############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Thu Jul 20 10:19:58 2017 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. NOsh_parseInput: Starting file parsing... NOsh: Parsing READ section NOsh: Storing molecule 0 path junk.pqr NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=1, ndiel=0, nkappa=0, ncharge=0, npot=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (353, 193, 289) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (353, 193, 289) NOsh: Done parsing ELEC section (nelec = 2) NOsh: Parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing PRINT section NOsh: Parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing PRINT section NOsh: Parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing file (got QUIT) ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Thu Jul 20 14:31:37 2017 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. NOsh_parseInput: Starting file parsing... NOsh: Parsing READ section NOsh: Storing molecule 0 path junk.pqr NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=1, ndiel=0, nkappa=0, ncharge=0, npot=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (353, 193, 289) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (353, 193, 289) NOsh: Done parsing ELEC section (nelec = 2) NOsh: Parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing PRINT section NOsh: Parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing PRINT section NOsh: Parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing file (got QUIT) ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Fri Aug 4 11:13:45 2017 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. NOsh_parseInput: Starting file parsing... NOsh: Parsing READ section NOsh: Storing molecule 0 path junk.pqr NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=1, ndiel=0, nkappa=0, ncharge=0, npot=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (353, 193, 289) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (353, 193, 289) NOsh: Done parsing ELEC section (nelec = 2) NOsh: Parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing PRINT section NOsh: Parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing PRINT section NOsh: Parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing file (got QUIT) ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Fri Aug 4 11:37:17 2017 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. NOsh_parseInput: Starting file parsing... NOsh: Parsing READ section NOsh: Storing molecule 0 path junk.pqr NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=1, ndiel=0, nkappa=0, ncharge=0, npot=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (353, 193, 289) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (353, 193, 289) NOsh: Done parsing ELEC section (nelec = 2) NOsh: Parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing PRINT section NOsh: Parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing PRINT section NOsh: Parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing file (got QUIT) ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Fri Aug 4 11:46:20 2017 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. NOsh_parseInput: Starting file parsing... NOsh: Parsing READ section NOsh: Storing molecule 0 path junk.pqr NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=1, ndiel=0, nkappa=0, ncharge=0, npot=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (353, 193, 289) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (353, 193, 289) NOsh: Done parsing ELEC section (nelec = 2) NOsh: Parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing PRINT section NOsh: Parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing PRINT section NOsh: Parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing file (got QUIT) ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Fri Aug 4 11:48:13 2017 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. NOsh_parseInput: Starting file parsing... NOsh: Parsing READ section NOsh: Storing molecule 0 path junk.pqr NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=1, ndiel=0, nkappa=0, ncharge=0, npot=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (353, 193, 289) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (353, 193, 289) NOsh: Done parsing ELEC section (nelec = 2) NOsh: Parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing PRINT section NOsh: Parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing PRINT section NOsh: Parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing file (got QUIT) ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Fri Aug 4 11:53:04 2017 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. NOsh_parseInput: Starting file parsing... NOsh: Parsing READ section NOsh: Storing molecule 0 path junk.pqr NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=1, ndiel=0, nkappa=0, ncharge=0, npot=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (353, 193, 289) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (353, 193, 289) NOsh: Done parsing ELEC section (nelec = 2) NOsh: Parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing PRINT section NOsh: Parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing PRINT section NOsh: Parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing file (got QUIT) ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Fri Aug 4 11:57:10 2017 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. NOsh_parseInput: Starting file parsing... NOsh: Parsing READ section NOsh: Storing molecule 0 path junk.pqr NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=1, ndiel=0, nkappa=0, ncharge=0, npot=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (353, 193, 289) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (353, 193, 289) NOsh: Done parsing ELEC section (nelec = 2) NOsh: Parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing PRINT section NOsh: Parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing PRINT section NOsh: Parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing file (got QUIT) ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Fri Aug 4 12:01:44 2017 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. NOsh_parseInput: Starting file parsing... NOsh: Parsing READ section NOsh: Storing molecule 0 path junk.pqr NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=1, ndiel=0, nkappa=0, ncharge=0, npot=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (353, 193, 289) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (353, 193, 289) NOsh: Done parsing ELEC section (nelec = 2) NOsh: Parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing PRINT section NOsh: Parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing PRINT section NOsh: Parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing file (got QUIT) Valist_readPQR: Counted 148 atoms Valist_getStatistics: Max atom coordinate: (2.018, 16.848, 1.37) Valist_getStatistics: Min atom coordinate: (-27.303, -2.918, -19.131) Valist_getStatistics: Molecule center: (-12.6425, 6.965, -8.8805) NOsh_setupCalcMGAUTO(nosh.c, 1597): coarse grid center = -12.6425 6.965 -8.8805 NOsh_setupCalcMGAUTO(nosh.c, 1602): fine grid center = -12.6425 6.965 -8.8805 NOsh_setupCalcMGAUTO (nosh.c, 1614): Coarse grid spacing = 0.141607, 0.175011, 0.121013 NOsh_setupCalcMGAUTO (nosh.c, 1616): Fine grid spacing = 0.108288, 0.133832, 0.0925392 NOsh_setupCalcMGAUTO (nosh.c, 1618): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.764706, 0.764706, 0.764706 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1712): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1714): coarse mesh center = -12.6425 6.965 -8.8805 NOsh_setupCalcMGAUTO (nosh.c, 1719): coarse mesh upper corner = 12.2803 23.7661 8.54535 NOsh_setupCalcMGAUTO (nosh.c, 1724): coarse mesh lower corner = -37.5653 -9.8361 -26.3064 NOsh_setupCalcMGAUTO (nosh.c, 1729): initial fine mesh upper corner = 6.41615 19.8129 4.44515 NOsh_setupCalcMGAUTO (nosh.c, 1734): initial fine mesh lower corner = -31.7011 -5.8829 -22.2062 NOsh_setupCalcMGAUTO (nosh.c, 1795): final fine mesh upper corner = 6.41615 19.8129 4.44515 NOsh_setupCalcMGAUTO (nosh.c, 1800): final fine mesh lower corner = -31.7011 -5.8829 -22.2062 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 0 (1) to calculation 1 (2) NOsh_setupCalcMGAUTO(nosh.c, 1597): coarse grid center = -12.6425 6.965 -8.8805 NOsh_setupCalcMGAUTO(nosh.c, 1602): fine grid center = -12.6425 6.965 -8.8805 NOsh_setupCalcMGAUTO (nosh.c, 1614): Coarse grid spacing = 0.141607, 0.175011, 0.121013 NOsh_setupCalcMGAUTO (nosh.c, 1616): Fine grid spacing = 0.108288, 0.133832, 0.0925392 NOsh_setupCalcMGAUTO (nosh.c, 1618): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.764706, 0.764706, 0.764706 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1712): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1714): coarse mesh center = -12.6425 6.965 -8.8805 NOsh_setupCalcMGAUTO (nosh.c, 1719): coarse mesh upper corner = 12.2803 23.7661 8.54535 NOsh_setupCalcMGAUTO (nosh.c, 1724): coarse mesh lower corner = -37.5653 -9.8361 -26.3064 NOsh_setupCalcMGAUTO (nosh.c, 1729): initial fine mesh upper corner = 6.41615 19.8129 4.44515 NOsh_setupCalcMGAUTO (nosh.c, 1734): initial fine mesh lower corner = -31.7011 -5.8829 -22.2062 NOsh_setupCalcMGAUTO (nosh.c, 1795): final fine mesh upper corner = 6.41615 19.8129 4.44515 NOsh_setupCalcMGAUTO (nosh.c, 1800): final fine mesh lower corner = -31.7011 -5.8829 -22.2062 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 1 (2) to calculation 3 (4) Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 20.7767 Vpbe_ctor2: solute dimensions = 32.287 x 22.406 x 22.936 Vpbe_ctor2: solute charge = -1 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.126889 Vpbe_ctor2: Debye length = 7.88093 Vpbe_ctor2: zkappa2 = 1.26455 Vpbe_ctor2: zmagic = 6999.55 Vpbe_ctor2: Constructing Vclist with 64 x 44 x 45 table Vclist_ctor2: Using 64 x 44 x 45 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.12 max radius Vclist_setupGrid: Grid lengths = (41.8028, 32.2478, 32.9828) Vclist_setupGrid: Grid lower corner = (-33.5439, -9.1589, -25.3719) Vclist_assignAtoms: Have 275810 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 242.732 Vacc_storeParms: Using 2466-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 2, mgsolv = 1 Setting PDE center to local center... Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vpmg_fillco: filling boundary arrays Vpmg_fillco: done filling boundary arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.815000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. Vbuildops: Fine: (353, 193, 289) Vbuildops: Operator stencil (lev, numdia) = (1, 4) Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.580000e+00 Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. Vbuildops: Galer: (177, 097, 145) Vbuildops: Galer: (089, 049, 073) Vbuildops: Galer: (045, 025, 037) Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.591000e+01 Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 9.547000e+01 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 2.087555e-01 Vprtstp: contraction number = 2.087555e-01 Vprtstp: iteration = 2 Vprtstp: relative residual = 3.792982e-02 Vprtstp: contraction number = 1.816950e-01 Vprtstp: iteration = 3 Vprtstp: relative residual = 8.172600e-03 Vprtstp: contraction number = 2.154664e-01 Vprtstp: iteration = 4 Vprtstp: relative residual = 1.797003e-03 Vprtstp: contraction number = 2.198814e-01 Vprtstp: iteration = 5 Vprtstp: relative residual = 4.235348e-04 Vprtstp: contraction number = 2.356896e-01 Vprtstp: iteration = 6 Vprtstp: relative residual = 1.000221e-04 Vprtstp: contraction number = 2.361602e-01 Vprtstp: iteration = 7 Vprtstp: relative residual = 2.435054e-05 Vprtstp: contraction number = 2.434516e-01 Vprtstp: iteration = 8 Vprtstp: relative residual = 5.893015e-06 Vprtstp: contraction number = 2.420076e-01 Vprtstp: iteration = 9 Vprtstp: relative residual = 1.474831e-06 