update aggregate data from latest data (#251)

* update aggregate data from latest data

* update ethanol data and matplotlibrc

* update plotting notebooks

Author: daico007

reproducibility_project/aggregate_summary/FinalFig.ipynb

@@ -1,7 +1,7 @@
 ,molecule,engine,temperature,pressure,ensemble,forcefield_name,cutoff_style,long_range_correction,r_cut,pressure-avg,pressure-std,pressure-sem,temperature-avg,temperature-std,temperature-sem,potential_energy-avg,potential_energy-std,potential_energy-sem,density-avg,density-std,density-sem
-15,benzeneUA,hoomd,450.0,2260.0,NPT,benzene-ua,hard,energy_pressure,1.4,2251.5109715634776,134.82018403402094,33.705046008505235,450.0315492437884,0.10726901893734267,0.026817254734335667,-8268.853515488903,2.756902247698143,0.6892255619245358,0.6977604365642096,0.0002410219365163394,6.025548412908485e-05
+15,benzeneUA,hoomd,450.0,2260.0,NPT,benzene-ua,hard,energy_pressure,1.4,2284.997850192821,134.60602199976364,33.65150549994091,449.95805169004507,0.10865277426801474,0.027163193567003686,-8288.26591745147,1.4432729143220793,0.3608182285805198,0.6991827368387439,0.00014795808066633067,3.6989520166582667e-05
 19,benzeneUA,cassandra,450.0,2260.0,NPT,benzene-ua,hard,energy_pressure,1.4,2235.812474062985,116.1144865920127,29.028621648003174,450.0,0.0,0.0,-8279.860781446354,10.994613044795699,2.7486532611989247,0.6984355226084895,0.0009722288849456309,0.00024305722123640772
 33,benzeneUA,gromacs,450.0,2260.0,NPT,benzene-ua,hard,energy_pressure,1.4,598.4628613056768,54.792266845144866,13.698066711286216,449.9749758293657,0.07962156893655552,0.01990539223413888,-4763.000351206376,35.14706410030546,8.786766025076364,0.6994750481091541,0.005320356104800141,0.0013300890262000352
-34,benzeneUA,gomc,450.0,2260.0,NPT,benzene-ua,hard,energy_pressure,1.4,2261.3261238725845,113.57359149858733,28.393397874646833,450.0,0.0,0.0,-996248.5051899063,1104.6892172880082,276.17230432200205,0.6986877138757969,0.0008168704743399857,0.00020421761858499643
-43,benzeneUA,mcccs,450.0,2260.0,NPT,benzene-ua,hard,energy_pressure,1.4,2194.916566386264,62.893504691808054,15.723376172952014,450.0,0.0,0.0,-6025.762650336912,11.953522211499461,2.9883805528748653,0.6983239878468144,0.0007810274199452238,0.00019525685498630594
+34,benzeneUA,gomc,450.0,2260.0,NPT,benzene-ua,hard,energy_pressure,1.4,2261.3261238725845,113.5735914985873,28.393397874646826,450.0,0.0,0.0,-996248.5051899063,1104.6892172880082,276.17230432200205,0.6986877138757969,0.0008168704743399857,0.00020421761858499643
+43,benzeneUA,mcccs,450.0,2260.0,NPT,benzene-ua,hard,energy_pressure,1.4,2194.916566386264,62.89350469180804,15.72337617295201,450.0,0.0,0.0,-6025.762650336912,11.953522211499195,2.9883805528747986,0.6983239878468144,0.0007810274199452439,0.00019525685498631099
 47,benzeneUA,lammps-VU,450.0,2260.0,NPT,benzene-ua,hard,energy_pressure,1.4,2275.7208916034388,190.05164979065881,47.512912447664704,450.5924355773069,0.2650670841539167,0.06626677103847918,-8268.001035948888,3.8592596056358226,0.9648149014089556,0.6976587115413384,0.00031912413669267124,7.978103417316781e-05

