[gmx-users] segfault(11) -- simulation blows up on first step

Inon Sharony InonShar at TAU.ac.IL
Tue Jun 2 13:20:53 CEST 2009



 Sorry for the previous mail, I guess the appended content was too long. Anyway, here it is as an attached file 

Sorry, and thanks again

-- 
Inon   Sharony
ינון     שרוני
+972(3)6407634
atto.TAU.ac.IL/~inonshar
Please consider your environmental responsibility before printing this e-mail.
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MDRUN_MPI STD-I/O:
==================

step 0
[hydrogen:15285] *** Process received signal ***
[hydrogen:15285] Signal: Segmentation fault (11)
[hydrogen:15285] Signal code: Address not mapped (1)
[hydrogen:15285] Failing at address: 0xfffffffe16c50a90
[hydrogen:15285] [ 0] /lib64/libpthread.so.0 [0x355c00de80]
[hydrogen:15285] [ 1] mdrun_mpi(gmx_pme_do+0x28b2) [0x4b56f2]
[hydrogen:15285] [ 2] mdrun_mpi(do_force_lowlevel+0x1023) [0x47f6f3]
[hydrogen:15285] [ 3] mdrun_mpi(do_force+0xe6e) [0x4c99ce]
[hydrogen:15285] [ 4] mdrun_mpi(do_md+0x48f0) [0x42c4a0]
[hydrogen:15285] [ 5] mdrun_mpi(mdrunner+0x831) [0x42d771]
[hydrogen:15285] [ 6] mdrun_mpi(main+0x3c0) [0x42e6a0]
[hydrogen:15285] [ 7] /lib64/libc.so.6(__libc_start_main+0xf4) [0x355b41d8b4]
[hydrogen:15285] [ 8] mdrun_mpi [0x4131a9]
[hydrogen:15285] *** End of error message ***
./test-2-6-09.sh: line 16: 15285 Segmentation fault      mdrun_mpi -c md -v


----------------------------------------------------------------------------------------------------------------

MD.MDP
======

integrator	=	sd	;stochastic dynamics (velocity Langevin) using a leap-frog algorithm
dt		=	0.0001
nsteps		=	10000						; [steps] ==> total (nsteps*dt) ps.
nstxout		=	1
nstvout		=	1
nstfout		=	1
; nstxtcout	=	1
nstenergy	=	1	; write energies to energy file every 1000 steps (default 100)
nstlog		=	1
energygrps	=	SL	SR
ns_type			=	simple
periodic_molecules	=	no
coulombtype	=	PME
tc-grps		=	SL	SR
tau_t		=	0	1	; mass/gamma
ref_t		=	0   	0	; refference (bath) temperature
Pcoupl		=	no
gen_vel		=	no
gen_seed	=	-1	; random seed based on computer clock
constraints	=	none

--------------------------------------------------------------------------------------------

1S2.itp
=======

[ atomtypes ]
;atomtype 	m (u) 	q (e)	part.type 	V(cr)	W(cr)
SX		32.0600	0.000	A		1E-03	1E-05

[ moleculetype ]
; Name nrexcl
1S2      2

[ atoms ]
;   nr	type  resnr resid  atom  cgnr   charge     mass
    1      SX     1  1S2     SL     1    0.000  32.0600
    2      SX     1  1S2     SR     2    0.000  32.0600

[ bonds ]
; ai  aj  fu    c0, c1, ...
   1   2   2    0.2040  5.3E+6    0.2040  5.3E+6 ;   SL SR

--------------------------------------------------------------------------------------------

TRAJ.TRR
========

traj.trr frame 0:
   natoms=         2  step=         0  time=0.0000000e+00  lambda=         0
   box (3x3):
      box[    0]={ 6.37511e+00,  0.00000e+00,  0.00000e+00}
      box[    1]={ 0.00000e+00,  6.37511e+00,  0.00000e+00}
      box[    2]={ 0.00000e+00,  0.00000e+00,  6.37511e+00}
   x (2x3):
      x[    0]={ 3.19756e+00,  3.20532e+00,  3.18725e+00}
      x[    1]={ 3.03044e+00,  3.21568e+00,  3.08875e+00}
   v (2x3):
      v[    0]={ 2.22763e+00, -2.56083e-01,  1.38905e+00}
      v[    1]={-2.22763e+00,  2.56083e-01, -1.38905e+00}
   f (2x3):
      f[    0]={ 3.43615e+03, -2.13216e+02,  2.02509e+03}
      f[    1]={-3.43615e+03,  2.13216e+02, -2.02509e+03}


--------------------------------------------------------------------------------------------

