Hi, I pushed the changes to the default branch (although I'd call it a fix rather than feature...). Let me know what you think. Cheers konstantin
Konstantin Koschke Schneckestr. 13 81737 München cell: +49 174 318 00 22 landline: +49 89 8092 8193 skype: der.konsi On Mon, Dec 30, 2013 at 10:25 PM, Christoph Junghans <[email protected]>wrote: > 2013/12/30 Konstantin Koschke <[email protected]>: > > Follow up question: > > > > I'm having trouble applying the described solution to systems with > >>=10000 particles. > > > > topol.xml: > > <topology base="conf.gro"> > > <topology base="conf.gro"> > > <molecules> > > <clear/> > > <define name="LJ" first="1" nbeads="1" nmols="46754"/> > > <define name="LJ2" first="46755" nbeads="1" nmols="222"/> > > </molecules> > > </topology> > > > > conf.gro (accepted by Gromacs) > > <comment> > > 46976 > > 1LJ LJ 1 1.501 0.898 39.020 -0.5403 -0.0643 -0.1237 > > 2LJ LJ 2 0.819 0.782 39.940 -0.1761 0.4613 0.8996 > > 3LJ LJ 3 25.569 0.223 78.723 -0.9311 0.6834 1.0154 > > 4LJ LJ 4 0.622 0.940 78.925 0.0867 -0.7893 -0.4776 > > 5LJ LJ 5 25.703 0.112 1.051 -1.4844 -1.3820 -0.2094 > > 6LJ LJ 6 0.746 0.884 0.850 -1.3114 -0.3018 -0.5255 > > 7LJ LJ 7 0.756 0.148 1.708 0.2187 1.2106 0.1784 > > 8LJ LJ 8 25.676 0.874 1.733 0.2661 0.0462 1.1449 > > 9LJ LJ 9 25.682 0.055 2.530 -0.7328 0.5694 0.2111 > > 10LJ LJ 10 0.772 0.907 2.567 -0.0130 -0.0032 0.8058 > > <snip> > > 46752LJ LJ46752 2.107 1.960 73.520 -1.5537 -0.1894 0.3724 > > 46753LJ LJ46753 0.101 4.070 73.973 -1.7185 0.4044 0.8888 > > 46754LJ LJ46754 20.944 22.353 77.453 -0.1121 0.2523 0.8406 > > 46755LJ2 LJ246755 21.629 4.264 77.401 1.2456 0.0706 -0.6452 > > 46756LJ2 LJ246756 20.918 25.072 48.823 -1.0657 0.5206 -0.2004 > > 46757LJ2 LJ246757 4.493 9.013 59.993 0.8699 0.2926 -0.3162 > > <snip> > > 46752LJ LJ46752 2.107 1.960 73.520 -1.5537 -0.1894 0.3724 > > 46753LJ LJ46753 0.101 4.070 73.973 -1.7185 0.4044 0.8888 > > 46754LJ LJ46754 20.944 22.353 77.453 -0.1121 0.2523 0.8406 > > 46755LJ2 LJ246755 21.629 4.264 77.401 1.2456 0.0706 -0.6452 > > 46756LJ2 LJ246756 20.918 25.072 48.823 -1.0657 0.5206 -0.2004 > > 46757LJ2 LJ246757 4.493 9.013 59.993 0.8699 0.2926 -0.3162 > > > > csg_dump --top topol.xml > > > > WARNING: topology created from .gro file, masses and charges are wrong! > > I have 46976 beads in 46976 molecules > > Boundary Condition: orthorhombic > > Box matix: 25.7134 0 0 > > 0 25.7636 0 > > 0 0 79.5886 > > > > List of molecules: > > molecule: 1 LJ beads: 1 > > 0 Name 1:LJ:LJ Type LJ Mass 1 > > molecule: 2 LJ beads: 1 > > 1 Name 1:LJ:LJ Type LJ Mass 1 > > molecule: 3 LJ beads: 1 > > <snip> > > 9997 Name 1:LJ:LJ Type LJ Mass 1 > > molecule: 9999 LJ beads: 1 > > 9998 Name 1:LJ:LJ Type LJ Mass 1 > > molecule: 10000 LJ beads: 1 > > 9999 Name 1:LJ:LJ10000 Type LJ10000 Mass 1 > > molecule: 10001 LJ beads: 1 > > 10000 Name 1:LJ:LJ10001 Type LJ10001 Mass 1 > > molecule: 10002 LJ beads: 1 > > <snip> > > 46752 Name 1:LJ:LJ46753 Type LJ46753 Mass 1 > > molecule: 46754 LJ beads: 1 > > 46753 Name 1:LJ:LJ46754 Type LJ46754 Mass 1 > > molecule: 46755 LJ2 beads: 1 > > 0 Name 1:LJ:LJ Type LJ Mass 1 > > molecule: 46756 LJ2 beads: 1 > > 1 Name 1:LJ:LJ Type LJ Mass 1 > > molecule: 46757 LJ2 beads: 1 > > <snip> > > 218 Name 1:LJ:LJ Type LJ Mass 1 > > molecule: 46974 LJ2 