reproducibility_project/aggregate_summary/MainDensities.ipynb

@@ -1,19 +1,19 @@
 ,molecule,engine,temperature,pressure,ensemble,forcefield_name,cutoff_style,long_range_correction,r_cut,pressure-avg,pressure-std,pressure-sem,temperature-avg,temperature-std,temperature-sem,potential_energy-avg,potential_energy-std,potential_energy-sem,density-avg,density-std,density-sem
 0,ethanolAA,gromacs,320.0,101.325,NPT,oplsaa,hard,energy_pressure,1.0,7.386085277182733,16.36290891398086,4.090727228495215,319.7222432843016,0.27728240727497183,0.06932060181874296,-3675.6252809287525,18.771018093961377,4.692754523490344,0.7736642320435503,0.00037277412529925744,9.319353132481436e-05
-3,ethanolAA,mcccs,300.0,101.325,NPT,oplsaa,hard,energy_pressure,1.0,144.10388789173697,142.38975855380298,35.597439638450744,300.0,0.0,0.0,-9636.586657425061,23.05769399077928,5.76442349769482,0.7915228869902695,0.0008904100983158416,0.0002226025245789604
-5,ethanolAA,mcccs,280.0,101.325,NPT,oplsaa,hard,energy_pressure,1.0,95.61641141756772,115.5419757027543,28.885493925688575,280.0,0.0,0.0,-10995.939734889276,22.679869112803736,5.669967278200934,0.8132799817630951,0.0009105163756624017,0.00022762909391560042
-13,ethanolAA,lammps-VU,320.0,101.325,NPT,oplsaa,hard,energy_pressure,1.0,0.24833346712508075,1.564784515992586,0.3911961289981465,320.0133517112167,0.045105272993998774,0.011276318248499693,-3105.911366040009,13.721818595408676,3.430454648852169,0.7737386886586286,0.0005190278846760177,0.00012975697116900442
-16,ethanolAA,lammps-VU,280.0,101.325,NPT,oplsaa,hard,energy_pressure,1.0,111.82732873174143,430.71588748003336,107.67897187000834,280.012746860633,0.045927991191355384,0.011481997797838846,-6552.472148956111,9.831177369535625,2.4577943423839064,0.8160460979302364,0.0003678107436767363,9.195268591918407e-05
+3,ethanolAA,mcccs,300.0,101.325,NPT,oplsaa,hard,energy_pressure,1.0,145.61546090485416,152.87990171580677,38.21997542895169,300.0,0.0,0.0,-9624.870357183845,21.492766343197125,5.373191585799281,0.7914265265542129,0.0008449434999277755,0.00021123587498194388
+5,ethanolAA,mcccs,280.0,101.325,NPT,oplsaa,hard,energy_pressure,1.0,9.334534096960937,262.56912429514097,65.64228107378524,280.0,0.0,0.0,-10993.896435283532,22.78806346124259,5.6970158653106475,0.8127366877433876,0.0009880063280023426,0.00024700158200058564
+13,ethanolAA,lammps-VU,320.0,101.325,NPT,oplsaa,hard,energy_pressure,1.0,0.24833346712508064,1.564784515992586,0.3911961289981465,320.0133517112167,0.045105272993998774,0.011276318248499693,-3105.911366040009,13.721818595408676,3.430454648852169,0.7737386886586286,0.0005190278846760177,0.00012975697116900442
+16,ethanolAA,lammps-VU,280.0,101.325,NPT,oplsaa,hard,energy_pressure,1.0,111.82732873174143,430.71588748003336,107.67897187000834,280.012746860633,0.045927991191355384,0.011481997797838846,-6552.472148956111,9.831177369535602,2.4577943423839006,0.8160460979302364,0.0003678107436767363,9.195268591918407e-05
