child):
    def __init__(self, name=None, children = [], parent=None, 
                 position = np.array((0,0,0)),
                 orientation = np.array(((1,0,0),(0,1,0),(0,0,1))),
    ):
        Transformable.__init__(self, position, orientation)
        Child.__init__(self, parent) # Initialize Child first
        Parent.__init__(self, children)
        self.name = name
        self.isClone = False

    def clone(self):
        return Clone(self)
        g = copy(self)
        g.isClone = True        # TODO: use?
        g.children = [copy(c) for c in g.children]
        for c in g.children:
            c.parent = g
        return g
        g = Group(position = self.position,
                  orientation = self.orientation)
        g.children = self.children # lists point to the same object

    def duplicate(self):
cmaffeo2's avatar
cmaffeo2 committed
378
379
380
381
        new = deepcopy(self)
        for c in new.children:
            c.parent = new
        return new
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
        # Group(position = self.position,
        #       orientation = self.orientation)
        # g.children = deepcopy self.children.deepcopy() # lists are the same object

        
        
    # def __getstate__(self):
    #     return (self.children, self.parent, self.position, self.orientation)

    # def __setstate__(self, state):
    #     self.children, self.parent, self.position, self.orientation = state

        
class PdbModel(Transformable, Parent):

    def __init__(self, children=[], dimensions=None):
        Transformable.__init__(self,(0,0,0))
        Parent.__init__(self, children)
        self.dimensions = dimensions
        self.particles = [p for p in self]
        self.cacheInvalid = True

    def _updateParticleOrder(self):
        pass

    def writePdb(self, filename):
        if self.cacheInvalid:
            self._updateParticleOrder()
        with open(filename,'w') as fh:
            ## Write header
cmaffeo2's avatar
cmaffeo2 committed
412
            fh.write("CRYST1    {:>5f}    {:>5f}    {:>5f}   90.00  90.00  90.00 P 1           1\n".format( *self.dimensions ))
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439

            ## Write coordinates
            formatString = "ATOM  {:>5d} {:^4s}{:1s}{:3s} {:1s}{:>5s}   {:8.3f}{:8.3f}{:8.3f}{:6.2f}{:6.2f}{:2s}{:2f}\n"
            for p in self.particles:
                ## http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM
                idx = p.idx+1
                name = p.type_.name
                resname = name[:3]
                chain = "A"
                charge = 0
                occ = 0
                beta = 0
                x,y,z = [x for x in p.collapsedPosition()]
                
                assert(idx < 1e5)
                resid = "{:<4d}".format(idx)

                fh.write( formatString.format(
                    idx, name[:1], "", resname, chain, resid, x, y, z, occ, beta, "", charge ))
        return
        
    def writePsf(self, filename):
        if self.cacheUpToDate == False:
            self._updateParticleOrder()
        with open(filename,'w') as fh:
            ## Write header
            fh.write("PSF NAMD\n\n") # create NAMD formatted psf
cmaffeo2's avatar
cmaffeo2 committed
440
            fh.write("{:>8d} !NTITLE\n\n".format(0))
441
442
443
444
445
446
447
448
449
450
451
452
453
            
            ## ATOMS section
            fh.write("{:>8d} !NATOM\n".format(len(self.particles)))

            ## From vmd/plugins/molfile_plugin/src/psfplugin.c
            ## "%d %7s %10s %7s %7s %7s %f %f"
            formatString = "{idx:>8d} {segname:7s} {resid:<10s} {resname:7s}" + \
                           " {name:7s} {type:7s} {charge:f} {mass:f}\n"
            for p in self.particles:
                idx = p.idx + 1
                data = dict(
                    idx     = idx,
                    segname = "A",
454
                    resid   = "%d%c%c" % (idx," "," "), # TODO: work with large indices
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
                    name    = p.type_.name[:1],
                    resname = p.type_.name[:3],
                    type    = p.type_.name[:1],
                    charge  = p.charge,
                    mass    = p.mass
                )
                fh.write(formatString.format( **data ))
            fh.write("\n")