Vprtstp: contraction number = 2.502677e-01 Vprtstp: iteration = 10 Vprtstp: relative residual = 3.644495e-07 Vprtstp: contraction number = 2.471127e-01 Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.467200e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.534780e+03 Vpmg_setPart: lower corner = (-37.5653, -9.8361, -26.3064) Vpmg_setPart: upper corner = (12.2803, 23.7661, 8.54535) Vpmg_setPart: actual minima = (-37.5653, -9.8361, -26.3064) Vpmg_setPart: actual maxima = (12.2803, 23.7661, 8.54535) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vpmg_energy: calculating only q-phi energy Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 3.810810091472E+04 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.000000e-01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 20.7767 Vpbe_ctor2: solute dimensions = 32.287 x 22.406 x 22.936 Vpbe_ctor2: solute charge = -1 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.126889 Vpbe_ctor2: Debye length = 7.88093 Vpbe_ctor2: zkappa2 = 1.26455 Vpbe_ctor2: zmagic = 6999.55 Vpbe_ctor2: Constructing Vclist with 64 x 44 x 45 table Vclist_ctor2: Using 64 x 44 x 45 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.12 max radius Vclist_setupGrid: Grid lengths = (41.8028, 32.2478, 32.9828) Vclist_setupGrid: Grid lower corner = (-33.5439, -9.1589, -25.3719) Vclist_assignAtoms: Have 275810 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 242.732 Vacc_storeParms: Using 2466-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 2, mgsolv = 1 Setting PDE center to local center... Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -31.7011, -5.8829, -22.2062 VPMG::focusFillBound -- New mesh maxs = 6.41615, 19.8129, 4.44515 VPMG::focusFillBound -- Old mesh mins = -37.5653, -9.8361, -26.3064 VPMG::focusFillBound -- Old mesh maxs = 12.2803, 23.7661, 8.54535 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-31.7011, -5.8829, -22.2062) Vpmg_setPart: upper corner = (6.41615, 19.8129, 4.44515) Vpmg_setPart: actual minima = (-37.5653, -9.8361, -26.3064) Vpmg_setPart: actual maxima = (12.2803, 23.7661, 8.54535) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 VPMG::extEnergy: Finding extEnergy dimensions... VPMG::extEnergy Disj part lower corner = (-31.7011, -5.8829, -22.2062) VPMG::extEnergy Disj part upper corner = (6.41615, 19.8129, 4.44515) VPMG::extEnergy Old lower corner = (-37.5653, -9.8361, -26.3064) VPMG::extEnergy Old upper corner = (12.2803, 23.7661, 8.54535) Vpmg_qmEnergy: Calculating linear energy VPMG::extEnergy: extQmEnergy = 0.328867 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.616592 kT Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.929000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. Vbuildops: Fine: (353, 193, 289) Vbuildops: Operator stencil (lev, numdia) = (1, 4) Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.310000e+00 Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. Vbuildops: Galer: (177, 097, 145) Vbuildops: Galer: (089, 049, 073) Vbuildops: Galer: (045, 025, 037) Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 6.575000e+01 Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.681940e+03 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 1.964084e-01 Vprtstp: contraction number = 1.964084e-01 Vprtstp: iteration = 2 Vprtstp: relative residual = 3.432681e-02 Vprtstp: contraction number = 1.747727e-01 Vprtstp: iteration = 3 Vprtstp: relative residual = 7.172083e-03 Vprtstp: contraction number = 2.089353e-01 Vprtstp: iteration = 4 Vprtstp: relative residual = 1.577378e-03 Vprtstp: contraction number = 2.199331e-01 ############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Fri Aug 4 12:04:04 2017 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. NOsh_parseInput: Starting file parsing... NOsh: Parsing READ section NOsh: Storing molecule 0 path junk.pqr NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=1, ndiel=0, nkappa=0, ncharge=0, npot=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (353, 193, 289) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing lpbe... PBEparm_parseToken: trying lpbe... NOsh: parsed lpbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (353, 193, 289) NOsh: Done parsing ELEC section (nelec = 2) NOsh: Parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing PRINT section NOsh: Parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing PRINT section NOsh: Parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing file (got QUIT) Valist_readPQR: Counted 148 atoms Valist_getStatistics: Max atom coordinate: (2.018, 16.848, 1.37) Valist_getStatistics: Min atom coordinate: (-27.303, -2.918, -19.131) Valist_getStatistics: Molecule center: (-12.6425, 6.965, -8.8805) NOsh_setupCalcMGAUTO(nosh.c, 1597): coarse grid center = -12.6425 6.965 -8.8805 NOsh_setupCalcMGAUTO(nosh.c, 1602): fine grid center = -12.6425 6.965 -8.8805 NOsh_setupCalcMGAUTO (nosh.c, 1614): Coarse grid spacing = 0.141607, 0.175011, 0.121013 NOsh_setupCalcMGAUTO (nosh.c, 1616): Fine grid spacing = 0.108288, 0.133832, 0.0925392 NOsh_setupCalcMGAUTO (nosh.c, 1618): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.764706, 0.764706, 0.764706 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1712): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1714): coarse mesh center = -12.6425 6.965 -8.8805 NOsh_setupCalcMGAUTO (nosh.c, 1719): coarse mesh upper corner = 12.2803 23.7661 8.54535 NOsh_setupCalcMGAUTO (nosh.c, 1724): coarse mesh lower corner = -37.5653 -9.8361 -26.3064 NOsh_setupCalcMGAUTO (nosh.c, 1729): initial fine mesh upper corner = 6.41615 19.8129 4.44515 NOsh_setupCalcMGAUTO (nosh.c, 1734): initial fine mesh lower corner = -31.7011 -5.8829 -22.2062 NOsh_setupCalcMGAUTO (nosh.c, 1795): final fine mesh upper corner = 6.41615 19.8129 4.44515 NOsh_setupCalcMGAUTO (nosh.c, 1800): final fine mesh lower corner = -31.7011 -5.8829 -22.2062 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 0 (1) to calculation 1 (2) NOsh_setupCalcMGAUTO(nosh.c, 