 17,ethanolAA,cassandra,320.0,101.325,NPT,oplsaa,hard,energy_pressure,1.0,1634.8622611289443,283.28092659352745,70.82023164838186,320.0,0.0,0.0,-8211.544145572916,24.794962810425634,6.1987407026064085,0.7687202859646355,0.0008468373536246669,0.00021170933840616672
 21,ethanolAA,gomc,300.0,101.325,NPT,oplsaa,hard,energy_pressure,1.0,189.33884519343806,160.73121090962596,40.18280272740649,300.0,0.0,0.0,-1153163.4855680207,4151.372410961057,1037.8431027402642,0.7913484722631563,0.0013261621823414586,0.00033154054558536466
 24,ethanolAA,gromacs,280.0,101.325,NPT,oplsaa,hard,energy_pressure,1.0,-0.1880251244876936,14.8946603224094,3.72366508060235,279.98895524102625,0.26090072711825657,0.06522518177956414,-7045.887545749052,22.953775808713953,5.738443952178488,0.8167763941860889,0.00023989817952917825,5.997454488229456e-05
-26,ethanolAA,cassandra,300.0,101.325,NPT,oplsaa,hard,energy_pressure,1.0,1306.5241974025141,326.08413793394254,81.52103448348564,300.0,0.0,0.0,-9618.100656297396,23.642645476418732,5.910661369104683,0.7912818525394791,0.0008829528154467213,0.00022073820386168033
-31,ethanolAA,hoomd,320.0,101.325,NPT,oplsaa,hard,energy_pressure,1.0,139.141174437068,620.2447448690797,155.06118621726992,318.0518146368627,0.0585342039959654,0.01463355099899135,-3638.707472577408,10.776813654689468,2.694203413672367,0.7737540395695532,0.0005696384060432825,0.00014240960151082062
-35,ethanolAA,hoomd,300.0,101.325,NPT,oplsaa,hard,energy_pressure,1.0,18.19520656087098,561.3429378651543,140.33573446628859,298.18270927920105,0.031193472226197085,0.007798368056549271,-5356.528356876066,12.728565429690816,3.182141357422704,0.795539037556105,0.0006699188454743484,0.0001674797113685871
+26,ethanolAA,cassandra,300.0,101.325,NPT,oplsaa,hard,energy_pressure,1.0,1306.5241974025141,326.0841379339425,81.52103448348562,300.0,0.0,0.0,-9618.100656297396,23.642645476418732,5.910661369104683,0.7912818525394791,0.0008829528154467213,0.00022073820386168033
+31,ethanolAA,hoomd,320.0,101.325,NPT,oplsaa,hard,energy_pressure,1.0,248.05444710657116,4508.844311809741,1127.2110779524353,319.9832139285838,0.20224047882474266,0.050560119706185666,-3444.1056338815515,500.760240794944,125.190060198736,0.7721643007287721,0.0011447004865814128,0.0002861751216453532
+35,ethanolAA,hoomd,300.0,101.325,NPT,oplsaa,hard,energy_pressure,1.0,194.85278910528027,5982.14146485386,1495.535366213465,300.0691625154075,0.22389518451464727,0.05597379612866182,-5170.099282012582,431.79370261079754,107.94842565269938,0.7941251333647472,0.0009700375981258833,0.00024250939953147083
 36,ethanolAA,cassandra,280.0,101.325,NPT,oplsaa,hard,energy_pressure,1.0,1100.9015507314693,355.4507643063722,88.86269107659305,280.0,0.0,0.0,-10989.091105359375,39.15544808085992,9.78886202021498,0.8134909356063542,0.0013345960311544694,0.00033364900778861734
