diff --git a/configure b/configure index c3a22683..de5b3d56 100755 --- a/configure +++ b/configure @@ -142,7 +142,7 @@ ezfio = Info( default_path=join(QP_ROOT_INSTALL, "EZFIO")) zeromq = Info( - url='http://download.zeromq.org/zeromq-4.0.7.tar.gz', + url='https://github.com/zeromq/zeromq4-1/releases/download/v4.1.4/zeromq-4.1.4.tar.gz', description=' ZeroMQ', default_path=join(QP_ROOT_LIB, "libzmq.a")) @@ -166,7 +166,7 @@ d_info = dict() for m in ["ocaml", "m4", "curl", "zlib", "patch", "irpf90", "docopt", "resultsFile", "ninja", "emsl", "ezfio", "p_graphviz", - "zeromq", "f77zmq","bats" ]: + "zeromq", "f77zmq","bats"]: exec ("d_info['{0}']={0}".format(m)) diff --git a/data/pseudo/tn_df b/data/pseudo/tn_df new file mode 100644 index 00000000..2ba941be --- /dev/null +++ b/data/pseudo/tn_df @@ -0,0 +1,785 @@ +H GEN 0 2 +6 + 1.00000000 1 34.44662515 + -0.89096601 2 40.13885591 + -4.35250792 2 24.66307521 + -11.58011743 2 20.49225491 + 12.58011743 2 30.23909011 + 34.44662515 3 22.28419700 +6 + -262.22422461 2 17.87367530 + 258.22981252 2 28.75598991 + 5613.63467960 2 19.10096571 + -4192.30569417 2 18.88256059 + -1341.04802395 2 20.95302325 + -79.28421640 2 34.10653707 +6 + -199.48848662 2 37.85954681 + 197.31066276 2 28.79454664 + 4870247.22276531 2 40.22839783 + -5277181.77014563 2 40.34690459 + -196566.81095176 2 39.13989706 + 603502.35555458 2 40.91315002 + +He GEN 0 2 +6 + 2.00000000 1 22.64777484 + -0.00700692 2 23.54196640 + -8.90169316 2 18.71556903 + 113.56926776 2 15.15150658 + -112.56926776 2 13.80465850 + 45.29554968 3 12.54192267 +6 + 747.63794984 2 13.33611411 + -753.70091072 2 23.45392111 + -397.08293819 2 12.23651194 + 10.35341837 2 14.87987639 + -1430.53848568 2 18.32138342 + 1818.26602949 2 21.24054054 +6 + 305.67933642 2 21.32319132 + -307.98355807 2 12.22370696 + 5957.66379729 2 14.11720170 + -6099.62872267 2 14.41269814 + 523.59639310 2 17.66028106 + -380.63505659 2 21.52626637 + +Li GEN 2 2 +6 + 1.00000000 1 0.78732101 + -2.23999912 2 0.79224763 + 0.10376190 2 1.79622268 + 4.27489122 2 1.83637465 + -3.27489122 2 1.91213904 + 0.78732101 3 0.79291624 +6 + 256.80790655 2 1.78312879 + -255.81956741 2 0.95553059 + 90.30361668 2 0.87617279 + 272.13155048 2 1.09621549 + -180.73373018 2 1.43900642 + -180.70146573 2 1.83085147 +6 + -4.80714862 2 1.53942961 + 3.36281864 2 0.84742021 + -305.38012622 2 0.78976831 + -509.40184487 2 0.98031681 + 436.16121675 2 0.81548364 + 379.61797456 2 1.02582853 + +Be GEN 2 2 +6 + 2.00000000 1 1.20639978 + -5.40313229 2 1.18425537 + 1.72394027 2 2.81826911 + 2.83884922 2 2.37513515 + -1.83884922 2 2.82920954 + 2.41279956 3 1.18219335 +6 + -1045.63679908 2 2.59240356 + 1047.85482764 2 1.41685787 + -1899.15859219 2 1.48536566 + 1398.06780686 2 1.70076501 + -696.13481389 2 2.03898674 + 1198.22571139 2 2.57766211 +6 + 630.90931326 2 1.84421403 + -632.78437074 2 1.13419132 + 441.35012255 2 1.13393716 + 435.97021325 2 1.22419150 + -353.63284449 2 1.39760436 + -522.69065435 2 1.88595068 + +B GEN 2 2 +6 + 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35.88691706 + -71.59603354 2 2.32679268 + 69.29537053 2 14.47120857 + -182.97334302 2 33.48566094 + 53.73921710 2 5.03596368 + 60.93980797 2 1.71252673 + +Ni GEN 18 2 +6 + 10.00000000 1 22.08639324 + -144.93688782 2 14.51813938 + 58.56151708 2 31.72005545 + 5.46467869 2 46.47610840 + -4.46467869 2 1.64348434 + 220.86393239 3 17.23929992 +6 + -1037.96291767 2 23.63013626 + 1112.68285967 2 22.54579447 + -202.88667032 2 10.67846148 + -1992.46747856 2 2.78611652 + 261.70081349 2 7.26891690 + 1934.65478930 2 2.71695433 +6 + -53.30731307 2 26.78098186 + 127.09013633 2 3.54449677 + -4806.85555998 2 9.97427088 + 4887.04372410 2 10.06368893 + -212.17359382 2 2.46160888 + 132.98697057 2 1.97486742 + +Cu GEN 18 2 +6 + 11.00000000 1 2.82733696 + -34.48196386 2 1.92614044 + -60.25585479 2 16.36117816 + 95.74606505 2 26.07073787 + -94.74606505 2 15.23964803 + 31.10070652 3 2.17204001 +6 + -45.62927216 2 31.69953680 + 125.91417027 2 1.14930323 + -14.54702824 2 1.62190112 + 4.20903863 2 5.04037704 + 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1.33657021 +6 + 13218.94379269 2 1.93743539 + -13214.39886844 2 1.06114866 + -12968.43207956 2 1.94924972 + 13915.97822491 2 1.06566409 + -954.00698285 2 1.23265097 + 7.46088753 2 4.89271387 +6 + 1464.46500602 2 1.99905491 + -1463.07044815 2 1.47578217 + 368.93680276 2 1.30626554 + -20015.22902646 2 1.76510607 + -4931.41969774 2 1.62454622 + 24578.71284776 2 1.71245824 + +Se GEN 28 2 +6 + 6.00000000 1 1.51096144 + 18985.66456772 2 2.92355341 + -18994.15945825 2 2.92032845 + -67662.27071451 2 3.11248219 + 67663.27071451 2 3.11189793 + 9.06576863 3 1.65761092 +6 + 9.98441274 2 1.51889669 + -2.50844675 2 1.97738476 + -180236.05319146 2 2.70806322 + 388717.66809223 2 2.76186155 + -395809.31847294 2 2.85646715 + 187328.70401255 2 2.90992434 +6 + -0.64003892 2 1.60286011 + 4.75615253 2 1.39335643 + -1221.08696720 2 2.09669307 + -10412.15615824 2 2.41527013 + 11345.50935270 2 2.36453165 + 288.73492615 2 3.03391531 + +Br GEN 28 2 +6 + 7.00000000 1 1.41289916 + -7.52651514 2 1.15658370 + 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173.21349705 3 11.94458523 +6 + -3233.03788910 2 12.39056574 + 3263.09949012 2 20.60119535 + 1065.47298248 2 11.30677784 + 846.05067282 2 12.27737462 + -34052.05079344 2 17.82669542 + 32141.52790433 2 17.34318949 +6 + 64989.42116117 2 20.31242587 + -65003.08394100 2 20.05277414 + -486.55828399 2 12.87396775 + 2895.04182579 2 15.84533388 + -261.91821074 2 19.42277681 + -2145.56672184 2 23.82700477 + +K GEN 18 2 +6 + 1.00000000 1 0.68724959 + 7665.13435390 2 0.62381187 + -7668.26785841 2 0.59278246 + -3877.60874288 2 0.63961163 + 3878.60874288 2 0.57860350 + 