1597): coarse grid center = -12.6425 6.965 -8.8805 NOsh_setupCalcMGAUTO(nosh.c, 1602): fine grid center = -12.6425 6.965 -8.8805 NOsh_setupCalcMGAUTO (nosh.c, 1614): Coarse grid spacing = 0.141607, 0.175011, 0.121013 NOsh_setupCalcMGAUTO (nosh.c, 1616): Fine grid spacing = 0.108288, 0.133832, 0.0925392 NOsh_setupCalcMGAUTO (nosh.c, 1618): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.764706, 0.764706, 0.764706 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1712): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1714): coarse mesh center = -12.6425 6.965 -8.8805 NOsh_setupCalcMGAUTO (nosh.c, 1719): coarse mesh upper corner = 12.2803 23.7661 8.54535 NOsh_setupCalcMGAUTO (nosh.c, 1724): coarse mesh lower corner = -37.5653 -9.8361 -26.3064 NOsh_setupCalcMGAUTO (nosh.c, 1729): initial fine mesh upper corner = 6.41615 19.8129 4.44515 NOsh_setupCalcMGAUTO (nosh.c, 1734): initial fine mesh lower corner = -31.7011 -5.8829 -22.2062 NOsh_setupCalcMGAUTO (nosh.c, 1795): final fine mesh upper corner = 6.41615 19.8129 4.44515 NOsh_setupCalcMGAUTO (nosh.c, 1800): final fine mesh lower corner = -31.7011 -5.8829 -22.2062 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 1 (2) to calculation 3 (4) Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 20.7767 Vpbe_ctor2: solute dimensions = 32.287 x 22.406 x 22.936 Vpbe_ctor2: solute charge = -1 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.126889 Vpbe_ctor2: Debye length = 7.88093 Vpbe_ctor2: zkappa2 = 1.26455 Vpbe_ctor2: zmagic = 6999.55 Vpbe_ctor2: Constructing Vclist with 64 x 44 x 45 table Vclist_ctor2: Using 64 x 44 x 45 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.12 max radius Vclist_setupGrid: Grid lengths = (41.8028, 32.2478, 32.9828) Vclist_setupGrid: Grid lower corner = (-33.5439, -9.1589, -25.3719) Vclist_assignAtoms: Have 275810 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 242.732 Vacc_storeParms: Using 2466-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 2, mgsolv = 1 Setting PDE center to local center... Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vprtstp: iteration = 5 Vprtstp: relative residual = 3.583379e-04 Vprtstp: contraction number = 2.271730e-01 Vprtstp: iteration = 6 Vprtstp: relative residual = 8.282883e-05 Vprtstp: contraction number = 2.311473e-01 Vprtstp: iteration = 7 Vprtstp: relative residual = 1.984240e-05 Vprtstp: contraction number = 2.395592e-01 Vpmg_fillco: done filling coefficient arrays Vpmg_fillco: filling boundary arrays Vpmg_fillco: done filling boundary arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.276000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. Vbuildops: Fine: (353, 193, 289) Vprtstp: iteration = 8 Vprtstp: relative residual = 4.795946e-06 Vprtstp: contraction number = 2.417019e-01 Vprtstp: iteration = 9 Vprtstp: relative residual = 1.178798e-06 Vprtstp: contraction number = 2.457905e-01 Vbuildops: Operator stencil (lev, numdia) = (1, 4) Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 4.400000e+00 Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. Vbuildops: Galer: (177, 097, 145) Vprtstp: iteration = 10 Vprtstp: relative residual = 2.905678e-07 Vprtstp: contraction number = 2.464949e-01 Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.539640e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.618720e+03 Vpmg_setPart: lower corner = (-31.7011, -5.8829, -22.2062) Vpmg_setPart: upper corner = (6.41615, 19.8129, 4.44515) Vpmg_setPart: actual minima = (-31.7011, -5.8829, -22.2062) Vpmg_setPart: actual maxima = (6.41615, 19.8129, 4.44515) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vpmg_energy: calculating only q-phi energy Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 5.114523037575E+04 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 7.000000e-02 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 20.7767 Vpbe_ctor2: solute dimensions = 32.287 x 22.406 x 22.936 Vpbe_ctor2: solute charge = -1 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.795157 Vpbe_ctor2: Debye length = 1.25761 Vpbe_ctor2: zkappa2 = 1.26455 Vpbe_ctor2: zmagic = 6999.55 Vpbe_ctor2: Constructing Vclist with 64 x 44 x 45 table Vclist_ctor2: Using 64 x 44 x 45 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.12 max radius Vclist_setupGrid: Grid lengths = (41.8028, 32.2478, 32.9828) Vclist_setupGrid: Grid lower corner = (-33.5439, -9.1589, -25.3719) Vclist_assignAtoms: Have 275810 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 242.732 Vacc_storeParms: Using 2466-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 2, mgsolv = 1 Setting PDE center to local center... Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vbuildops: Galer: (089, 049, 073) Vbuildops: Galer: (045, 025, 037) Vpmg_fillco: done filling coefficient arrays Vpmg_fillco: filling boundary arrays Vpmg_fillco: done filling boundary arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 2.619000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. Vbuildops: Fine: (353, 193, 289) Vbuildops: Operator stencil (lev, numdia) = (1, 4) Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.610000e+00 Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. Vbuildops: Galer: (177, 097, 145) Vbuildops: Galer: (089, 049, 073) Vbuildops: Galer: (045, 025, 037) Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.517000e+01 Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.016800e+02 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 2.087555e-01 Vprtstp: contraction number = 2.087555e-01 Vprtstp: iteration = 2 Vprtstp: relative residual = 3.792982e-02 Vprtstp: contraction number = 1.816950e-01 Vprtstp: iteration = 3 Vprtstp: relative residual = 8.172600e-03 Vprtstp: contraction number = 2.154664e-01 Vprtstp: iteration = 4 Vprtstp: relative residual = 1.797003e-03 Vprtstp: contraction number = 2.198814e-01 Vprtstp: iteration = 5 Vprtstp: relative residual = 4.235348e-04 Vprtstp: contraction number = 2.356896e-01 Vprtstp: iteration = 6 