 37,ethanolAA,gromacs,300.0,101.325,NPT,oplsaa,hard,energy_pressure,1.0,0.48879268702858414,18.88738372413123,4.721845931032807,299.9842745059775,0.33296690752590247,0.08324172688147562,-5383.192305854824,30.97299823399313,7.743249558498283,0.7956309742518117,0.0003515280944911218,8.788202362278045e-05
 41,ethanolAA,gomc,280.0,101.325,NPT,oplsaa,hard,energy_pressure,1.0,73.82676037295047,229.41972307688044,57.35493076922011,280.0,0.0,0.0,-1316410.1096084896,4920.244044398107,1230.0610110995267,0.8131313624791041,0.0014130531794989858,0.00035326329487474646
-45,ethanolAA,lammps-VU,300.0,101.325,NPT,oplsaa,hard,energy_pressure,1.0,-7.467739908959722,269.38193292433175,67.34548323108294,300.015323409767,0.06284411712385393,0.015711029280963483,-4854.502013981132,7.479035537092114,1.8697588842730286,0.7954329437061574,0.0002927443340395005,7.318608350987512e-05
-49,ethanolAA,gomc,320.0,101.325,NPT,oplsaa,hard,energy_pressure,1.0,187.7324407434529,235.43716134138515,58.85929033534629,320.0,0.0,0.0,-982220.6171556511,3957.009782240972,989.252445560243,0.7680116167513229,0.0011735365258760796,0.0002933841314690199
-51,ethanolAA,hoomd,280.0,101.325,NPT,oplsaa,hard,energy_pressure,1.0,-213.60666293220967,622.6881733188677,155.67204332971693,278.280373216568,0.048639019260606924,0.012159754815151731,-7019.56063054578,15.701777553793786,3.9254443884484465,0.8162973288982891,0.0006679099141502698,0.00016697747853756744
-52,ethanolAA,mcccs,320.0,101.325,NPT,oplsaa,hard,energy_pressure,1.0,237.10278940694064,130.13928396070077,32.53482099017519,320.0,0.0,0.0,-8229.879840892247,20.393359453562393,5.098339863390598,0.7687308005306762,0.0008008656849902207,0.00020021642124755517
+45,ethanolAA,lammps-VU,300.0,101.325,NPT,oplsaa,hard,energy_pressure,1.0,-7.467739908959722,269.38193292433175,67.34548323108294,300.015323409767,0.06284411712385393,0.015711029280963483,-4854.502013981132,7.4790355370920905,1.8697588842730226,0.7954329437061574,0.0002927443340395005,7.318608350987512e-05
+49,ethanolAA,gomc,320.0,101.325,NPT,oplsaa,hard,energy_pressure,1.0,187.7324407434529,235.43716134138512,58.85929033534628,320.0,0.0,0.0,-982220.6171556511,3957.009782240972,989.252445560243,0.7680116167513229,0.0011735365258760796,0.0002933841314690199
+51,ethanolAA,hoomd,280.0,101.325,NPT,oplsaa,hard,energy_pressure,1.0,670.7770420599928,4480.434574077588,1120.108643519397,280.00804607872556,0.12654941147904664,0.03163735286976166,-6744.059667433118,311.4286143203445,77.85715358008612,0.814962736060654,0.0009422609413402352,0.0002355652353350588
+52,ethanolAA,mcccs,320.0,101.325,NPT,oplsaa,hard,energy_pressure,1.0,125.21204106083076,145.75684610579142,36.439211526447856,320.0,0.0,0.0,-8217.886733415391,22.632590743446148,5.658147685861537,0.7683967713807014,0.0008251837054924887,0.00020629592637312218