0.68724959 3 0.50008691 +6 + 477943.00813868 2 0.60446875 + -477941.36080643 2 0.55281419 + -533027.54468668 2 0.57763214 + 644866.44840953 2 0.56624742 + -347063.87255621 2 0.60823749 + 235225.96911606 2 0.54903924 +6 + 5177368.01138896 2 0.56835236 + -5177366.94506877 2 0.57395949 + 479730.23987439 2 0.65183506 + 1027151.48932830 2 0.60393420 + -737636.25038898 2 0.55451546 + -769244.47868615 2 0.64345811 + +Ca GEN 18 2 +6 + 2.00000000 1 1.02097432 + -10036.20006734 2 0.76570985 + 10030.67757963 2 0.83608195 + -8136.00883920 2 0.84362927 + 8137.00883920 2 0.75729596 + 2.04194863 3 0.94514267 +6 + -34706.02643508 2 0.85912364 + 34710.12533681 2 0.50000000 + 860.68953329 2 0.79227941 + 33806.87817612 2 0.85997136 + -34747.30927870 2 0.50004940 + 80.74228959 2 1.01833438 +6 + 514.89542915 2 0.50045897 + -511.93073005 2 0.57886998 + -1374495660.24999190 2 0.50000000 + 687246875.87136328 2 0.50000000 + 595.96081232 2 0.56402502 + 687248189.41960287 2 0.50000000 + +Sc GEN 18 2 +6 + 3.00000000 1 8.57059896 + 39.59298139 2 7.59719947 + -67.37349200 2 5.06179469 + 3.54689568 2 11.85222547 + -2.54689568 2 0.70815643 + 25.71179688 3 5.04858060 +6 + 414.99811890 2 5.58945823 + -389.30527335 2 5.93611719 + 8.74915776 2 0.56803113 + -23.92388226 2 0.60868170 + 42.12589000 2 0.76957270 + -25.95178014 2 1.21300456 +6 + 87.05758924 2 1.12946939 + -62.19670511 2 8.56362761 + 66.37833241 2 7.27494713 + 16.41391965 2 0.74327556 + 43.70031508 2 2.03252459 + -125.49197853 2 1.19227023 + +Ti GEN 18 2 +6 + 4.00000000 1 4.77516915 + 28.34758957 2 10.86929502 + -63.21363466 2 5.37319310 + 5.17935660 2 6.86168513 + -4.17935660 2 0.95669336 + 19.10067660 3 3.52162434 +6 + 211.66189616 2 7.01854391 + -179.82099411 2 1.03880358 + -185.28466640 2 8.02474194 + 43.44334388 2 1.22490803 + -44.06205312 2 0.73917909 + 186.90335758 2 0.89595855 +6 + 49.26886952 2 4.65596397 + -18.32131307 2 12.03001514 + -5.50633295 2 2.16547114 + -342.25486254 2 0.92182600 + 304.90681508 2 0.90099079 + 43.85505055 2 0.99684289 + +V GEN 18 2 +6 + 5.00000000 1 7.54069430 + 35.58763613 2 13.63949328 + -78.03044429 2 6.35551182 + 6.53716910 2 2.59423528 + -5.53716910 2 1.16176108 + 37.70347150 3 6.00940761 +6 + 194.57815114 2 8.18606241 + -156.25972501 2 0.95585889 + -162.29334861 2 9.81441300 + -7.74379387 2 0.70017858 + 244.84040986 2 0.97854682 + -73.80312462 2 1.14925292 +6 + 58.91069981 2 5.48333809 + -21.55840127 2 14.40777862 + -10.12891199 2 2.12080402 + 2.52953175 2 0.69388688 + 109.28174657 2 1.01378564 + -100.68144081 2 1.02780261 + +Cr GEN 18 2 +6 + 6.00000000 1 5.86829616 + -3.09900314 2 0.98487638 + -44.94655388 2 6.96616660 + 135.46731129 2 13.59887742 + -134.46731129 2 11.34882544 + 35.20977696 3 8.91110617 +6 + -526.12421414 2 1.73784849 + 568.24328209 2 32.55674074 + -4019.88240027 2 29.55364033 + 495.64908693 2 1.64707294 + 3445.48735974 2 29.05037955 + 79.74580069 2 3.85284016 +6 + 31.31844062 2 19.50625909 + 10.30743573 2 0.86978393 + -81.88780266 2 15.20370471 + 461.22634080 2 10.28610919 + 1.00599253 2 29.84121604 + -379.34381792 2 10.93761710 + +Mn GEN 18 2 +6 + 7.00000000 1 15.05016398 + 76.91199595 2 15.84783194 + -135.08366030 2 9.80426007 + 5.12036990 2 21.62193241 + -4.12036990 2 1.26331891 + 105.35114786 3 9.24698903 +6 + 4.45077705 2 37.07900996 + 46.93892122 2 10.09409180 + -59.63952162 2 18.98557107 + 47.25376130 2 10.16267391 + 2270.38024432 2 0.79460121 + -2256.99438460 2 0.79345224 +6 + 43.65884288 2 39.18960573 + 6.58957965 2 5.88646925 + 273.41973132 2 12.35978155 + -27.85882166 2 45.92825074 + -255.64090683 2 15.10051906 + 11.08093098 2 0.96083847 + +Fe GEN 18 2 +6 + 8.00000000 1 20.13246747 + 61.79343671 2 20.09868712 + -128.55600523 2 10.70685691 + 4.84472314 2 28.79726611 + -3.84472314 2 1.31374323 + 161.05973977 3 11.74858936 +6 + -20.21006220 2 30.42214774 + 78.68908034 2 10.18491881 + -104.38370168 2 6.69228251 + 11879.61125830 2 2.98725076 + 4067.63536025 2 2.63900793 + -15841.86182474 2 2.88538957 +6 + 52.35701571 2 38.26448010 + 4.85142656 2 5.90250183 + 2169.08154283 2 14.09502191 + -40.04038813 2 42.65213493 + -2140.34005623 2 14.44188153 + 12.29991314 2 1.06050818 + +Co GEN 18 2 +6 + 9.00000000 1 18.31609159 + 47.84627034 2 26.91264651 + -123.98809879 2 11.91957078 + 5.09540361 2 38.50128360 + -4.09540361 2 1.45636943 + 164.84482431 3 13.41744556 +6 + -22.55314559 2 34.07535172 + 88.75521276 2 10.45260699 + -158.32924566 2 5.91087540 + -53402.80058080 2 3.13684604 + 49767.17959800 2 3.16692544 + 3794.95155282 2 2.81533596 +6 + 61.92019742 2 38.11279103 + 2.85881103 2 5.82898971 + -387.27158530 2 15.59733227 + -64.65478412 2 38.57519906 + 439.30094674 2 13.98109833 + 13.62664636 2 1.17046441 + +Ni GEN 18 2 +6 + 10.00000000 1 19.84291404 + -195.32353012 2 16.02128656 + 108.98533897 2 26.59513762 + 6.08469364 2 39.39261550 + -5.08469364 2 1.73812596 + 198.42914037 3 16.63287860 +6 + 636.14358475 2 21.00974643 + -561.54325704 2 22.88188409 + -146.65571659 2 11.08963477 + 1590.91833845 2 2.66405882 + 203.15470938 2 6.84512029 + -1646.41568069 2 2.74451213 +6 + 67.70992628 2 28.31556957 + 5.37743585 2 4.16521410 + 374.49405320 2 17.37825451 + -389.83846114 2 21.96153313 + 1.91671522 2 49.74424984 + 14.42906054 2 1.27579002 + +Cu GEN 18 2 +6 + 11.00000000 1 35.47715926 + -18105.91023962 2 21.73013363 + 18011.23386368 2 21.83870561 + 6.01228206 2 18.42008793 + -5.01228206 2 1.78198604 + 390.24875182 3 20.58922180 +6 + -51.41016015 2 31.92243640 + 131.47547623 2 14.07215286 + -100490.54220540 2 4.21909683 + 20675.75763691 2 3.56801887 + 263590.56712535 2 4.06536588 + -183774.78117039 2 3.92650866 +6 + 68.62159615 2 31.47726702 + 10.70810140 2 4.95987737 + 233.01753836 2 17.95562228 + -258.78181256 2 26.97191776 + 12.01106739 