Vprtstp: relative residual = 1.000221e-04 Vprtstp: contraction number = 2.361602e-01 Vprtstp: iteration = 7 Vprtstp: relative residual = 2.435054e-05 Vprtstp: contraction number = 2.434516e-01 Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 6.782000e+01 Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.326020e+03 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 8 Vprtstp: relative residual = 5.893015e-06 Vprtstp: contraction number = 2.420076e-01 Vprtstp: iteration = 1 Vprtstp: relative residual = 3.554901e-01 Vprtstp: contraction number = 3.554901e-01 Vprtstp: iteration = 9 Vprtstp: relative residual = 1.474831e-06 Vprtstp: contraction number = 2.502677e-01 Vprtstp: iteration = 10 Vprtstp: relative residual = 3.644495e-07 Vprtstp: contraction number = 2.471127e-01 Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.214690e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.283620e+03 Vpmg_setPart: lower corner = (-37.5653, -9.8361, -26.3064) Vpmg_setPart: upper corner = (12.2803, 23.7661, 8.54535) Vpmg_setPart: actual minima = (-37.5653, -9.8361, -26.3064) Vpmg_setPart: actual maxima = (12.2803, 23.7661, 8.54535) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vprtstp: iteration = 2 Vprtstp: relative residual = 9.138493e-02 Vprtstp: contraction number = 2.570675e-01 Vnm_tstart: starting timer 29 (Energy timer).. Vpmg_energy: calculating only q-phi energy Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 3.810810091472E+04 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.300000e-01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 20.7767 Vpbe_ctor2: solute dimensions = 32.287 x 22.406 x 22.936 Vpbe_ctor2: solute charge = -1 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.126889 Vpbe_ctor2: Debye length = 7.88093 Vpbe_ctor2: zkappa2 = 1.26455 Vpbe_ctor2: zmagic = 6999.55 Vpbe_ctor2: Constructing Vclist with 64 x 44 x 45 table Vclist_ctor2: Using 64 x 44 x 45 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.12 max radius Vclist_setupGrid: Grid lengths = (41.8028, 32.2478, 32.9828) Vclist_setupGrid: Grid lower corner = (-33.5439, -9.1589, -25.3719) Vclist_assignAtoms: Have 275810 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 242.732 Vacc_storeParms: Using 2466-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 2, mgsolv = 1 Setting PDE center to local center... Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -31.7011, -5.8829, -22.2062 VPMG::focusFillBound -- New mesh maxs = 6.41615, 19.8129, 4.44515 VPMG::focusFillBound -- Old mesh mins = -37.5653, -9.8361, -26.3064 VPMG::focusFillBound -- Old mesh maxs = 12.2803, 23.7661, 8.54535 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-31.7011, -5.8829, -22.2062) Vpmg_setPart: upper corner = (6.41615, 19.8129, 4.44515) Vpmg_setPart: actual minima = (-37.5653, -9.8361, -26.3064) Vpmg_setPart: actual maxima = (12.2803, 23.7661, 8.54535) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 VPMG::extEnergy: Finding extEnergy dimensions... VPMG::extEnergy Disj part lower corner = (-31.7011, -5.8829, -22.2062) VPMG::extEnergy Disj part upper corner = (6.41615, 19.8129, 4.44515) VPMG::extEnergy Old lower corner = (-37.5653, -9.8361, -26.3064) VPMG::extEnergy Old upper corner = (12.2803, 23.7661, 8.54535) Vpmg_qmEnergy: Calculating linear energy VPMG::extEnergy: extQmEnergy = 0.328867 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.616592 kT Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vprtstp: iteration = 3 Vprtstp: relative residual = 5.159303e-02 Vprtstp: contraction number = 5.645682e-01 Vprtstp: iteration = 4 Vprtstp: relative residual = 2.475547e-02 Vprtstp: contraction number = 4.798219e-01 Vprtstp: iteration = 5 Vprtstp: relative residual = 1.820392e-02 Vprtstp: contraction number = 7.353495e-01 Vpmg_fillco: done filling coefficient arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.909000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. Vbuildops: Fine: (353, 193, 289) Vprtstp: iteration = 6 Vprtstp: relative residual = 9.799940e-03 Vprtstp: contraction number = 5.383423e-01 Vbuildops: Operator stencil (lev, numdia) = (1, 4) Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.190000e+00 Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. Vbuildops: Galer: (177, 097, 145) Vprtstp: iteration = 7 Vprtstp: relative residual = 7.307795e-03 Vprtstp: contraction number = 7.456979e-01 Vprtstp: iteration = 8 Vprtstp: relative residual = 4.031109e-03 Vprtstp: contraction number = 5.516177e-01 Vbuildops: Galer: (089, 049, 073) Vbuildops: Galer: (045, 025, 037) Vprtstp: iteration = 9 Vprtstp: relative residual = 3.031149e-03 Vprtstp: contraction number = 7.519394e-01 Vprtstp: iteration = 10 Vprtstp: relative residual = 1.686500e-03 Vprtstp: contraction number = 5.563896e-01 Vprtstp: iteration = 11 Vprtstp: relative residual = 1.278034e-03 Vprtstp: contraction number = 7.578026e-01 Vprtstp: iteration = 12 Vprtstp: relative residual = 7.113484e-04 Vprtstp: contraction number = 5.565957e-01 Vprtstp: iteration = 13 Vprtstp: relative residual = 5.438667e-04 Vprtstp: contraction number = 7.645575e-01 Vprtstp: iteration = 14 Vprtstp: relative residual = 3.016318e-04 Vprtstp: contraction number = 5.546062e-01 Vprtstp: iteration = 15 Vprtstp: relative residual = 2.328897e-04 Vprtstp: contraction number = 7.720991e-01 Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 6.903000e+01 Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.436300e+03 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 16 Vprtstp: relative residual = 1.284291e-04 Vprtstp: contraction number = 5.514588e-01 Vprtstp: iteration = 1 Vprtstp: relative residual = 1.964084e-01 Vprtstp: contraction number = 1.964084e-01 Vprtstp: iteration = 17 Vprtstp: relative residual = 1.002052e-04 Vprtstp: contraction number = 7.802377e-01 Vprtstp: iteration = 2 Vprtstp: relative residual = 3.432681e-02 Vprtstp: contraction number = 1.747727e-01 Vprtstp: iteration = 18 Vprtstp: relative residual = 5.487411e-05 