reproducibility_project/aggregate_summary/aggregate_summary_all.csv

@@ -1,7 +1,7 @@
 ,molecule,engine,temperature,pressure,ensemble,forcefield_name,cutoff_style,long_range_correction,r_cut,pressure-avg,pressure-std,pressure-sem,temperature-avg,temperature-std,temperature-sem,potential_energy-avg,potential_energy-std,potential_energy-sem,density-avg,density-std,density-sem
 22,methaneUA,lammps-VU,140.0,1318.0,NPT,trappe-ua,hard,energy_pressure,1.4,1.3727125266159015,0.1451022781692951,0.03627556954232378,140.0187312234737,0.06909822894426526,0.017274557236066315,-5699.011530679262,0.8883769467881574,0.22209423669703934,0.37597173850147536,5.600563041526528e-05,1.400140760381632e-05
-25,methaneUA,hoomd,140.0,1318.0,NPT,trappe-ua,hard,energy_pressure,1.4,1345.1464581169503,84.93437741138331,21.233594352845827,139.99489781041444,0.027113603946789334,0.006778400986697334,-5698.978934502496,1.537298743603749,0.38432468590093727,0.3759024878229348,8.351549941558764e-05,2.087887485389691e-05
+25,methaneUA,hoomd,140.0,1318.0,NPT,trappe-ua,hard,energy_pressure,1.4,1313.6256886675899,54.56001389414809,13.640003473537023,139.98810848678062,0.02789268211118877,0.006973170527797192,-5698.725201951535,0.6103091268099518,0.15257728170248794,0.3759534543582492,4.223753591654779e-05,1.0559383979136947e-05
 27,methaneUA,gomc,140.0,1318.0,NPT,trappe-ua,hard,energy_pressure,1.4,1301.81422061616,58.83067456113999,14.707668640284998,140.0,0.0,0.0,-685093.8421600625,208.00218845104496,52.00054711276124,0.3757889993377083,0.00011691176661201252,2.922794165300313e-05
 39,methaneUA,cassandra,140.0,1318.0,NPT,trappe-ua,hard,energy_pressure,1.4,1292.1047136521488,31.592770246951666,7.8981925617379165,140.0,0.0,0.0,-5695.189620521354,2.915553296563871,0.7288883241409677,0.3757235620453125,0.0001751962404427804,4.37990601106951e-05
-54,methaneUA,mcccs,140.0,1318.0,NPT,trappe-ua,hard,energy_pressure,1.4,1285.4831025069893,37.20743432388115,9.301858580970288,140.0,0.0,0.0,-5695.738792702148,3.029363327288005,0.7573408318220013,0.37575936057731646,0.0001837137385027993,4.592843462569983e-05
+54,methaneUA,mcccs,140.0,1318.0,NPT,trappe-ua,hard,energy_pressure,1.4,1285.4831025069893,37.20743432388115,9.301858580970288,140.0,0.0,0.0,-5695.738792702148,3.029363327288005,0.7573408318220013,0.37575936057731646,0.00018371373850279828,4.592843462569957e-05
 55,methaneUA,gromacs,140.0,1318.0,NPT,trappe-ua,hard,energy_pressure,1.4,13.588645423936484,1.0591647556941834,0.26479118892354586,140.00376846643206,0.051552152017493635,0.012888038004373409,-5698.862840276335,1.6907945007949114,0.42269862519872786,0.3759555197390835,5.592110954235338e-05,1.3980277385588345e-05