2 46.85069031 + 14.75422657 2 1.35614623 + +Zn GEN 18 2 +6 + 12.00000000 1 26.60492300 + -196.98442222 2 17.93401272 + 89.18558790 2 36.25784521 + 6.19159911 2 49.96784160 + -5.19159911 2 1.99109193 + 319.25907600 3 19.77027094 +6 + -177.37971474 2 32.01501166 + 269.42130045 2 23.08836163 + 60361.29701582 2 4.67975974 + 1343973.13568915 2 5.29114502 + -619902.07009680 2 5.11539109 + -784431.36064381 2 5.38368747 +6 + 46.22045015 2 19.08371294 + 43.98275320 2 50.00000000 + 103.59052598 2 16.88459979 + -129.86700605 2 37.83300205 + 11.83058445 2 5.11918008 + 15.44716451 2 1.45112568 + +Ga GEN 28 2 +6 + 3.00000000 1 1.29464779 + 1852.96920182 2 1.20541500 + -1856.15440251 2 1.17879070 + -513.51787928 2 1.21964580 + 514.51787928 2 1.12868888 + 3.88394338 3 1.06946118 +6 + -10.41248284 2 0.75266853 + 13.44253658 2 0.82344143 + -163070.82529640 2 1.96346903 + 118782.06261627 2 1.90761481 + 72439.51450979 2 2.00432013 + -28149.75180125 2 1.83309310 +6 + -55.43707314 2 0.98715132 + 55.68679311 2 1.18143237 + 95.35935510 2 1.24163917 + -111.55606197 2 1.48647971 + 6.22134153 2 1.87957113 + 10.97737885 2 2.24689865 + +Ge GEN 28 2 +6 + 4.00000000 1 0.64699203 + 1042.65966555 2 1.17600365 + -1045.50742663 2 1.40672708 + -522.21837337 2 1.06148136 + 523.21837337 2 1.52689039 + 2.58796812 3 0.70634661 +6 + 298.52031462 2 1.37488700 + -295.91758286 2 3.05395101 + -65778.83466330 2 1.99750874 + 253302.61962618 2 2.10159773 + 25864.29161720 2 2.35028323 + -213387.07659768 2 2.16152517 +6 + -1416.87913796 2 1.43279054 + 1416.49405157 2 1.27947333 + -4677.12774504 2 1.39756889 + 6758.57740664 2 1.50728327 + -2630.12555402 2 1.70834188 + 549.67778384 2 1.92912262 + +As GEN 28 2 +6 + 5.00000000 1 1.90897798 + -8.55267316 2 1.59326524 + 3.44617934 2 1.10844459 + -8.94709126 2 1.02625257 + 9.94709126 2 1.90897549 + 9.54488990 3 1.18318262 +6 + -299.57003383 2 1.31601774 + 303.89084920 2 0.88992491 + 34018.91875930 2 0.82417957 + -44808.38727678 2 0.87058735 + 19528.43031171 2 0.91644709 + -8737.95845690 2 0.77833472 +6 + 46094.50987530 2 1.90902784 + -46093.10097169 2 1.56895782 + -1934.82978262 2 1.41134047 + -240427.05172601 2 1.84187044 + 36043.17172862 2 1.53235052 + 206319.71069040 2 1.81590910 + +Se GEN 28 2 +6 + 6.00000000 1 1.73885845 + -4868.76631948 2 3.10952817 + 4860.07291481 2 2.76656612 + 247376.94576273 2 2.93723435 + -247375.94576273 2 2.93039894 + 10.43315069 3 1.80783830 +6 + 43.48906338 2 1.54256367 + -36.07303722 2 1.99876644 + -1338.16209913 2 2.22244851 + 88855.15492433 2 3.01653570 + -93322.17292948 2 3.00370283 + 5806.18068397 2 2.62760372 +6 + 101.24952978 2 1.51703915 + -96.89194467 2 1.50669503 + -561.81915381 2 2.17759706 + 1474.30831735 2 2.47900419 + -87533.83638244 2 3.02701983 + 86622.34849171 2 3.03071493 + +Br GEN 28 2 +6 + 7.00000000 1 1.29861066 + -8.22129971 2 1.15959643 + 0.21335410 2 2.29768788 + -14617.16154553 2 2.88622041 + 14618.16154553 2 2.88664159 + 9.09027461 3 1.38987227 +6 + 1993.56030565 2 1.99554365 + -1988.14839885 2 2.18330258 + 62338.94920254 2 2.78298975 + 91516.94063906 2 2.50252605 + -109846.25447802 2 2.70576408 + -44008.63516555 2 2.38434210 +6 + 17.36412726 2 1.29580803 + -14.67327121 2 1.60078690 + -6128.76923065 2 2.16344915 + 12563.02678529 2 2.26961184 + 757.63553722 2 2.83383736 + -7190.89195704 2 2.41971949 + +Kr GEN 28 2 +6 + 8.00000000 1 6.82429532 + 2245.94610147 2 4.82301962 + -2257.24927570 2 3.38163452 + 1889.52842356 2 3.29088128 + -1888.52842356 2 4.98656184 + 54.59436254 3 3.01373570 +6 + -2003.10975854 2 6.01573226 + 2010.79212346 2 4.07497664 + 13467772.94730707 2 4.47273823 + -18464141.82809087 2 4.45030979 + -2607955.84552628 2 4.28291762 + 7604325.72641131 2 4.35368575 +6 + -6512.57971257 2 5.33963561 + 6517.54562224 2 4.41831473 + 55170.14413687 2 3.66247372 + -35314.20447418 2 3.56293692 + -27094.88743738 2 3.99199621 + 7239.94695795 2 5.23539786 + +Al GEN 10 2 +6 + 3.00000000 1 0.90167530 + -12.07740634 2 1.08338853 + 6.60507677 2 2.07851308 + -13877404.00590185 2 2.08053590 + 13877405.00590186 2 2.08053570 + 2.70502591 3 0.92748596 +6 + -41.26842670 2 2.04866185 + 45.70193781 2 1.11866688 + 2946.69575922 2 1.71721106 + -376.01922297 2 1.36753958 + 4331.41613799 2 1.93292012 + -6901.09265568 2 1.86705782 +6 + 504.79904464 2 1.88548919 + -502.69536383 2 1.42616967 + -769.46860271 2 1.80548694 + -17.66088618 2 0.95520911 + 101.43853505 2 1.20112583 + 686.69150206 2 1.52824179 + +Si GEN 10 2 +6 + 4.00000000 1 2.54461774 + -2902.58084906 2 2.24978528 + 2895.18838752 2 2.53789008 + 7161.72254279 2 2.34887222 + -7160.72254279 2 2.46336277 + 10.17847098 3 1.52421025 +6 + 4.24352962 2 1.08064949 + 2.05989979 2 1.33341749 + 88608.14855737 2 2.39993059 + -849.93508619 2 1.92845396 + -1434647.87047626 2 2.35634772 + 1346890.65714548 2 2.35320332 +6 + -15264.86061936 2 1.82998100 + 15267.99758945 2 1.91566514 + -0.49522434 2 1.35066217 + 2807.17037795 2 2.16756956 + 6912.45723497 2 1.79762600 + -9718.13169060 2 2.03990309 + +P GEN 10 2 +6 + 5.00000000 1 2.20104239 + -14571.76154266 2 3.30954781 + 14561.08785293 2 3.65491917 + -21023.88213100 2 3.60582863 + 21024.88213100 2 3.36814532 + 11.00521195 3 2.06883762 +6 + -214.99423753 2 3.00175595 + 224.31212541 2 1.90508764 + -1320.42895216 2 2.23252373 + 2262.27394007 2 2.56842585 + -5217.11058123 2 3.22957222 + 4276.26614237 2 3.32169865 +6 + -4655.41288683 2 1.51251059 + 4660.80718311 2 1.51289861 + -994.25816078 2 3.31761981 + -19.30793578 2 2.04639527 + 311.57919748 2 3.70626860 + 702.98798215 2 3.09154453 + +S GEN 10 2 +6 + 6.00000000 1 3.76431332 + 518.21506704 2 2.91975646 + -532.35656437 2 2.26777538 + 14394.84387811 2 2.49556645 + -14393.84387811 2 2.51698479 + 22.58587994 3 2.71241239 +6 + -104.19902150 