            ## Write out bonds
            bonds = self.get_bonds()
            fh.write("{:>8d} !NBOND\n".format(len(bonds)))
            counter = 0
            for p1,p2,b,ex in bonds:
                fh.write( "{:d} {:d} ".format(p1.idx+1,p2.idx+1) )
                counter += 1
                if counter == 3:
                    fh.write("\n")
                    counter = 0
            fh.write("\n")

cmaffeo2's avatar
cmaffeo2 committed
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
            ## Write out angles
            angles = self.get_angles()
            fh.write("{:>8d} !NTHETA\n".format(len(angles)))
            counter = 0
            for p1,p2,p3,a in angles:
                fh.write( "{:d} {:d} {:d}".format(p1.idx+1,p2.idx+1,p3.idx+1) )
                counter += 1
                if counter == 2:
                    fh.write("\n")
                    counter = 0
            fh.write("\n")

            ## Write out dihedrals
            dihedrals = self.get_dihedrals()
            fh.write("{:>8d} !NPHI\n".format(len(dihedrals)))
            counter = 0
            for p1,p2,p3,p4,a in dihedrals:
                fh.write( "{:d} {:d} {:d} {:d}".format(p1.idx+1,p2.idx+1,p3.idx+1,p4.idx+1) )
                counter += 1
                if counter == 2:
                    fh.write("\n")
                    counter = 0
            fh.write("\n")

            ## Write out impropers
            impropers = self.get_impropers()
            fh.write("{:>8d} !NIMPHI\n".format(len(impropers)))
            counter = 0
            for p1,p2,p3,p4,a in impropers:
                fh.write( "{:d} {:d} {:d} {:d}".format(p1.idx+1,p2.idx+1,p3.idx+1,p4.idx+1) )
                counter += 1
                if counter == 2:
                    fh.write("\n")
                    counter = 0
            fh.write("\n")
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538


class ArbdModel(PdbModel):
    def __init__(self, children, dimensions=(1000,1000,1000), temperature=291, timestep=50e-6, cutoff=50, decompPeriod=10000, pairlistDistance=None, nonbondedResolution=0.1):
        PdbModel.__init__(self, children, dimensions)
        self.temperature = temperature

        self.timestep = timestep
        self.cutoff  =  cutoff

        if pairlistDistance == None:
            pairlistDistance = cutoff+2
        
        self.decompPeriod = decompPeriod
        self.pairlistDistance = pairlistDistance

        self.numParticles = 0
        self.particles = []
        self.type_counts = None

        self.nbSchemes = []
        self._nbParamFiles = [] # This could be made more robust
        self.nbResolution = 0.1

        self._written_bond_files = dict()        

        self.cacheUpToDate = False

539
540
541
542
543
544
545
    def clear_all(self, keep_children=False):
        Parent.clear_all(self, keep_children=keep_children)
        self.particles = []
        self.numParticles = 0
        self.type_counts = None
        self._nbParamFiles = []
        self._written_bond_files = dict()
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574

    def _getNbScheme(self, typeA, typeB):
        scheme = None
        for s,A,B in self.nbSchemes:
            if A is None or B is None:
                if A is None and B is None:
                    return s
                elif A is None and typeB == B:
                    return s
                elif B is None and typeA == A:
                    return s
            elif typeA == A and typeB == B:
                return s
        raise Exception("No nonbonded scheme found for %s and %s" % (typeA.name, typeB.name))

    def _countParticleTypes(self):
        ## TODO: check for modifications to particle that require
        ## automatic generation of new particle type
        type_counts = dict()
        for p in self:
            t = p.type_
            if t in type_counts:
                type_counts[t] += 1
            else:
                type_counts[t] = 1
        self.type_counts = type_counts

    def _updateParticleOrder(self):
        ## Create ordered list
575
576
        self.particles = [p for p in self]
        # self.particles = sorted(particles, key=lambda p: (p.type_, p.idx))
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
        
