Error Insufficient Jacobi Rotations For Rigid Body

for 31 timesteps before I get "nan" from the thermo output. Then at the end of the output I get the Jacobi rotations error. If the Jacobi routine is run just once at the beginning of the run, then I don't understand why things work for a bit, then fail, then I get this error. If I run a simulation for 30 timesteps, then the simulation exits cleanly with no error. I checked the configurations and it doesn't make sense why it should cause a problem. My guess is that the Jacobi error is a red herring? thanks for the help. I will investigate other possibilities for the nan's, Joyce PS: SHAKE cannot handle an angle constraint of exactly 180 degrees. Steve Plimpton wrote: The jacobi calculation is only done once before a run begins, on each rigid body. So I don't know what you mean by it happens on a certain timestep. If there is one (or more) bodies that are failing in jacobi(), then you should be able to reproduce it on a 0-timestep run, where the 3 atoms are in a restart file or data file, and the whole simluation is just those 3 atoms. Can you create such an input script or print out the coords of the 3 atoms before the jacobi routine is called on them? Steve On Nov 7, 2007 5:43 PM, Joyce Noah-Vanhoucke wrote: Dear Lammps-users, I am doing simulations on a system of 3-member linear rigid bodies using fix rigid and the lj/cut/coul/long pair potential. I get the following error during equilibration: "ERROR: Insufficient Jacobi rotations for rigid body", which means that "Eigensolve for rigid body was not sufficiently accurate." I checked the configuration of my rigid bodies and they are as they should be (exactly co-linear). I've tried changing MAXJACOBI in fix_rigid.cpp from the original 50 to 100, 200 and 250, but the problem seems to be independent of this value. (I get the error at the same timestep irrespective of the MAXJACOBI value). The other thermodynamic quantities seem normal up until the timestep where I get "nan," so I am not sure what is causing this error. If anyone has any insights into why the Jacobi routine would fail, please let me know. I appreciate any help! Thanks, Joyce ------------------------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now >> http://get.splunk.com/ _______________________________________________ lam

instructions: Windows Mac Red Hat Linux Ubuntu Click URL instructions: Right-click on ad, choose "Copy Link", then paste here → (This may not be possible with some types of ads) More information about our ad policies X You seem to have CSS turned off. Please don't fill out this field. You seem to have CSS turned off. Please don't fill out this field. Briefly describe the problem (required): Upload screenshot of ad (required): Select a file, or drag & drop file here. ✔ ✘ Please provide http://lammps.sandia.gov/threads/msg02531.html the ad click URL, if possible: Home Browse LAMMPS Mailing Lists LAMMPS Brought to you by: sjplimp Summary Files Reviews Support Wiki Mailing Lists News Discussion lammps-users Re: [lammps-users] ERROR: Insufficient Jacobi rotations for rigid body Re: [lammps-users] ERROR: Insufficient Jacobi rotations for rigid body From: Steve Plimpton - 2010-03-22 17:28:43 Please post your data file, so I can https://sourceforge.net/p/lammps/mailman/message/24828519/ try to reproduce the error message. Steve On Sat, Mar 20, 2010 at 8:05 AM, Mantzalis, Dimitrios wrote: > Dear all, > > i am trying to simulate a single wall nanotube with a 3 site CO2 model. I tried to use the same approach that i have used for one site CO2 and argon interacting with a swnt. But when i am trying to simulate these i am getting an error."ERROR: Insufficient Jacobi rotations for rigid body". what should i do for this? i thought to erase the fix rigid or the bond and angles from the nanotube. But then i thought of this works for one site or for argon why here it doesn't? > > Regards > Dimitris > > > > ##################################################### > # Initialisation file for CO2 melecules in a nanotube > ##################################################### > > #Periodic boundary conditions for z, fixed simulation boundary for x and y, 3D case > > dimension       3 > boundary p p p > units real > > neighbor      

Sign in Pricing Blog Support Search GitHub This repository Watch 7 Star 7 Fork 13 CFDEMproject/LAMMPS Code Issues 0 Pull requests 0 Projects 0 Pulse https://github.com/CFDEMproject/LAMMPS/blob/master/src/RIGID/fix_rigid_small.h Graphs Permalink Branch: master Switch branches/tags Branches Tags master Nothing to show https://github.com/CFDEMproject/LAMMPS/blob/master/src/USER-OMP/fix_rigid_small_omp.h Nothing to show Find file Copy path LAMMPS/src/RIGID/fix_rigid_small.h Fetching contributors… Cannot retrieve contributors at this time Raw Blame History 230 lines (168 sloc) 7.06 KB /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator http://lammps.sandia.gov, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms error insufficient of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains certain rights in this software. This software is distributed under the GNU General Public License. See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ #ifdef FIX_CLASS FixStyle(rigid/small,FixRigidSmall) #else #ifndef LMP_FIX_RIGID_SMALL_H #define LMP_FIX_RIGID_SMALL_H #include "fix.h" // replace this later #include

Sign in Pricing Blog Support Search GitHub This repository Watch 7 Star 7 Fork 13 CFDEMproject/LAMMPS Code Issues 0 Pull requests 0 Projects 0 Pulse Graphs Permalink Branch: master Switch branches/tags Branches Tags master Nothing to show Nothing to show Find file Copy path LAMMPS/src/USER-OMP/fix_rigid_small_omp.h Fetching contributors… Cannot retrieve contributors at this time Raw Blame History 135 lines (81 sloc) 3.23 KB /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator http://lammps.sandia.gov, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains certain rights in this software. This software is distributed under the GNU General Public License. See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ #ifdef FIX_CLASS FixStyle(rigid/small/omp,FixRigidSmallOMP) #else #ifndef LMP_FIX_RIGID_SMALL_OMP_H #define LMP_FIX_RIGID_SMALL_OMP_H #include "fix_rigid_small.h" namespace LAMMPS_NS { class FixRigidSmallOMP : public FixRigidSmall { public: FixRigidSmallOMP(class LAMMPS *lmp, int narg, char **args) : FixRigidSmall(lmp,narg,args) {}; virtual ~FixRigidSmallOMP() {}; virtual void initial_integrate(int); virtual void final_integrate(); private: template void set_xv_thr(); template void set_v_thr(); }; } #endif #endif /* ERROR/WARNING messages: E: Illegal ... command Self-explanatory. Check the input script syntax and compare to the documentation for the command. You can use -echo screen as a command-line option when running LAMMPS to see the offending line. E: Fix rigid molecule requires atom attribute molecule Self-explanatory. E: Could not find fix rigid group ID A