2 4.55895180 + 116.57081427 2 2.10503756 + -994.81335242 2 2.63814508 + 2203.13414043 2 3.11140569 + -1617.61176296 2 3.62963239 + 410.29160018 2 4.55921172 +6 + 723.09548214 2 4.48128068 + -715.46568241 2 3.35956681 + 9063.41201304 2 3.83857196 + -16.38228027 2 1.92699416 + 44.06704522 2 2.30670170 + -9090.09577098 2 3.92706305 + +Cl GEN 10 2 +6 + 7.00000000 1 4.77392870 + 719885.76609499 2 4.74019033 + -719903.82223984 2 4.74189768 + -37102.89380181 2 4.67979490 + 37103.89380181 2 4.71510215 + 33.41750090 3 3.29732864 +6 + 959.05010082 2 5.01134618 + -943.54843009 2 3.64529189 + -6456.16063099 2 4.20510279 + 637.70704529 2 2.74283267 + -1479.66774202 2 3.00605599 + 7299.12201388 2 3.90198120 +6 + -121.63220275 2 3.86324469 + 131.70125226 2 3.08695111 + 5447.27282828 2 5.92092153 + -52.94814165 2 2.63467524 + 559.83762330 2 5.08437179 + -5953.16139883 2 5.86183616 + +Ar GEN 10 2 +6 + 8.00000000 1 5.17746158 + -76.72264736 2 5.90884243 + 56.16280755 2 3.53735685 + -660.63282107 2 4.53072721 + 661.63282107 2 4.90879705 + 41.41969264 3 3.95156133 +6 + 496.48392385 2 3.21092458 + -479.29969508 2 3.39224537 + -12086.26924659 2 4.28061928 + 37151.97923364 2 4.62803105 + 496310.90908097 2 5.10487541 + -521375.61810527 2 5.08995306 +6 + -1901.02320099 2 5.53714820 + 1911.87432982 2 4.52372637 + -127.53875733 2 2.45115265 + 198.78501467 2 2.62001527 + -976.26297293 2 3.97593759 + 906.01814260 2 6.12659776 + + + + diff --git a/install/scripts/install_ocaml.sh b/install/scripts/install_ocaml.sh index 86e4e8b7..a7462b2e 100755 --- a/install/scripts/install_ocaml.sh +++ b/install/scripts/install_ocaml.sh @@ -6,6 +6,7 @@ cd - # Normal installation PACKAGES="core cryptokit ocamlfind sexplib ZMQ" +#ppx_sexp_conv # Needed for ZeroMQ export C_INCLUDE_PATH="${QP_ROOT}"/lib:"${C_INCLUDE_PATH}" diff --git a/install/scripts/install_zeromq.sh b/install/scripts/install_zeromq.sh index 73b59019..3bf2a715 100755 --- a/install/scripts/install_zeromq.sh +++ b/install/scripts/install_zeromq.sh @@ -15,14 +15,14 @@ function _install() ./configure --without-libsodium || exit 1 make -j 8 || exit 1 rm -f -- "${QP_ROOT}"/lib/libzmq.a "${QP_ROOT}"/lib/libzmq.so "${QP_ROOT}"/lib/libzmq.so.? -# cp .libs/libzmq.a "${QP_ROOT}"/lib -# cp .libs/libzmq.so "${QP_ROOT}"/lib/libzmq.so.5 - cp src/.libs/libzmq.a "${QP_ROOT}"/lib - cp src/.libs/libzmq.so "${QP_ROOT}"/lib/libzmq.so.4 + cp .libs/libzmq.a "${QP_ROOT}"/lib + cp .libs/libzmq.so "${QP_ROOT}"/lib/libzmq.so.5 +# cp src/.libs/libzmq.a "${QP_ROOT}"/lib +# cp src/.libs/libzmq.so "${QP_ROOT}"/lib/libzmq.so.4 cp include/{zmq.h,zmq_utils.h} "${QP_ROOT}"/lib cd "${QP_ROOT}"/lib -# ln -s libzmq.so.5 libzmq.so - ln -s libzmq.so.4 libzmq.so + ln -s libzmq.so.5 libzmq.so +# ln -s libzmq.so.4 libzmq.so cd ${ORIG} return 0 } diff --git a/ocaml/Atom.ml b/ocaml/Atom.ml index 832cfa5b..72932b1f 100644 --- a/ocaml/Atom.ml +++ b/ocaml/Atom.ml @@ -1,4 +1,4 @@ -open Core.Std;; +open Core.Std exception AtomError of string @@ -27,12 +27,18 @@ let of_string ~units s = coord = Point3d.of_string ~units (String.concat [x; y; z] ~sep:" ") } | _ -> raise (AtomError s) -;; + let to_string ~units a = [ Element.to_string a.element ; Charge.to_string a.charge ; Point3d.to_string ~units a.coord ] |> String.concat ~sep:" " -;; + + +let to_xyz a = + Printf.sprintf "%-3s %s" + (Element.to_string a.element) + (Point3d.to_string ~units:Units.Angstrom a.coord) + diff --git a/ocaml/Atom.mli b/ocaml/Atom.mli index 28915993..4b1963d5 100644 --- a/ocaml/Atom.mli +++ b/ocaml/Atom.mli @@ -7,3 +7,4 @@ val sexp_of_t : t -> Sexplib.Sexp.t val of_string : units:Units.units -> string -> t val to_string : units:Units.units -> t -> string +val to_xyz : t -> string diff --git a/ocaml/Basis.ml b/ocaml/Basis.ml index 237e5547..869fb132 100644 --- a/ocaml/Basis.ml +++ b/ocaml/Basis.ml @@ -35,11 +35,11 @@ let read_element in_channel at_number element = read in_channel at_number -let to_string b = + +let to_string_general ~fmt ~atom_sep b = let new_nucleus n = Printf.sprintf "Atom %d" n in - let rec do_work accu current_nucleus = function | [] -> List.rev accu | (g,n)::tail -> @@ -47,15 +47,27 @@ let to_string b = in let accu = if (n <> current_nucleus) then - (new_nucleus n)::""::accu + (new_nucleus n)::atom_sep::accu else accu in - do_work ((Gto.to_string g)::accu) n tail + do_work ((Gto.to_string ~fmt g)::accu) n tail in do_work [new_nucleus 1] 1 b |> String.concat ~sep:"\n" +let to_string_gamess = + to_string_general ~fmt:Gto.Gamess ~atom_sep:"" + +let to_string_gaussian b = + String.concat ~sep:"\n" + [ to_string_general ~fmt:Gto.Gaussian ~atom_sep:"****" b ; "****" ] + +let to_string ?(fmt=Gto.Gamess) = + match fmt with + | Gto.Gamess -> to_string_gamess + | Gto.Gaussian -> to_string_gaussian + include To_md5 let to_md5 = to_md5 sexp_of_t diff --git a/ocaml/Basis.mli b/ocaml/Basis.mli index 4da99266..249c14f9 100644 --- a/ocaml/Basis.mli +++ b/ocaml/Basis.mli @@ -14,7 +14,7 @@ val read_element : in_channel -> Nucl_number.t -> Element.t -> (Gto.t * Nucl_number.t) list (** Convert the basis to a string *) -val to_string : (Gto.t * Nucl_number.t) list -> string +val to_string : ?fmt:Gto.fmt -> (Gto.t * Nucl_number.t) list -> string (** Convert the basis to an MD5 hash *) val to_md5 : (Gto.t * Nucl_number.t) list -> MD5.t diff --git a/ocaml/Gto.ml b/ocaml/Gto.ml index 69aeba37..fb576ee7 100644 --- a/ocaml/Gto.ml +++ b/ocaml/Gto.ml @@ -4,6 +4,10 @@ open Qptypes exception GTO_Read_Failure of string exception End_Of_Basis +type fmt = +| Gamess +| Gaussian + type t = { sym : Symmetry.t ; lc : ((Primitive.t * AO_coef.t) list) @@ -68,8 +72,8 @@ let read_one in_channel = -(** Transform the gto to a string *) -let to_string { sym = sym ; lc = lc } = +(** Write the GTO in Gamess format *) +let to_string_gamess { sym = sym ; lc = lc } = let result = Printf.sprintf "%s %3d" (Symmetry.to_string sym) (List.length lc) in @@ -88,3 +92,30 @@ let to_string { sym = sym ; lc = lc } = |> String.concat ~sep:"\n" +(** Write the GTO in Gaussian format *) +let to_string_gaussian { sym = sym ; lc = lc } = + let result = + Printf.sprintf "%s %3d 1.00" (Symmetry.to_string sym) (List.length lc) + in + let rec do_work accu i = function + | [] -> List.rev accu + | (p,c)::tail -> + let p = AO_expo.to_float p.Primitive.expo + and c = AO_coef.to_float c + in + let result = + Printf.sprintf "%15.7f %15.7f" p c + in + do_work (result::accu) (i+1) tail + in + (do_work [result] 1 lc) + |> String.concat ~sep:"\n" + + +(** Transform the gto to a string *) +let to_string ?