        ## Update particle indices
        for p,i in zip(self.particles,range(len(self.particles))):
            p.idx = i
            
        # self.initialCoords = np.array([p.initialPosition for p in self.particles])

    def useNonbondedScheme(self, nbScheme, typeA=None, typeB=None):
        self.nbSchemes.append( (nbScheme, typeA, typeB) )
        if typeA != typeB:
            self.nbSchemes.append( (nbScheme, typeB, typeA) )

    def simulate(self, outputPrefix, outputDirectory='output', numSteps=100000000, timestep=100e-6, gpu=0, outputPeriod=1e4, arbd=None):
        assert(type(gpu) is int)
        numSteps = int(numSteps)

593
        if self.cacheUpToDate == False: # TODO: remove cache?
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
            self._countParticleTypes()
            self._updateParticleOrder()

        if outputDirectory == '': outputDirectory='.'
            
        if arbd is None:
            for path in os.environ["PATH"].split(os.pathsep):
                path = path.strip('"')
                fname = os.path.join(path, "arbd")
                if os.path.isfile(fname) and os.access(fname, os.X_OK):
                    arbd = fname
                    break 

        if arbd is None: raise Exception("ARBD was not found")

        if not os.path.exists(arbd):
            raise Exception("ARBD was not found")
        if not os.path.isfile(arbd):
            raise Exception("ARBD was not found")
        if not os.access(arbd, os.X_OK):
            raise Exception("ARBD is not executable")

        if not os.path.exists(outputDirectory):
            os.makedirs(outputDirectory)
        elif not os.path.isdir(outputDirectory):
            raise Exception("outputDirectory '%s' is not a directory!" % outputDirectory)
            

        self.writePdb( outputPrefix + ".pdb" )
        self.writePsf( outputPrefix + ".psf" )
        self.writeArbdFiles( outputPrefix, numSteps=numSteps, outputPeriod=outputPeriod )

        ## http://stackoverflow.com/questions/18421757/live-output-from-subprocess-command
        cmd = (arbd, '-g', "%d" % gpu, "%s.bd" % outputPrefix, "%s/%s" % (outputDirectory, outputPrefix))
        cmd = tuple(str(x) for x in cmd)

        print("Running ARBD with: %s" % " ".join(cmd))
        process = subprocess.Popen(cmd, stdout=subprocess.PIPE, universal_newlines=True)
        for line in process.stdout:
            sys.stdout.write(line)
            sys.stdout.flush()

    # -------------------------- #
    # Methods for printing model #
    # -------------------------- #

    def writeArbdFiles(self, prefix, numSteps=100000000, outputPeriod=10000):
        ## TODO: save and reference directories and prefixes using member data
        d = "potentials"
643
644
        if not os.path.exists(d):
            os.makedirs(d)
645
646
647
648
649
        self._bond_filename = "%s/%s.bonds.txt" % (d, prefix)
        self._angle_filename = "%s/%s.angles.txt" % (d, prefix)
        self._dihedral_filename = "%s/%s.dihedrals.txt" % (d, prefix)
        self._exclusion_filename = "%s/%s.exculsions.txt" % (d, prefix)
        
650
651
        # self._writeArbdCoordFile( prefix + ".coord.txt" )
        self._writeArbdParticleFile( prefix + ".particles.txt" )
652
653
654
655
656
657
658
        self._writeArbdBondFile()
        self._writeArbdAngleFile()
        self._writeArbdDihedralFile()
        self._writeArbdExclusionFile()
        self._writeArbdPotentialFiles( prefix, directory = d )
        self._writeArbdConf( prefix, numSteps=numSteps, outputPeriod=outputPeriod )
        
659
660
661
662
663
664
    # def _writeArbdCoordFile(self, filename):
    #     with open(filename,'w') as fh:
    #         for p in self.particles:
    #             fh.write("%f %f %f\n" % tuple(x for x in p.collapsedPosition()))

    def _writeArbdParticleFile(self, filename):
665
666
        with open(filename,'w') as fh:
            for p in self.particles:
667
668
669
                data = tuple([p.idx,p.name] + [x for x in p.collapsedPosition()])
                fh.write("ATOM %d %s %f %f %f\n" % data)