Vprtstp: contraction number = 5.476175e-01 Vprtstp: iteration = 3 Vprtstp: relative residual = 7.172083e-03 Vprtstp: contraction number = 2.089353e-01 Vprtstp: iteration = 19 Vprtstp: relative residual = 4.328885e-05 Vprtstp: contraction number = 7.888757e-01 Vprtstp: iteration = 4 Vprtstp: relative residual = 1.577378e-03 Vprtstp: contraction number = 2.199331e-01 Vprtstp: iteration = 20 Vprtstp: relative residual = 2.351905e-05 Vprtstp: contraction number = 5.433050e-01 Vprtstp: iteration = 5 Vprtstp: relative residual = 3.583379e-04 Vprtstp: contraction number = 2.271730e-01 Vprtstp: iteration = 21 Vprtstp: relative residual = 1.876738e-05 Vprtstp: contraction number = 7.979651e-01 Vprtstp: iteration = 6 Vprtstp: relative residual = 8.282883e-05 Vprtstp: contraction number = 2.311473e-01 Vprtstp: iteration = 22 Vprtstp: relative residual = 1.010866e-05 Vprtstp: contraction number = 5.386294e-01 Vprtstp: iteration = 7 Vprtstp: relative residual = 1.984240e-05 Vprtstp: contraction number = 2.395592e-01 Vprtstp: iteration = 23 Vprtstp: relative residual = 8.162741e-06 Vprtstp: contraction number = 8.074995e-01 Vprtstp: iteration = 8 Vprtstp: relative residual = 4.795946e-06 Vprtstp: contraction number = 2.417019e-01 Vprtstp: iteration = 24 Vprtstp: relative residual = 4.356067e-06 Vprtstp: contraction number = 5.336524e-01 Vprtstp: iteration = 9 Vprtstp: relative residual = 1.178798e-06 Vprtstp: contraction number = 2.457905e-01 Vprtstp: iteration = 25 Vprtstp: relative residual = 3.561022e-06 Vprtstp: contraction number = 8.174857e-01 Vprtstp: iteration = 26 Vprtstp: relative residual = 1.881709e-06 Vprtstp: contraction number = 5.284181e-01 Vprtstp: iteration = 10 Vprtstp: relative residual = 2.905678e-07 Vprtstp: contraction number = 2.464949e-01 Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 1.319780e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 1.399590e+03 Vpmg_setPart: lower corner = (-31.7011, -5.8829, -22.2062) Vpmg_setPart: upper corner = (6.41615, 19.8129, 4.44515) Vpmg_setPart: actual minima = (-31.7011, -5.8829, -22.2062) Vpmg_setPart: actual maxima = (6.41615, 19.8129, 4.44515) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vpmg_energy: calculating only q-phi energy Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 5.114523037575E+04 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.000000e-02 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 20.7767 Vpbe_ctor2: solute dimensions = 32.287 x 22.406 x 22.936 Vpbe_ctor2: solute charge = -1 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.795157 Vpbe_ctor2: Debye length = 1.25761 Vpbe_ctor2: zkappa2 = 1.26455 Vpbe_ctor2: zmagic = 6999.55 Vpbe_ctor2: Constructing Vclist with 64 x 44 x 45 table Vclist_ctor2: Using 64 x 44 x 45 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.12 max radius Vclist_setupGrid: Grid lengths = (41.8028, 32.2478, 32.9828) Vclist_setupGrid: Grid lower corner = (-33.5439, -9.1589, -25.3719) Vclist_assignAtoms: Have 275810 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 242.732 Vacc_storeParms: Using 2466-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 2, mgsolv = 1 Setting PDE center to local center... Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vprtstp: iteration = 27 Vprtstp: relative residual = 1.557925e-06 Vprtstp: contraction number = 8.279313e-01 Vprtstp: iteration = 28 Vprtstp: relative residual = 8.147479e-07 Vprtstp: contraction number = 5.229698e-01 Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.201930e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.278700e+03 Vpmg_setPart: lower corner = (-37.5653, -9.8361, -26.3064) Vpmg_setPart: upper corner = (12.2803, 23.7661, 8.54535) Vpmg_setPart: actual minima = (-37.5653, -9.8361, -26.3064) Vpmg_setPart: actual maxima = (12.2803, 23.7661, 8.54535) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vpmg_energy: calculating only q-phi energy Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 3.855558488887E+04 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 1.300000e-01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 20.7767 Vpbe_ctor2: solute dimensions = 32.287 x 22.406 x 22.936 Vpbe_ctor2: solute charge = -1 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.795157 Vpbe_ctor2: Debye length = 1.25761 Vpbe_ctor2: zkappa2 = 1.26455 Vpbe_ctor2: zmagic = 6999.55 Vpbe_ctor2: Constructing Vclist with 64 x 44 x 45 table Vclist_ctor2: Using 64 x 44 x 45 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.12 max radius Vclist_setupGrid: Grid lengths = (41.8028, 32.2478, 32.9828) Vclist_setupGrid: Grid lower corner = (-33.5439, -9.1589, -25.3719) Vclist_assignAtoms: Have 275810 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 242.732 Vacc_storeParms: Using 2466-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 2, mgsolv = 1 Setting PDE center to local center... Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -31.7011, -5.8829, -22.2062 VPMG::focusFillBound -- New mesh maxs = 6.41615, 19.8129, 4.44515 VPMG::focusFillBound -- Old mesh mins = -37.5653, -9.8361, -26.3064 VPMG::focusFillBound -- Old mesh maxs = 12.2803, 23.7661, 8.54535 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-31.7011, -5.8829, -22.2062) Vpmg_setPart: upper corner = (6.41615, 19.8129, 4.44515) Vpmg_setPart: actual minima = (-37.5653, -9.8361, -26.3064) Vpmg_setPart: actual maxima = (12.2803, 23.7661, 8.54535) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 VPMG::extEnergy: Finding extEnergy dimensions... VPMG::extEnergy Disj part lower corner = (-31.7011, -5.8829, -22.2062) VPMG::extEnergy Disj part upper corner = (6.41615, 19.8129, 4.44515) VPMG::extEnergy Old lower corner = (-37.5653, -9.8361, -26.3064) VPMG::extEnergy Old upper corner = (12.2803, 23.7661, 8.54535) Vpmg_qmEnergy: Calculating linear energy VPMG::extEnergy: extQmEnergy = 71.1094 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 73.2589 kT Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vpmg_fillco: filling boundary arrays Vpmg_fillco: done filling boundary arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.143000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. Vbuildops: Fine: (353, 193, 289) Vbuildops: Operator stencil (lev, numdia) = (1, 4) Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.590000e+00 Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. Vbuildops: Galer: (177, 097, 145) Vpmg_fillco: done filling coefficient arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.108000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vbuildops: Galer: (089, 049, 073) Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. Vbuildops: Fine: (353, 193, 289) Vbuildops: Galer: (045, 025, 037) Vbuildops: Operator stencil (lev, numdia) = (1, 4) Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 2.540000e+00 Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. Vbuildops: Galer: (177, 097, 145) Vbuildops: Galer: (089, 049, 073) Vbuildops: Galer: (045, 025, 037) Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 5.511000e+01 Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.853360e+03 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 1 Vprtstp: relative residual = 3.554901e-01 Vprtstp: contraction number = 3.554901e-01 Vprtstp: iteration = 2 Vprtstp: relative residual = 9.138493e-02 Vprtstp: contraction number = 2.570675e-01 Vprtstp: iteration = 3 Vprtstp: relative residual = 5.159303e-02 Vprtstp: contraction number = 5.645682e-01 Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup). CPU TIME = 6.030000e+01 Vnm_tstart: starting timer 30 (Vmgdrv2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.640210e+03 Vprtstp: iteration = 0 Vprtstp: relative residual = 1.000000e+00 Vprtstp: contraction number = 1.000000e+00 Vprtstp: iteration = 4 Vprtstp: relative residual = 2.475547e-02 Vprtstp: contraction number = 4.798219e-01 Vprtstp: iteration = 1 Vprtstp: relative residual = 5.354783e-01 Vprtstp: contraction number = 5.354783e-01 Vprtstp: iteration = 5 Vprtstp: relative residual = 1.820392e-02 Vprtstp: contraction number = 7.353495e-01 Vprtstp: iteration = 2 Vprtstp: relative residual = 1.205700e-01 Vprtstp: contraction number = 2.251633e-01 Vprtstp: iteration = 6 Vprtstp: relative residual = 9.799940e-03 Vprtstp: contraction number = 5.383423e-01 Vprtstp: iteration = 3 Vprtstp: relative residual = 4.353701e-02 Vprtstp: contraction number = 3.610931e-01 Vprtstp: iteration = 7 Vprtstp: relative residual = 7.307795e-03 Vprtstp: contraction number = 7.456979e-01 Vprtstp: iteration = 4 Vprtstp: relative residual = 2.216528e-02 Vprtstp: contraction number = 5.091135e-01 Vprtstp: iteration = 8 Vprtstp: relative residual = 4.031109e-03 Vprtstp: contraction number = 5.516177e-01 Vprtstp: iteration = 5 Vprtstp: relative residual = 1.394017e-02 Vprtstp: contraction number = 6.289192e-01 Vprtstp: iteration = 9 Vprtstp: relative residual = 3.031149e-03 Vprtstp: contraction number = 7.519394e-01 Vprtstp: iteration = 6 Vprtstp: relative residual = 8.623667e-03 Vprtstp: contraction number = 6.186200e-01 Vprtstp: iteration = 10 Vprtstp: relative residual = 1.686500e-03 Vprtstp: contraction number = 5.563896e-01 Vprtstp: iteration = 7 Vprtstp: relative residual = 5.894723e-03 Vprtstp: contraction number = 6.835517e-01 Vprtstp: iteration = 11 Vprtstp: relative residual = 1.278034e-03 Vprtstp: contraction number = 7.578026e-01 Vprtstp: iteration = 8 Vprtstp: relative residual = 3.830412e-03 Vprtstp: contraction number = 6.498035e-01 Vprtstp: iteration = 12 Vprtstp: relative residual = 7.113484e-04 Vprtstp: contraction number = 5.565957e-01 Vprtstp: iteration = 13 Vprtstp: relative residual = 5.438667e-04 Vprtstp: contraction number = 7.645575e-01 Vprtstp: iteration = 9 Vprtstp: relative residual = 2.655652e-03 Vprtstp: contraction number = 6.933073e-01 Vprtstp: iteration = 14 Vprtstp: relative residual = 3.016318e-04 Vprtstp: contraction number = 5.546062e-01 Vprtstp: iteration = 10 Vprtstp: relative residual = 1.764094e-03 Vprtstp: contraction number = 6.642790e-01 Vprtstp: iteration = 15 Vprtstp: relative residual = 2.328897e-04 Vprtstp: contraction number = 7.720991e-01 Vprtstp: iteration = 16 Vprtstp: relative residual = 1.284291e-04 Vprtstp: contraction number = 5.514588e-01 Vprtstp: iteration = 11 Vprtstp: relative residual = 1.228826e-03 Vprtstp: contraction number = 6.965765e-01 Vprtstp: iteration = 17 Vprtstp: relative residual = 1.002052e-04 Vprtstp: contraction number = 7.802377e-01 Vprtstp: iteration = 12 Vprtstp: relative residual = 8.259923e-04 Vprtstp: contraction number = 6.721799e-01 Vprtstp: iteration = 18 Vprtstp: relative residual = 5.487411e-05 Vprtstp: contraction number = 5.476175e-01 Vprtstp: iteration = 13 Vprtstp: relative residual = 5.765563e-04 Vprtstp: contraction number = 6.980165e-01 Vprtstp: iteration = 19 Vprtstp: relative residual = 4.328885e-05 Vprtstp: contraction number = 7.888757e-01 Vprtstp: iteration = 14 Vprtstp: relative residual = 3.901673e-04 Vprtstp: contraction number = 6.767203e-01 Vprtstp: iteration = 20 Vprtstp: relative residual = 2.351905e-05 Vprtstp: contraction number = 5.433050e-01 Vprtstp: iteration = 15 Vprtstp: relative residual = 2.726832e-04 Vprtstp: contraction number = 6.988878e-01 Vprtstp: iteration = 21 Vprtstp: relative residual = 1.876738e-05 Vprtstp: contraction number = 7.979651e-01 Vprtstp: iteration = 16 Vprtstp: relative residual = 1.852756e-04 Vprtstp: contraction number = 6.794535e-01 Vprtstp: iteration = 17 Vprtstp: relative residual = 1.296257e-04 Vprtstp: contraction number = 6.996374e-01 Vprtstp: iteration = 22 Vprtstp: relative residual = 1.010866e-05 Vprtstp: contraction number = 5.386294e-01 Vprtstp: iteration = 18 Vprtstp: relative residual = 8.828744e-05 Vprtstp: contraction number = 6.810952e-01 Vprtstp: iteration = 23 Vprtstp: relative residual = 8.162741e-06 Vprtstp: contraction number = 8.074995e-01 Vprtstp: iteration = 19 Vprtstp: relative residual = 6.183914e-05 Vprtstp: contraction number = 7.004296e-01 Vprtstp: iteration = 24 Vprtstp: relative residual = 4.356067e-06 Vprtstp: contraction number = 5.336524e-01 Vprtstp: iteration = 25 Vprtstp: relative residual = 3.561022e-06 Vprtstp: contraction number = 8.174857e-01 Vprtstp: iteration = 20 Vprtstp: relative residual = 4.217560e-05 Vprtstp: contraction number = 6.820212e-01 Vprtstp: iteration = 26 Vprtstp: relative residual = 1.881709e-06 Vprtstp: contraction number = 5.284181e-01 Vprtstp: iteration = 21 Vprtstp: relative residual = 2.957890e-05 Vprtstp: contraction number = 7.013272e-01 Vprtstp: iteration = 22 Vprtstp: relative residual = 2.018611e-05 Vprtstp: contraction number = 6.824497e-01 Vprtstp: iteration = 27 Vprtstp: relative residual = 1.557925e-06 Vprtstp: contraction number = 8.279313e-01 Vprtstp: iteration = 23 Vprtstp: relative residual = 1.417765e-05 Vprtstp: contraction number = 7.023467e-01 Vprtstp: iteration = 28 Vprtstp: relative residual = 8.147479e-07 Vprtstp: contraction number = 5.229698e-01 Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 3.453210e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 3.518820e+03 Vpmg_setPart: lower corner = (-37.5653, -9.8361, -26.3064) Vpmg_setPart: upper corner = (12.2803, 23.7661, 8.54535) Vpmg_setPart: actual minima = (-37.5653, -9.8361, -26.3064) Vpmg_setPart: actual maxima = (12.2803, 23.7661, 8.54535) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vpmg_energy: calculating only q-phi energy Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 3.855558488887E+04 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.100000e-01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 20.7767 Vpbe_ctor2: solute dimensions = 32.287 x 22.406 x 22.936 Vpbe_ctor2: solute charge = -1 Vpbe_ctor2: bulk ionic strength = 0.15 Vpbe_ctor2: xkappa = 0.795157 Vpbe_ctor2: Debye length = 1.25761 Vpbe_ctor2: zkappa2 = 1.26455 Vpbe_ctor2: zmagic = 6999.55 Vpbe_ctor2: Constructing Vclist with 64 x 44 x 45 table Vclist_ctor2: Using 64 x 44 x 45 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.12 max radius Vclist_setupGrid: Grid lengths = (41.8028, 32.2478, 32.9828) Vclist_setupGrid: Grid lower corner = (-33.5439, -9.1589, -25.3719) Vclist_assignAtoms: Have 275810 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 242.732 Vacc_storeParms: Using 2466-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 2, mgsolv = 1 Setting PDE center to local center... Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -31.7011, -5.8829, -22.2062 VPMG::focusFillBound -- New mesh maxs = 6.41615, 19.8129, 4.44515 VPMG::focusFillBound -- Old mesh mins = -37.5653, -9.8361, -26.3064 VPMG::focusFillBound -- Old mesh maxs = 12.2803, 23.7661, 8.54535 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-31.7011, -5.8829, -22.2062) Vpmg_setPart: upper corner = (6.41615, 19.8129, 4.44515) Vpmg_setPart: actual minima = (-37.5653, -9.8361, -26.3064) Vpmg_setPart: actual maxima = (12.2803, 23.7661, 8.54535) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 VPMG::extEnergy: Finding extEnergy dimensions... VPMG::extEnergy Disj part lower corner = (-31.7011, -5.8829, -22.2062) VPMG::extEnergy Disj part upper corner = (6.41615, 19.8129, 4.44515) VPMG::extEnergy Old lower corner = (-37.5653, -9.8361, -26.3064) VPMG::extEnergy Old upper corner = (12.2803, 23.7661, 8.54535) Vpmg_qmEnergy: Calculating linear energy VPMG::extEnergy: extQmEnergy = 71.1094 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 73.2589 kT Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vprtstp: iteration = 24 Vprtstp: relative residual = 9.676470e-06 Vprtstp: contraction number = 6.825159e-01 Vprtstp: iteration = 25 Vprtstp: relative residual = 6.807246e-06 Vprtstp: contraction number = 7.034844e-01 Vprtstp: iteration = 26 Vprtstp: relative residual = 4.644635e-06 Vprtstp: contraction number = 6.823075e-01 Vpmg_fillco: done filling coefficient arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 4.242000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vprtstp: iteration = 27 Vprtstp: relative residual = 3.273216e-06 Vprtstp: contraction number = 7.047306e-01 Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup).. Vbuildops: Fine: (353, 193, 289) Vprtstp: iteration = 28 Vprtstp: relative residual = 2.231955e-06 Vprtstp: contraction number = 6.818844e-01 Vbuildops: Operator stencil (lev, numdia) = (1, 4) Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup). CPU TIME = 3.740000e+00 Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup).. Vbuildops: Galer: (177, 097, 145) Vprtstp: iteration = 29 Vprtstp: relative residual = 1.575924e-06 Vprtstp: contraction number = 7.060731e-01 Vprtstp: iteration = 30 Vprtstp: relative residual = 1.073660e-06 Vprtstp: contraction number = 6.812891e-01 Vbuildops: Galer: (089, 049, 073) Vbuildops: Galer: (045, 025, 037) Vprtstp: iteration = 31 Vprtstp: relative residual = 7.596163e-07 Vprtstp: contraction number = 7.075019e-01 Vnm_tstop: stopping timer 30 (Vmgdrv2: solve). CPU TIME = 4.085380e+03 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 4.155520e+03 Vpmg_setPart: lower corner = (-31.7011, -5.8829, -22.2062) Vpmg_setPart: upper corner = (6.41615, 19.8129, 4.44515) Vpmg_setPart: actual minima = (-31.7011, -5.8829, -22.2062) Vpmg_setPart: actual maxima = (6.41615, 19.8129, 4.44515) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vpmg_energy: calculating only q-phi energy Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 5.159214314839E+04 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 9.000000e-02 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 printEnergy: Performing global reduction (sum) Vcom_reduce: Not compiled with MPI, doing simple copy. printEnergy: Performing global reduction (sum) Vcom_reduce: Not compiled with MPI, doing simple copy. printEnergy: Performing global reduction (sum) Vcom_reduce: Not compiled with MPI, doing simple copy. Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 1.172609e+04