(fmt=Gamess) = + match fmt with + | Gamess -> to_string_gamess + | Gaussian -> to_string_gaussian + + diff --git a/ocaml/Gto.mli b/ocaml/Gto.mli index fad133a3..753cd81a 100644 --- a/ocaml/Gto.mli +++ b/ocaml/Gto.mli @@ -1,5 +1,9 @@ exception GTO_Read_Failure of string exception End_Of_Basis +type fmt = +| Gamess +| Gaussian + type t = { sym : Symmetry.t ; lc : (Primitive.t * Qptypes.AO_coef.t) list; @@ -13,4 +17,4 @@ val of_prim_coef_list : val read_one : in_channel -> t (** Convert to string for printing *) -val to_string : t -> string +val to_string : ?fmt:fmt -> t -> string diff --git a/ocaml/Input_ao_basis.ml b/ocaml/Input_ao_basis.ml index 82bc4964..88e277ee 100644 --- a/ocaml/Input_ao_basis.ml +++ b/ocaml/Input_ao_basis.ml @@ -17,6 +17,7 @@ module Ao_basis : sig ;; val read : unit -> t option val to_string : t -> string + val to_basis : t -> Basis.t val write : t -> unit val to_md5 : t -> MD5.t val to_rst : t -> Rst_string.t diff --git a/ocaml/Input_nuclei.ml b/ocaml/Input_nuclei.ml index d050ded9..ca81629e 100644 --- a/ocaml/Input_nuclei.ml +++ b/ocaml/Input_nuclei.ml @@ -13,6 +13,7 @@ module Nuclei : sig val read : unit -> t option val write : t -> unit val to_string : t -> string + val to_atom_list : t -> Atom.t list val to_rst : t -> Rst_string.t val of_rst : Rst_string.t -> t option end = struct @@ -134,6 +135,22 @@ end = struct ;; + let to_atom_list b = + let rec loop accu (coord, charge, label) = function + | -1 -> accu + | i -> + let atom = + { Atom.element = label.(i) ; + Atom.charge = charge.(i) ; + Atom.coord = coord.(i) ; + } + in + loop (atom::accu) (coord, charge, label) (i-1) + in + loop [] (b.nucl_coord, b.nucl_charge, b.nucl_label) + ( (Nucl_number.to_int b.nucl_num) - 1) + ;; + let to_string b = Printf.sprintf " nucl_num = %s diff --git a/ocaml/Molecule.ml b/ocaml/Molecule.ml index f0800f7f..a9d73432 100644 --- a/ocaml/Molecule.ml +++ b/ocaml/Molecule.ml @@ -85,7 +85,7 @@ let name m = String.concat (result) -let to_string m = +let to_string_general ~f m = let { nuclei ; elec_alpha ; elec_beta } = m in let n = @@ -94,10 +94,15 @@ let to_string m = let title = name m in - [ Int.to_string n ; title ] @ - (List.map ~f:(fun x -> Atom.to_string Units.Angstrom x) nuclei) + [ Int.to_string n ; title ] @ (List.map ~f nuclei) |> String.concat ~sep:"\n" +let to_string = + to_string_general ~f:(fun x -> Atom.to_string Units.Angstrom x) + +let to_xyz = + to_string_general ~f:Atom.to_xyz + let of_xyz_string ?(charge=(Charge.of_int 0)) ?(multiplicity=(Multiplicity.of_int 1)) diff --git a/ocaml/Molecule.mli b/ocaml/Molecule.mli index 1a3d9715..f81f28a3 100644 --- a/ocaml/Molecule.mli +++ b/ocaml/Molecule.mli @@ -20,6 +20,7 @@ val name : t -> string (** Conversion for printing *) val to_string : t -> string +val to_xyz : t -> string (** Creates a molecule from an xyz file *) diff --git a/ocaml/TaskServer.mli b/ocaml/TaskServer.mli new file mode 100644 index 00000000..f16ddaab --- /dev/null +++ b/ocaml/TaskServer.mli @@ -0,0 +1,84 @@ +type t = +{ + queue : Queuing_system.t ; + state : Message.State.t option ; + address_tcp : Address.Tcp.t option ; + address_inproc : Address.Inproc.t option ; + psi : Message.Psi.t option; + progress_bar : Progress_bar.t option ; + running : bool; +} + + +(** {1} Debugging *) + +(** Fetch the QP_TASK_DEBUG environment variable *) +val debug_env : bool + +(** Print a debug message *) +val debug : string -> unit + +(** {1} ZMQ *) + +(** ZeroMQ context *) +val zmq_context : ZMQ.Context.t + +(** Bind a ZMQ socket *) +val bind_socket : + socket_type:string -> socket:'a ZMQ.Socket.t -> address:string -> unit + +(** Name of the host on which the server runs *) +val hostname : string lazy_t + +(** IP address of the current host *) +val ip_address : string lazy_t + +(** Standard messages *) +val reply_ok : [> `Req ] ZMQ.Socket.t -> unit +val reply_wrong_state : [> `Req ] ZMQ.Socket.t -> unit + +(** Stop server *) +val stop : port:int -> unit + +(** {1} Server functions *) + +(** Create a new job *) +val new_job : Message.Newjob_msg.t -> t -> [> `Req ] ZMQ.Socket.t -> t + +(** Finish a running job *) +val end_job : Message.Endjob_msg.t -> t -> [> `Req ] ZMQ.Socket.t -> t + +(** Connect a client *) +val connect: Message.Connect_msg.t -> t -> [> `Req ] ZMQ.Socket.t -> t + +(** Disconnect a client *) +val disconnect: Message.Disconnect_msg.t -> t -> [> `Req ] ZMQ.Socket.t -> t + +(** Add a task to the pool *) +val add_task: Message.AddTask_msg.t -> t -> [> `Req ] ZMQ.Socket.t -> t + +(** Mark the task as done by the client *) +val task_done: Message.TaskDone_msg.t -> t -> [> `Req ] ZMQ.Socket.t -> t + +(** Delete a task when it has been pulled by the collector *) +val del_task: Message.DelTask_msg.t -> t -> [> `Req ] ZMQ.Socket.t -> t + +(** The client get a new task to execute *) +val get_task: Message.GetTask_msg.t -> t -> [> `Req ] ZMQ.Socket.t -> t + +(** Terminate server *) +val