beads: 1 > > 219 Name 1:LJ:LJ Type LJ Mass 1 > > molecule: 46975 LJ2 beads: 1 > > 220 Name 1:LJ:LJ Type LJ Mass 1 > > molecule: 46976 LJ2 beads: 1 > > 221 Name 1:LJ:LJ Type LJ Mass 1 > > $ csg_stat --top to > > on rdf-grid.xml --trj conf.gro > > begin to calculate distribution functions > > # of bonded interactions: 0 > > # of non-bonded interactions: 1 > > > > WARNING: topology created from .gro file, masses and charges are wrong! > > I have 46976 beads in 46976 molecules > > Reading frames from gro file 'LJ liq stitched to LJ ice along z', 46976 > > atoms. > > Reading frame 0 time 0.000 > > an error occurred: > > Topology does not have beads of type "LJ2" > > This was specified in type2 of interaction "unknown" > > > > (all files are also attached) > > > > I may have an obvious mistake in topol.xml. Any hints? > I see, I guess the problem starts if there is no space between the > residue name and the atom id. > If I remember correctly votca uses an ifstream to read the file, which > uses white spaces as separators, but gro files are fixed-format. > Can you go ahead an fix that in grotopologyreader.cc > (csg/src/libcsg/modules/io)? (See the recently added pdbtopology > reader on how to read fixed format file correctly.) > > Christoph > > > > Thanks! > > > > Konstantin Koschke > > Schneckestr. 13 > > 81737 München > > > > cell: +49 174 318 00 22 > > landline: +49 89 8092 8193 > > skype: der.konsi > > > > > > On Sun, Dec 29, 2013 at 12:29 AM, Konstantin Koschke > > <[email protected]> wrote: > >> > >> Thank you! > >> > >> Worked as described. > >> > >> Best > >> konstantin > >> Konstantin Koschke > >> Schneckestr. 13 > >> 81737 München > >> > >> cell: +49 174 318 00 22 > >> landline: +49 89 8092 8193 > >> skype: der.konsi > >> > >> > >> On Sat, Dec 28, 2013 at 12:30 AM, Christoph Junghans < > [email protected]> > >> wrote: > >> > 2013/12/27 Konstantin Koschke <[email protected]>: > >> >> Dear all, > >> >> > >> >> I've been using Espresso++ for my simulations, saving the trajectory > >> >> to a .gro file. > >> >> > >> >> I would like to use csg_stat to compute the radial distribution > >> >> function, but do not know how to specify the different types of atoms > >> >> for which the rdf should be computed. > >> >> > >> >> Sample (single frame) .gro file: > >> >> > >> >> system description, current step=1, length unit=LJ > >> >> 1872 > >> >> 1T0 T0 1 0.284 7.798 0.208 0.1758 -0.0315 -1.8179 > >> >> 2T0 T0 2 0.759 11.851 2.541 -0.3331 0.5601 -0.1017 > >> >> 3T0 T0 3 4.468 3.993 9.966 -2.0515 -0.5443 0.5865 > >> >> 4T0 T0 4 1.191 8.928 7.218 0.6759 -0.1850 0.7744 > >> >> 5T0 T0 5 2.372 1.933 11.360 0.3106 -0.1728 -2.0392 > >> >> 6T0 T0 6 8.341 1.811 10.498 0.2489 0.3545 1.7114 > >> >> 7T0 T0 7 7.774 11.684 11.541 0.9694 -1.0832 -1.7319 > >> >> 8T0 T0 8 6.976 5.328 0.700 -1.9203 -2.2488 0.1209 > >> >> 9T0 T0 9 9.434 6.609 5.760 -0.0652 1.8154 0.5061 > >> >> <snip> > >> >> 1864T1 T1 1864 9.047 0.116 5.381 0.5089 -1.8502 1.9424 > >> >> 1865T1 T1 1865 6.681 0.467 9.574 -2.1365 -0.1400 0.1403 > >> >> 1866T1 T1 1866 4.985 6.904 10.216 2.5356 -2.8845 -0.6594 > >> >> 1867T1 T1 1867 2.153 8.618 9.314 -2.1215 -1.8006 -0.8942 > >> >> 1868T1 T1 1868 0.297 0.925 2.052 -1.7950 -1.6092 0.3049 > >> >> 1869T1 T1 1869 1.739 5.657 10.281 0.6179 -1.4787 2.2130 > >> >> 1870T1 T1 1870 5.681 12.372 2.197 -2.1709 0.0992 2.2873 > >> >> 1871T1 T1 1871 2.140 2.912 8.940 -0.2329 -0.4645 -3.2850 > >> >> 1872T1 T1 1872 2.026 9.238 1.335 -0.0400 -0.0488 0.5568 > >> >> > >> >> relevant part of settings.xml: > >> >> <!