i0ddlZddlmZddlmZmZddlmZddlZ ddl Z ddl Z ddl mZGddeZGd d eZd Zd Zd ZdZdS)N)SynchronizedArray)ProcessManager) cpu_count) MemoryReadercZeZdZdZddZdZdZdZdZdZ d Z d Z d Z d Z e Zd ZdS)TriangularMatrixaTriangular matrix class. This class is designed to provide a memory-efficient representation of a triangular matrix that still behaves as a square symmetric one. The class wraps a numpy.array object, in which data are memorized in row-major order. It also has few additional facilities to conveniently load/write a matrix from/to file. It can be accessed using the [] and () operators, similarly to a normal numpy array. Nc nt|tr3tj|t |_n||_||_|r||dSt|tj r7||_tj |dz|zdztj |_ dSt|trxtj|tj |_ t!tjddt%|zzdz dz |_dSt|tjrH||_ t!tjddt%|zzdz dz |_dSt()aClass constructor. Parameters ---------- size : int / array_like Size of the matrix (number of rows or columns). If an array is provided instead, the size of the triangular matrix will be calculated and the array copied as the matrix elements. Otherwise, the matrix is just initialized to zero. metadata : dict or None Metadata dictionary. Used to generate the metadata attribute. loadfile : str or None Load the matrix from this file. All the attributes and data will be determined by the matrix file itself (i.e. metadata will be ignored); size has to be provided though. )dtypeN) isinstancedictnparrayitemsobjectmetadatasizeloadznumbersIntegralzerosfloat64 _elementsrget_objintsqrtlenndarray TypeError)selfrrloadfiles j/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/analysis/encore/utils.py__init__zTriangularMatrix.__init__,sk& h % % %HX^^%5%5VDDDDMM$DM   JJx g. / / DIXtax4&71&z0ParallelCalculation.__init__..s111!2111r()n_jobsr functionshasattrr!r,kwargsnruns)r$rgfunctionr,rjs r&r'zParallelCalculation.__init__s$ ;"  #++DK!t~z22 :"n-D 9DN t~  #d)) + +!^AAA.D S000DN <D   2 DKK11ty111DKYY r(c  |}|dkrdS|||j||j|i|j|f[)a Generic worker. Will run function with the prescribed args and kwargs. Parameters ---------- q : multiprocessing.Manager.Queue object work queue, from which the worker fetches arguments and messages results : multiprocessing.Manager.Queue object results queue, where results are put after each calculation is finished TSTOPN)getputrhr,rj)r$qresultsres r&workerzParallelCalculation.workersh  AF{{ KK%DN1%ty|Ft{1~FFG     r(c 2g}jdkrWtjD]@}||j|j|ij|fAnt}||fdtjD}tjD]} ||D]} d|D]}| |D]}|  dtj dD]}||tt|dS)a Run parallel calculation. Returns ------- results : tuple of ordered tuples (int, object) int is the number of the calculation corresponding to a certain argument in the args list, and object is the result of corresponding calculation. For instance, in (3, output), output is the return of function(\*args[3], \*\*kwargs[3]). r c@g|]}tjfS))targetr,)rrs)rdrerqrrr$s r&rfz+ParallelCalculation.run..6s<t{!W>>>r(rnc|dS)Nrr?)r-s r&z)ParallelCalculation.run..Js !r()key)rgrangerkappendrhr,rjrQueuerpstartjoiniterrotuplesorted)r$ results_listremanagerworkerswrqrrs` @@r&runzParallelCalculation.runs ;!  4:&&  ##)q)49Q<J4;q>JJK  iiG AmmooGt{++G 4:&&  a  f       KK   '+v.. ' '##A&&&&VLnn===>>>r(rX)rYrZr[r\r'rsrr?r(r&r_r_sQ0))))V2,?,?,?,?,?r(r_c#K|\}}||dkr+||kr||fVd}|dz }n ||fV|dz }||dk+||dkr||fV|dz }||dkdSdS)a Generate (i,j) indeces of a triangular matrix, between elements a and b. The matrix size is automatically determined from the number of elements. For instance: trm_indices((0,0),(2,1)) yields (0,0) (1,0) (1,1) (2,0) (2,1). Parameters ---------- a : (int i, int j) tuple starting matrix element. b : (int i, int j) tuple final matrix element. rr Nr?)r7brejs r& trm_indicesrMs DAq ad(( 66a&LLLA FAAa&LLL FA ad(( qt))!f  Q qt))))))r(c#`Ktd|D]}t|D]}||fV dS)zgenerate (i,j) indeces of a triangular matrix of n rows (or columns), without diagonal (e.g. no elements (0,0),(1,1),...,(n,n)) Parameters ---------- n : int Matrix size r Nrznrers r&trm_indices_nodiagrksR1a[[q  Aa&LLLL r(c#fKtd|D]}t|dzD]}||fV dS)zgenerate (i,j) indeces of a triangular matrix of n rows (or columns), with diagonal Parameters ---------- n : int Matrix size rr Nrrs r&trm_indices_diagr{sV1a[[q1u  Aa&LLLL r(c |D]}|tj|djt jt d|DdtS)z Merge list of universes into one Parameters ---------- universes : list of Universe objects Returns ---------- Universe object rcDg|]}|jdS)fac)order) trajectory timeseries)rdes r&rfz#merge_universes..s+KKKA1<***77KKKr()axis)format)transfer_to_memorymdaUniversefilenamer concatenaterr) universesuniverses r&merge_universesrs&&##%%%% <!   KKKKK L L       r()rmultiprocessing.sharedctypesrmultiprocessingrrjoblibrnumpyrsys MDAnalysisrcoordinates.memoryrrr r_rrrrr?r(r&rs+.::::::,,,,,,,, ......\$\$\$\$\$v\$\$\$~I?I?I?I?I?&I?I?I?X<       r(