terminate : t -> [> `Req ] ZMQ.Socket.t -> t + +(** Put a wave function in the task server *) +val put_psi : + Message.PutPsi_msg.t -> string list -> t -> [> `Req ] ZMQ.Socket.t -> t + +(** Get the wave function stored in the task server *) +val get_psi : Message.GetPsi_msg.t -> t -> [> `Req ] ZMQ.Socket.t -> t + +(** Reply an Error message *) +val error : string -> t -> [> `Req ] ZMQ.Socket.t -> t + +(** Run server *) +val run : port:int -> unit + diff --git a/ocaml/_tags b/ocaml/_tags index fd4c4804..3f5cd9b6 100644 --- a/ocaml/_tags +++ b/ocaml/_tags @@ -1,3 +1,3 @@ -true: package(core,sexplib.syntax,cryptokit,ZMQ) +true: package(core,cryptokit,ZMQ,sexplib.syntax) true: thread false: profile diff --git a/plugins/Full_CI/micro_pt2.irp.f b/plugins/Full_CI/micro_pt2.irp.f index 1d4d7eaa..14cc52bf 100644 --- a/plugins/Full_CI/micro_pt2.irp.f +++ b/plugins/Full_CI/micro_pt2.irp.f @@ -35,6 +35,8 @@ subroutine run_wf call provide_everything integer :: rc, i + print *, 'Contribution to PT2 running' + !$OMP PARALLEL PRIVATE(i) i = omp_get_thread_num() call H_apply_FCI_PT2_slave_tcp(i) diff --git a/plugins/QmcChem/e_curve_qmc.irp.f b/plugins/QmcChem/e_curve_qmc.irp.f new file mode 100644 index 00000000..4beed3fa --- /dev/null +++ b/plugins/QmcChem/e_curve_qmc.irp.f @@ -0,0 +1,102 @@ +program e_curve + use bitmasks + implicit none + integer :: i,j,k, nab, m, l + double precision :: norm, E, hij, num, ci, cj + integer, allocatable :: iorder(:) + double precision , allocatable :: norm_sort(:) + nab = n_det_alpha_unique+n_det_beta_unique + allocate ( norm_sort(0:nab), iorder(0:nab) ) + + + norm_sort(0) = 0.d0 + iorder(0) = 0 + do i=1,n_det_alpha_unique + norm_sort(i) = det_alpha_norm(i) + iorder(i) = i + enddo + + do i=1,n_det_beta_unique + norm_sort(i+n_det_alpha_unique) = det_beta_norm(i) + iorder(i+n_det_alpha_unique) = -i + enddo + + call dsort(norm_sort(1),iorder(1),nab) + + if (.not.read_wf) then + stop 'Please set read_wf to true' + endif + + PROVIDE psi_bilinear_matrix_values nuclear_repulsion + print *, '' + print *, '==============================' + print *, 'Energies at different cut-offs' + print *, '==============================' + print *, '' + print *, '==========================================================' + print '(A8,2X,A8,2X,A12,2X,A10,2X,A12)', 'Thresh.', 'Ndet', 'Cost', 'Norm', 'E' + print *, '==========================================================' + double precision :: thresh + integer(bit_kind), allocatable :: det_i(:,:), det_j(:,:) + thresh = 1.d-10 + do j=0,nab + i = iorder(j) + if (i<0) then + do k=1,n_det + if (psi_bilinear_matrix_columns(k) == -i) then + psi_bilinear_matrix_values(k,1) = 0.d0 + endif + enddo + else + do k=1,n_det + if (psi_bilinear_matrix_rows(k) == i) then + psi_bilinear_matrix_values(k,1) = 0.d0 + endif + enddo + endif + if (thresh > norm_sort(j)) then + cycle + endif + num = 0.d0 + norm = 0.d0 + m = 0 + !$OMP PARALLEL DEFAULT(SHARED) PRIVATE(k,l,det_i,det_j,ci,cj,hij) REDUCTION(+:norm,m,num) + allocate( det_i(N_int,2), det_j(N_int,2)) + !$OMP DO SCHEDULE(guided) + do k=1,n_det + if (psi_bilinear_matrix_values(k,1) == 0.d0) then + cycle + endif + ci = psi_bilinear_matrix_values(k,1) + det_i(:,1) = psi_det_alpha_unique(:,psi_bilinear_matrix_rows(k)) + det_i(:,2) = psi_det_beta_unique(:,psi_bilinear_matrix_columns(k)) + do l=1,n_det + if (psi_bilinear_matrix_values(l,1) == 0.d0) then + cycle + endif + cj = psi_bilinear_matrix_values(l,1) + det_j(:,1) = psi_det_alpha_unique(:,psi_bilinear_matrix_rows(l)) + det_j(:,2) = psi_det_beta_unique(:,psi_bilinear_matrix_columns(l)) + call i_h_j(det_i, det_j, N_int, hij) + num = num + ci*cj*hij + enddo + norm = norm + ci*ci + m = m+1 + enddo + !$OMP END DO + deallocate (det_i,det_j) + !$OMP END PARALLEL + if (m == 0) then + exit + endif + E = num / norm + nuclear_repulsion + print '(E9.1,2X,I8,2X,F10.2,2X,F10.8,2X,F12.6)', thresh, m, & + dble( elec_alpha_num**3 + elec_alpha_num**2 * (nab-1) ) / & + dble( elec_alpha_num**3 + elec_alpha_num**2 * (j-1)), norm, E + thresh = thresh * 2.d0 + enddo + print *, '==========================================================' + + deallocate (iorder, norm_sort) +end + diff --git a/plugins/QmcChem/save_for_qmcchem.irp.f b/plugins/QmcChem/save_for_qmcchem.irp.f index c8ddb4d9..a281a184 100644 --- a/plugins/QmcChem/save_for_qmcchem.irp.f +++ b/plugins/QmcChem/save_for_qmcchem.irp.f @@ -1,9 +1,46 @@ program save_for_qmc - read_wf = .True. - TOUCH read_wf - print *, "N_det = ", N_det - call write_spindeterminants - if (do_pseudo) then - call write_pseudopotential - endif + + integer :: iunit + integer, external :: get_unit_and_open + logical :: exists + double precision :: e_ref + + ! Determinants + read_wf = .True. + TOUCH read_wf + print *, "N_det = ", N_det + call write_spindeterminants + + ! Reference Energy + if (do_pseudo) then + call write_pseudopotential + endif + call system( & + 'mkdir -p '//trim(ezfio_filename)//'/simulation ;' // & + 'cp '//trim(ezfio_filename)//'/.version '//trim(ezfio_filename)//'/simulation/.version ; ' // & + 'mkdir -p '//trim(ezfio_filename)//'/properties ;' // & + 'cp '//trim(ezfio_filename)//'/.version '//trim(ezfio_filename)//'/properties/.version ; ' // & + 'echo T > '//trim(ezfio_filename)//'/properties/e_loc' & + ) + iunit = 13 + open(unit=iunit,file=trim(ezfio_filename)//'/simulation/e_ref',action='write') + call ezfio_has_full_ci_energy_pt2(exists) + if (exists) then + call ezfio_get_full_ci_energy_pt2(e_ref) + else + call ezfio_has_full_ci_energy(exists) + if (exists) then + call ezfio_get_full_ci_energy(e_ref) + else + call ezfio_has_hartree_fock_energy(exists) + if (exists) then + call ezfio_get_hartree_fock_energy(e_ref) + else + e_ref = 0.d0 + endif + endif + endif + write(iunit,*) e_ref + close(iunit) + end diff --git a/plugins/qmcpack/qp_convert_qmcpack_to_ezfio.py b/plugins/qmcpack/qp_convert_qmcpack_to_ezfio.py index 0dc99029..a140ec1e 100755 --- a/plugins/qmcpack/qp_convert_qmcpack_to_ezfio.py +++ b/plugins/qmcpack/qp_convert_qmcpack_to_ezfio.py @@ -183,6 +183,9 @@ def get_nb_permutation(str_): def order_l_l_sym(l_l_sym): + + l_order_mo = [i for i,_ in enumerate(l_l_sym)] + n = 1 for i in range(len(l_l_sym)): if n != 1: @@ -192,11 +195,11 @@ def order_l_l_sym(l_l_sym): l = l_l_sym[i] n = get_nb_permutation(l[2]) - l_l_sym[i:i + n] = sorted(l_l_sym[i:i + n], - key=lambda x: x[2], - cmp=compare_gamess_style) + l_l_sym[i:i + n], l_order_mo[i:i+n] = zip(*sorted(zip(l_l_sym[i:i + n],l_order_mo[i:i+n]), + key=lambda x: x[0][2], + cmp=compare_gamess_style)) - return l_l_sym + return l_l_sym, l_order_mo #========================== @@ -205,8 +208,13 @@ def order_l_l_sym(l_l_sym): l_sym_without_header = sym_raw.split("\n")[3:-2] l_l_sym_raw = [i.split() for i in l_sym_without_header] +print len(l_l_sym_raw) + l_l_sym_expend_sym = expend_sym_l(l_l_sym_raw) -l_l_sym_ordered = order_l_l_sym(l_l_sym_expend_sym) +print len(l_l_sym_expend_sym) + +l_l_sym_ordered, l_order_mo = order_l_l_sym(l_l_sym_expend_sym) + #======== #MO COEF @@ -348,6 +356,7 @@ d_rep={"+":"1","-":"0"} det_without_header = det_raw[pos+2::] + for line_raw in det_without_header.split("\n"): line = line_raw @@ -355,8 +364,14 @@ for line_raw in det_without_header.split("\n"): try: float(line) except ValueError: + + print line_raw.strip(), len(line_raw.strip()) + print l_order_mo, len(l_order_mo) + + line_order = [line_raw[i] for i in l_order_mo] line= "".join([d_rep[x] if x in d_rep else x for x in line_raw]) print line.strip() print "END_DET" + diff --git a/scripts/compilation/qp_create_ninja.py b/scripts/compilation/qp_create_ninja.py index adcfb6f7..cc1c8aa8 100755 --- a/scripts/compilation/qp_create_ninja.py +++ b/scripts/compilation/qp_create_ninja.py @@ -37,7 +37,7 @@ from qp_path import QP_ROOT, QP_SRC, QP_EZFIO LIB = "" # join(QP_ROOT, "lib", "rdtsc.o") EZFIO_LIB = join(QP_ROOT, "lib", "libezfio_irp.a") -ZMQ_LIB = join(QP_ROOT, "lib", "libf77zmq.a") + " " + join(QP_ROOT, "lib", "libzmq.a") + " -lstdc++ -lrt" +ZMQ_LIB = join(QP_ROOT, "lib", "libf77zmq.a") + " " + join(QP_ROOT, "lib", "libzmq.a") + " -lstdc++ -lrt" ROOT_BUILD_NINJA = join(QP_ROOT, "config", "build.ninja") header = r"""# @@ -96,7 +96,8 @@ def ninja_create_env_variable(pwd_config_file): l_string.append(str_) lib_lapack = get_compilation_option(pwd_config_file, "LAPACK_LIB") - l_string.append("LIB = {0} {1} {2} {3}".format(LIB, lib_lapack, EZFIO_LIB, ZMQ_LIB)) + str_lib = " ".join([LIB, lib_lapack, EZFIO_LIB, ZMQ_LIB]) + l_string.append("LIB = {0} ".format(str_lib)) l_string.append("") @@ -387,6 +388,8 @@ def get_l_file_for_module(path_module): l_src.append(f) obj = '{0}.o'.format(os.path.splitext(f)[0]) l_obj.append(obj) + elif f.lower().endswith(".o"): + l_obj.append(join(path_module.abs, f)) elif f == "EZFIO.cfg": l_depend.append(join(path_module.abs, "ezfio_interface.irp.f")) diff --git a/scripts/ezfio_interface/qp_edit_template b/scripts/ezfio_interface/qp_edit_template index 408ca3f7..9c7a1386 100644 --- a/scripts/ezfio_interface/qp_edit_template +++ b/scripts/ezfio_interface/qp_edit_template @@ -6,7 +6,7 @@ open Core.Std;; WARNING This file is autogenerad by -`${{QP_ROOT}}/script/ezfio_interface/ei_handler.py` +`${{QP_ROOT}}/scripts/ezfio_interface/ei_handler.py` *) @@ -120,7 +120,7 @@ let set str s = | Nuclei -> write Nuclei.(of_rst, write) s | Ao_basis -> () (* TODO *) | Mo_basis -> () (* TODO *) - end + end ;; @@ -169,7 +169,9 @@ let run check_only ezfio_filename = in (* Create the temp file *) - let temp_filename = create_temp_file ezfio_filename tasks in + let temp_filename = + create_temp_file ezfio_filename tasks + in (* Open the temp file with external editor *) let editor = @@ -193,7 +195,7 @@ let run check_only ezfio_filename = List.iter ~f:(fun x -> set temp_string x) tasks; (* Remove temp_file *) - Sys.remove temp_filename; + Sys.remove temp_filename ;; diff --git a/scripts/generate_h_apply.py b/scripts/generate_h_apply.py index 0a024cab..244b090b 100755 --- a/scripts/generate_h_apply.py +++ b/scripts/generate_h_apply.py @@ -248,13 +248,13 @@ class H_apply(object): """ self.data["deinit_thread"] = """ - !$ call omp_set_lock(lck) + !$OMP CRITICAL do k=1,N_st sum_e_2_pert_in(k) = sum_e_2_pert_in(k) + sum_e_2_pert(k) sum_norm_pert_in(k) = sum_norm_pert_in(k) + sum_norm_pert(k) sum_H_pert_diag_in(k) = sum_H_pert_diag_in(k) + sum_H_pert_diag(k) enddo - !$ call omp_unset_lock(lck) + !$OMP END CRITICAL deallocate (e_2_pert_buffer, coef_pert_buffer) """ self.data["size_max"] = "8192" @@ -356,12 +356,12 @@ class H_apply(object): self.data["skip"] = """ if (i_generator < size_select_max) then if (select_max(i_generator) < selection_criterion_min*selection_criterion_factor) then - !$ call omp_set_lock(lck) + !$OMP CRITICAL do k=1,N_st norm_psi(k) = norm_psi(k) + psi_coef_generators(i_generator,k)*psi_coef_generators(i_generator,k) pt2_old(k) = 0.d0 enddo - !$ call omp_unset_lock(lck) + !