670
671
672
673
674
675
676
677
678
679
680
681
682
683
        
    def _writeArbdConf(self, prefix, randomSeed=None, numSteps=100000000, outputPeriod=10000, restartCoordinateFile=None):
        ## TODO: raise exception if _writeArbdPotentialFiles has not been called
        filename = "%s.bd" % prefix

        ## Prepare a dictionary to fill in placeholders in the configuration file
        params = self.__dict__.copy() # get parameters from System object

        if randomSeed is None:
            params['randomSeed']     = ""
        else:
            params['randomSeed'] = "seed %s" % randomSeed
        params['numSteps']       = int(numSteps)

684
685
        # params['coordinateFile'] = "%s.coord.txt" % prefix
        params['particleFile'] = "%s.particles.txt" % prefix
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
        if restartCoordinateFile is None:
            params['restartCoordinates'] = ""
        else:
            params['restartCoordinates'] = "restartCoordinates %s" % restartCoordinateFile
        params['outputPeriod'] = outputPeriod

        for k,v in zip('XYZ', self.dimensions):
            params['origin'+k] = -v*0.5
            params['dim'+k] = v

        ## Actually write the file
        with open(filename,'w') as fh:
            fh.write("""{randomSeed}
timestep {timestep}
steps {numSteps}
numberFluct 0                   # deprecated

interparticleForce 1            # other values deprecated
fullLongRange 0                 # deprecated
temperature {temperature}

outputPeriod {outputPeriod}
## Energy doesn't actually get printed!
outputEnergyPeriod {outputPeriod}
outputFormat dcd

## Infrequent domain decomposition because this kernel is still very slow
decompPeriod {decompPeriod}
cutoff {cutoff}
pairlistDistance {pairlistDistance}

origin {originX} {originY} {originZ}
systemSize {dimX} {dimY} {dimZ}
\n""".format(**params))
            
            ## Write entries for each type of particle
            for pt,num in self.getParticleTypesAndCounts():
                particleParams = pt.__dict__.copy()
                particleParams['num'] = num
                fh.write("""
particle {name}
num {num}
diffusion {diffusivity}
""".format(**particleParams))
                if 'grid' in particleParams:
                    for g in pt['grid']:
                        fh.write("gridFile {}\n".format(g))
                else:
                    fh.write("gridFile null.dx\n")

            ## Write coordinates and interactions
            fh.write("""
## Input coordinates
739
inputParticles {particleFile}
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
{restartCoordinates}

## Interaction potentials
tabulatedPotential  1
## The i@j@file syntax means particle type i will have NB interactions with particle type j using the potential in file
""".format(**params))
            for pair,f in zip(self._particleTypePairIter(), self._nbParamFiles):
                i,j,t1,t2 = pair
                fh.write("tabulatedFile %d@%d@%s\n" % (i,j,f))

            ## Bonded interactions
            bonds = self.get_bonds()
            angles = self.get_angles()
            dihedrals = self.get_dihedrals()
            exclusions = self.get_exclusions()

            if len(bonds) > 0:
                for b in list(set([b for i,j,b,ex in bonds])):
                    fh.write("tabulatedBondFile %s\n" % b)

            if len(angles) > 0:
                for b in list(set([b for i,j,k,b in angles])):
                    fh.write("tabulatedAngleFile %s\n" % b)

            if len(dihedrals) > 0:
                for b in list(set([b for i,j,k,l,b in dihedrals])):
                    fh.write("tabulatedDihedralFile %s\n" % b)

            fh.write("inputBonds %s\n" % self._bond_filename)
            fh.write("inputAngles %s\n" % self._angle_filename)
            fh.write("inputDihedrals %s\n" % self._dihedral_filename)
            fh.write("inputExcludes %s\n" % self._exclusion_filename)
     