-- types involved in this interaction --> > >> >> <type1>*</type1> > >> >> <type2>*</type2> > >> >> > >> >> $ csg_dump --top traj.gro > >> >> WARNING: topology created from .gro file, masses and charges are > wrong! > >> >> I have 1872 beads in 0 molecules > >> >> > >> >> List of molecules: > >> > gro files contain no molecular information, you will need to create an > >> > xml topology based on your gro file. > >> > (see topol.xml in csg-tutorials/spce/ibi_espressopp as an example). > >> > > >> >> csg_dump does not find the two types of atoms (T0, T1) and I don't > >> >> know what to put into the 'type' tags in the settings.xml. I would > >> >> like to compute the rdf between T0 and T1. Any suggestions? > >> > Once molecules are setup csg_dump will show you the types it found: > >> > $ csg_dump --top topol.xml > >> > ... > >> > molecule: 2180 SOL beads: 1 > >> > 2179 Name 1:SOL:CG Type CG Mass 1 > >> > > >> > These types can be used in your settings.xml. > >> > > >> > Cheers, > >> > > >> > Christoph > >> >> > >> >> > >> >> Thank you! > >> >> konstantin > >> >> > >> >> PS. If necessary, I'll code. > >> >> > >> >> Konstantin Koschke > >> >> Schneckestr. 13 > >> >> 81737 München > >> >> > >> >> cell: +49 174 318 00 22 > >> >> landline: +49 89 8092 8193 > >> >> skype: der.konsi > >> >> > >> >> -- > >> >> You received this message because you are subscribed to the Google > >> >> Groups "votca" group. > >> >> To unsubscribe from this group and stop receiving emails from it, > send > >> >> an email to [email protected]. > >> >> To post to this group, send email to [email protected]. > >> >> Visit this group at http://groups.google.com/group/votca. > >> >> For more options, visit https://groups.google.com/groups/opt_out. > >> > > >> > > >> > > >> > -- > >> > Christoph Junghans > >> > Web: http://www.compphys.de > >> > > >> > -- > >> > You received this message because you are subscribed to the Google > >> > Groups "votca" group. > >> > To unsubscribe from this group and stop receiving emails from it, send > >> > an email to [email protected]. > >> > To post to this group, send email to [email protected]. > >> > Visit this group at http://groups.google.com/group/votca. > >> > For more options, visit https://groups.google.com/groups/opt_out. > > > > > > -- > > You received this message because you are subscribed to the Google Groups > > "votca" group. > > To unsubscribe from this group and stop receiving emails from it, send an > > email to [email protected]. > > To post to this group, send email to [email protected]. > > Visit this group at http://groups.google.com/group/votca. > > For more options, visit https://groups.google.com/groups/opt_out. > > > > -- > Christoph Junghans > Web: http://www.compphys.de > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/votca. > For more options, visit https://groups.google.com/groups/opt_out. > -- You received this message because you are subscribed to the Google Groups "votca" group. 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