$OMP END CRITICAL cycle endif select_max(i_generator) = 0.d0 diff --git a/src/AO_Basis/aos.irp.f b/src/AO_Basis/aos.irp.f index aa805093..67ccf03c 100644 --- a/src/AO_Basis/aos.irp.f +++ b/src/AO_Basis/aos.irp.f @@ -25,7 +25,7 @@ END_PROVIDER BEGIN_DOC ! Coefficients including the AO normalization END_DOC - double precision :: norm, norm2,overlap_x,overlap_y,overlap_z,C_A(3), c + double precision :: norm,overlap_x,overlap_y,overlap_z,C_A(3), c integer :: l, powA(3), nz integer :: i,j,k nz=100 @@ -34,9 +34,11 @@ END_PROVIDER C_A(3) = 0.d0 ao_coef_normalized = 0.d0 do i=1,ao_num + powA(1) = ao_power(i,1) powA(2) = ao_power(i,2) powA(3) = ao_power(i,3) + do j=1,ao_prim_num(i) call overlap_gaussian_xyz(C_A,C_A,ao_expo(i,j),ao_expo(i,j),powA,powA,overlap_x,overlap_y,overlap_z,norm,nz) ao_coef_normalized(i,j) = ao_coef(i,j)/sqrt(norm) @@ -51,8 +53,42 @@ END_PROVIDER enddo ao_coef_normalization_factor(i) = 1.d0/sqrt(norm) enddo + END_PROVIDER +BEGIN_PROVIDER [ double precision, ao_coef_normalization_libint_factor, (ao_num) ] + implicit none + BEGIN_DOC + ! Coefficients including the AO normalization + END_DOC + double precision :: norm,overlap_x,overlap_y,overlap_z,C_A(3), c + integer :: l, powA(3), nz + integer :: i,j,k + nz=100 + C_A(1) = 0.d0 + C_A(2) = 0.d0 + C_A(3) = 0.d0 + + do i=1,ao_num + powA(1) = ao_l(i) + powA(2) = 0 + powA(3) = 0 + + ! Normalization of the contracted basis functions + norm = 0.d0 + do j=1,ao_prim_num(i) + do k=1,ao_prim_num(i) + call overlap_gaussian_xyz(C_A,C_A,ao_expo(i,j),ao_expo(i,k),powA,powA,overlap_x,overlap_y,overlap_z,c,nz) + norm = norm+c*ao_coef_normalized(i,j)*ao_coef_normalized(i,k) + enddo + enddo + ao_coef_normalization_libint_factor(i) = ao_coef_normalization_factor(i) * sqrt(norm) + + enddo + +END_PROVIDER + + BEGIN_PROVIDER [ double precision, ao_coef_normalized_ordered, (ao_num_align,ao_prim_num_max) ] &BEGIN_PROVIDER [ double precision, ao_expo_ordered, (ao_num_align,ao_prim_num_max) ] implicit none diff --git a/src/Determinants/H_apply.irp.f b/src/Determinants/H_apply.irp.f index abb251db..cadf84b4 100644 --- a/src/Determinants/H_apply.irp.f +++ b/src/Determinants/H_apply.irp.f @@ -214,8 +214,13 @@ subroutine remove_duplicates_in_psi_det(found_duplicates) duplicate(i) = .False. enddo - do i=1,N_det-1 + found_duplicates = .False. + i=0 + j=0 + do while (i 2.d0) then $printout_now wall_0 = wall_1 endif - !$ call omp_unset_lock(lck) + !$OMP END CRITICAL enddo !$OMP END DO deallocate( mask, fock_diag_tmp ) !$OMP END PARALLEL - !$ call omp_destroy_lock(lck) $copy_buffer $generate_psi_guess diff --git a/src/Determinants/H_apply_zmq.template.f b/src/Determinants/H_apply_zmq.template.f index c1f6ceed..2faceb77 100644 --- a/src/Determinants/H_apply_zmq.template.f +++ b/src/Determinants/H_apply_zmq.template.f @@ -13,7 +13,6 @@ subroutine $subroutine($params_main) integer :: i integer :: i_generator double precision :: wall_0, wall_1 - integer(omp_lock_kind) :: lck integer(bit_kind), allocatable :: mask(:,:,:) integer :: ispin, k integer :: rc diff --git a/src/Determinants/s2.irp.f b/src/Determinants/s2.irp.f index 9810b219..9a60dbd9 100644 --- a/src/Determinants/s2.irp.f +++ b/src/Determinants/s2.irp.f @@ -301,13 +301,21 @@ subroutine diagonalize_s2_betweenstates(keys_tmp,psi_coefs_inout,n,nmax_keys,nma print*,'' print*,'nstates = ',nstates allocate(s2(nstates,nstates),overlap(nstates,nstates)) - do i = 1, nstates - overlap(i,i) = u_dot_u(psi_coefs_inout(1,i),n) - do j = i+1, nstates - overlap(i,j) = u_dot_v(psi_coefs_inout(1,j),psi_coefs_inout(1,i),n) - overlap(j,i) = overlap(i,j) - enddo - enddo + !$OMP PARALLEL DO COLLAPSE(2) DEFAULT(NONE) SCHEDULE(dynamic) & + !$OMP PRIVATE(i,j) SHARED(overlap,psi_coefs_inout,nstates,n) + do i = 1, nstates + do j = 1, nstates + if (i < j) then + cycle + else if (i == j) then + overlap(i,i) = u_dot_u(psi_coefs_inout(1,i),n) + else + overlap(i,j) = u_dot_v(psi_coefs_inout(1,j),psi_coefs_inout(1,i),n) + overlap(j,i) = overlap(i,j) + endif + enddo + enddo + !$OMP END PARALLEL DO print*,'Overlap matrix in the basis of the states considered' do i = 1, nstates write(*,'(10(F16.10,X))')overlap(i,:) @@ -315,13 +323,21 @@ subroutine diagonalize_s2_betweenstates(keys_tmp,psi_coefs_inout,n,nmax_keys,nma call ortho_lowdin(overlap,size(overlap,1),nstates,psi_coefs_inout,size(psi_coefs_inout,1),n) print*,'passed ortho' - do i = 1, nstates - overlap(i,i) = u_dot_u(psi_coefs_inout(1,i),n) - do j = i+1, nstates - overlap(i,j) = u_dot_v(psi_coefs_inout(1,j),psi_coefs_inout(1,i),n) - overlap(j,i) = overlap(i,j) - enddo - enddo + !$OMP PARALLEL DO COLLAPSE(2) DEFAULT(NONE) SCHEDULE(dynamic) & + !$OMP PRIVATE(i,j) SHARED(overlap,psi_coefs_inout,nstates,n) + do i = 1, nstates + do j = 1, nstates + if (i < j) then + cycle + else if (i == j) then + overlap(i,i) = u_dot_u(psi_coefs_inout(1,i),n) + else + overlap(i,j) = u_dot_v(psi_coefs_inout(1,j),psi_coefs_inout(1,i),n) + overlap(j,i) = overlap(i,j) + endif + enddo + enddo + !$OMP END PARALLEL DO print*,'Overlap matrix in the basis of the Lowdin orthonormalized states ' do i = 1, nstates write(*,'(10(F16.10,X))')overlap(i,:) diff --git a/src/Integrals_Bielec/ao_bi_integrals.irp.f b/src/Integrals_Bielec/ao_bi_integrals.irp.f index 3b754dfc..b7c75fb8 100644 --- a/src/Integrals_Bielec/ao_bi_integrals.irp.f +++ b/src/Integrals_Bielec/ao_bi_integrals.irp.f @@ -4,6 +4,7 @@ double precision function ao_bielec_integral(i,j,k,l) ! integral of the AO basis or (ij|kl) ! i(r1) j(r1) 1/r12 k(r2) l(r2) END_DOC + integer,intent(in) :: i,j,k,l integer :: p,q,r,s double precision :: I_center(3),J_center(3),K_center(3),L_center(3) diff --git a/src/ZMQ/utils.irp.f b/src/ZMQ/utils.irp.f index 0bbba56e..ae1de6e7 100644 --- a/src/ZMQ/utils.irp.f +++ b/src/ZMQ/utils.irp.f @@ -350,11 +350,11 @@ subroutine end_zmq_pull_socket(zmq_socket_pull) ! endif rc = f77_zmq_unbind(zmq_socket_pull,zmq_socket_pull_tcp_address) - if (rc /= 0) then - print *, rc - print *, irp_here, 'f77_zmq_unbind(zmq_socket_pull,zmq_socket_pull_tcp_address)' - stop 'error' - endif +! if (rc /= 0) then +! print *, rc +! print *, irp_here, 'f77_zmq_unbind(zmq_socket_pull,zmq_socket_pull_tcp_address)' +! stop 'error' +! endif call sleep(1) ! see https://github.com/zeromq/libzmq/issues/1922