        write_null_dx = False
        for pt,num in self.getParticleTypesAndCounts():
            if "grid" not in pt.__dict__: 
                with open("null.dx",'w') as fh:
                    fh.write("""object 1 class gridpositions counts  2 2 2
origin {originX} {originY} {originZ}
delta  {dimX} 0.000000 0.000000
delta  0.000000 {dimY} 0.000000
delta  0.000000 0.000000 {dimZ}
object 2 class gridconnections counts  2 2 2
object 3 class array type float rank 0 items 8 data follows
0.0	0.0	0.0	
0.0	0.0	0.0	
0.0	0.0	
attribute "dep" string "positions"
object "density" class field 
component "positions" value 1
component "connections" value 2
component "data" value 3
""".format(**params))
                    break

    def getParticleTypesAndCounts(self):
        ## TODO: remove(?)
        return sorted( self.type_counts.items(), key=lambda x: x[0] )

    def _particleTypePairIter(self):
        typesAndCounts = self.getParticleTypesAndCounts()
        for i in range(len(typesAndCounts)):
            t1 = typesAndCounts[i][0]
            for j in range(i,len(typesAndCounts)):
                t2 = typesAndCounts[j][0]
                yield( (i,j,t1,t2) )
    
    def _writeArbdPotentialFiles(self, prefix, directory = "potentials"):
        try: 
            os.makedirs(directory)
        except OSError:
            if not os.path.isdir(directory):
                raise

        pathPrefix = "%s/%s" % (directory,prefix)
        self._writeNonbondedParameterFiles( pathPrefix + "-nb" )
        # self._writeBondParameterFiles( pathPrefix )
        # self._writeAngleParameterFiles( pathPrefix )
        # self._writeDihedralParameterFiles( pathPrefix )
                
    def _writeNonbondedParameterFiles(self, prefix):
        x = np.arange(0, self.cutoff, self.nbResolution)
        for i,j,t1,t2 in self._particleTypePairIter():
            f = "%s.%s-%s.dat" % (prefix, t1.name, t2.name)
            scheme = self._getNbScheme(t1,t2)
            scheme.write_file(f, t1, t2, rMax = self.cutoff)
            self._nbParamFiles.append(f)

    def _getNonbondedPotential(self,x,a,b):
        return a*(np.exp(-x/b))    

    def _writeArbdBondFile( self ):
        for b in list( set( [b for i,j,b,ex in self.get_bonds()] ) ):
            if type(b) is not str:
                b.write_file()

        with open(self._bond_filename,'w') as fh:
            for i,j,b,ex in self.get_bonds():
                item = (i.idx, j.idx, str(b))
                if ex:
                    fh.write("BOND REPLACE %d %d %s\n" % item)
                else:
                    fh.write("BOND ADD %d %d %s\n" % item)

    def _writeArbdAngleFile( self ):
        for b in list( set( [b for i,j,k,b in self.get_angles()] ) ):
            if type(b) is not str:
                b.write_file()

        with open(self._angle_filename,'w') as fh:
            for b in self.get_angles():
                item = tuple([p.idx for p in b[:-1]] + [str(b[-1])])
                fh.write("ANGLE %d %d %d %s\n" % item)

    def _writeArbdDihedralFile( self ):
        for b in list( set( [b for i,j,k,l,b in self.get_dihedrals()] ) ):
            if type(b) is not str:
                b.write_file()

        with open(self._dihedral_filename,'w') as fh:
            for b in self.get_dihedrals():
                item = tuple([p.idx for p in b[:-1]] + [str(b[-1])])
                fh.write("DIHEDRAL %d %d %d %d %s\n" % item)

    def _writeArbdExclusionFile( self ):
        with open(self._exclusion_filename,'w') as fh:
            for ex in self.get_exclusions():
                item = tuple(int(p.idx) for p in ex)
                fh.write("EXCLUDE %d %d\n" % item)
cmaffeo2's avatar
cmaffeo2 committed
869
870
871
872
873
874
875
876
877

    def atomic_simulate(self, outputPrefix, outputDirectory='output'):
        if self.cacheUpToDate == False: # TODO: remove cache?
            self._countParticleTypes()
            self._updateParticleOrder()

        if outputDirectory == '': outputDirectory='.'
        self.writePdb( outputPrefix + ".pdb" )
        self.writePsf( outputPrefix + ".psf" )