reproducibility_project/aggregate_summary/aggregate_summary_benzeneUA.csv

@@ -1,6 +1,6 @@
 ,molecule,engine,temperature,pressure,ensemble,forcefield_name,cutoff_style,long_range_correction,r_cut,pressure-avg,pressure-std,pressure-sem,temperature-avg,temperature-std,temperature-sem,potential_energy-avg,potential_energy-std,potential_energy-sem,density-avg,density-std,density-sem
 7,pentaneUA-constrain_bonds,gomc,372.0,1402.0,NPT,trappe-ua,hard,energy_pressure,1.4,1402.1451191031786,122.33555496765892,30.58388874191473,372.0,0.0,0.0,-289476.5306132031,695.9399642321441,173.98499105803603,0.540849320879125,0.0005165323368682392,0.0001291330842170598
 9,pentaneUA-constrain_bonds,gromacs,372.0,1402.0,NPT,trappe-ua,hard,energy_pressure,1.4,14.357145017690527,3.1597071853930756,0.7899267963482689,371.96957083362616,0.1266716916298173,0.03166792290745433,-2425.9794197016618,6.719675700234463,1.6799189250586157,0.5419011696532579,0.00032131570087705043,8.032892521926261e-05
-23,pentaneUA-constrain_bonds,hoomd,372.0,1402.0,NPT,trappe-ua,hard,energy_pressure,1.4,1371.946960694772,400.5795327139803,100.14488317849508,371.88057372250626,0.16990409362951864,0.04247602340737966,-2426.950978718094,2.7282250208703003,0.6820562552175751,0.5419898727782437,0.00030186004689047055,7.546501172261764e-05
-32,pentaneUA-constrain_bonds,mcccs,372.0,1402.0,NPT,trappe-ua,hard,energy_pressure,1.4,1405.6732120732916,62.34335707970884,15.58583926992721,372.0,0.0,0.0,-2417.163109475033,4.0531456026239985,1.0132864006559996,0.5410886453415661,0.0003461206838981674,8.653017097454186e-05
-48,pentaneUA-constrain_bonds,cassandra,372.0,1402.0,NPT,trappe-ua,hard,energy_pressure,1.4,1348.1548122757595,70.96284002873008,17.74071000718252,372.0,0.0,0.0,-2423.008360798958,8.612346519187353,2.1530866297968383,0.541189253940625,0.0008495282868671981,0.00021238207171679952
+23,pentaneUA-constrain_bonds,hoomd,372.0,1402.0,NPT,trappe-ua,hard,energy_pressure,1.4,1384.849960890102,161.50869416714798,40.377173541786995,371.9813495927463,0.07157094608209967,0.017892736520524918,-2422.8959021289934,2.2316870527198835,0.5579217631799709,0.5416574660552227,0.00013949047379420166,3.4872618448550415e-05
+32,pentaneUA-constrain_bonds,mcccs,372.0,1402.0,NPT,trappe-ua,hard,energy_pressure,1.4,1405.6732120732916,62.34335707970884,15.58583926992721,372.0,0.0,0.0,-2417.163109475033,4.053145602623963,1.0132864006559907,0.5410886453415661,0.00034612068389815707,8.653017097453927e-05
+48,pentaneUA-constrain_bonds,cassandra,372.0,1402.0,NPT,trappe-ua,hard,energy_pressure,1.4,1348.1548122757595,70.96284002873007,17.740710007182518,372.0,0.0,0.0,-2423.008360798958,8.612346519187353,2.1530866297968383,0.541189253940625,0.0008495282868671981,0.00021238207171679952

reproducibility_project/aggregate_summary/aggregate_summary_ethanolAA.csv

@@ -1,4 +1,4 @@
 ,molecule,engine,temperature,pressure,ensemble,forcefield_name,cutoff_style,long_range_correction,r_cut,pressure-avg,pressure-std,pressure-sem,temperature-avg,temperature-std,temperature-sem,potential_energy-avg,potential_energy-std,potential_energy-sem,density-avg,density-std,density-sem
 8,pentaneUA-flexible_bonds,gromacs,372.0,1402.0,NPT,trappe-ua,hard,energy_pressure,1.4,17.49920310190135,13.276552718944716,3.319138179736179,372.0263139499642,0.13134130495187382,0.032835326237968455,-499.8800451010373,10.719653087484343,2.6799132718710856,0.5339952516891766,0.001211795303466543,0.00030294882586663575
-20,pentaneUA-flexible_bonds,hoomd,372.0,1402.0,NPT,trappe-ua,hard,energy_pressure,1.4,1857.8986043278728,1029.4136806403035,257.35342016007587,370.07282272345594,0.06753494307570201,0.016883735768925504,-598.348686676936,18.29546292690224,4.57386573172556,0.5444344331662561,0.0016273073789420784,0.0004068268447355196
+20,pentaneUA-flexible_bonds,hoomd,372.0,1402.0,NPT,trappe-ua,hard,energy_pressure,1.4,1131.9989328054967,379.4199257278238,94.85498143195595,371.98529055816607,0.07766550766568893,0.019416376916422232,-344.570792844545,3.511947951179613,0.8779869877949033,0.5174152365081742,0.0004982751667635888,0.0001245687916908972
 44,pentaneUA-flexible_bonds,lammps-VU,372.0,1402.0,NPT,trappe-ua,hard,energy_pressure,1.4,928.9680976970318,2861.1272486888683,715.2818121722171,371.9753474023654,0.20884629272470256,0.05221157318117564,-452.67791782923,15.456058650662392,3.864014662665598,0.5432271222473475,0.0018561358209731838,0.00046403395524329596