MD.LOG
======



Input Parameters:
   integrator           = sd
   nsteps               = 10000
   init_step            = 0
   ns_type              = Simple
   nstlist              = 10
   ndelta               = 2
   nstcomm              = 1
   comm_mode            = Linear
   nstlog               = 1
   nstxout              = 1
   nstvout              = 1
   nstfout              = 1
   nstenergy            = 1
   nstxtcout            = 0
   init_t               = 0
   delta_t              = 0.0001
   xtcprec              = 1000
   nkx                  = 54
   nky                  = 54
   nkz                  = 54
   pme_order            = 4
   ewald_rtol           = 1e-05
   ewald_geometry       = 0
   epsilon_surface      = 0
   optimize_fft         = FALSE
   ePBC                 = xyz
   bPeriodicMols        = FALSE
   bContinuation        = FALSE
   bShakeSOR            = FALSE
   etc                  = No
   epc                  = No
   epctype              = Isotropic
   tau_p                = 1
   ref_p (3x3):
      ref_p[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      ref_p[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      ref_p[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   compress (3x3):
      compress[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      compress[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      compress[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   refcoord_scaling     = No
   posres_com (3):
      posres_com[0]= 0.00000e+00
      posres_com[1]= 0.00000e+00
      posres_com[2]= 0.00000e+00
   posres_comB (3):
      posres_comB[0]= 0.00000e+00
      posres_comB[1]= 0.00000e+00
      posres_comB[2]= 0.00000e+00
   andersen_seed        = 815131
   rlist                = 1
   rtpi                 = 0.05
   coulombtype          = PME
   rcoulomb_switch      = 0
   rcoulomb             = 1
   vdwtype              = Cut-off
   rvdw_switch          = 0
   rvdw                 = 1
   epsilon_r            = 1
   epsilon_rf           = 1
   tabext               = 1
   implicit_solvent     = No
   gb_algorithm         = Still
   gb_epsilon_solvent   = 80
   nstgbradii           = 1
   rgbradii             = 2
   gb_saltconc          = 0
   gb_obc_alpha         = 1
   gb_obc_beta          = 0.8
   gb_obc_gamma         = 4.85
   sa_surface_tension   = 2.092
   DispCorr             = No
   free_energy          = no
   init_lambda          = 0
   sc_alpha             = 0
   sc_power             = 0
   sc_sigma             = 0.3
   delta_lambda         = 0
   nwall                = 0
   wall_type            = 9-3
   wall_atomtype[0]     = -1
   wall_atomtype[1]     = -1
   wall_density[0]      = 0
   wall_density[1]      = 0
   wall_ewald_zfac      = 3
   pull                 = no
   disre                = No
   disre_weighting      = Conservative
   disre_mixed          = FALSE
   dr_fc                = 1000
   dr_tau               = 0
   nstdisreout          = 100
   orires_fc            = 0
   orires_tau           = 0
   nstorireout          = 100
   dihre-fc             = 1000
   em_stepsize          = 0.01
   em_tol               = 10
   niter                = 20
   fc_stepsize          = 0
   nstcgsteep           = 1000
   nbfgscorr            = 10
   ConstAlg             = Lincs
   shake_tol            = 0.0001
   lincs_order          = 4
   lincs_warnangle      = 30
   lincs_iter           = 1
   bd_fric              = 0
   ld_seed              = 1993
   cos_accel            = 0
   deform (3x3):
      deform[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      deform[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      deform[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   userint1             = 0
   userint2             = 0
   userint3             = 0
   userint4             = 0
   userreal1            = 0
   userreal2            = 0
   userreal3            = 0
   userreal4            = 0
grpopts:
   nrdf:         1.5         1.5
   ref_t:           0           0
   tau_t:           0           1
anneal:          No          No
ann_npoints:           0           0
   acc:	           0           0           0
   nfreeze:           N           N           N
   energygrp_flags[  0]: 0 0
   energygrp_flags[  1]: 0 0
   efield-x:
      n = 0
   efield-xt:
      n = 0
   efield-y:
      n = 0
   efield-yt:
      n = 0
   efield-z:
      n = 0
   efield-zt:
      n = 0
   bQMMM                = FALSE
   QMconstraints        = 0
   QMMMscheme           = 0
   scalefactor          = 1
qm_opts:
   ngQM                 = 0
Table routines are used for coulomb: TRUE
Table routines are used for vdw:     FALSE
Will do PME sum in reciprocal space.

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen 
A smooth particle mesh Ewald method
J. Chem. Phys. 103 (1995) pp. 8577-8592
-------- -------- --- Thank You --- -------- --------

Using a Gaussian width (1/beta) of 0.320163 nm for Ewald
Cut-off's:   NS: 1   Coulomb: 1   LJ: 1
System total charge: 0.000
Generated table with 4000 data points for Ewald.
Tabscale = 2000 points/nm
Generated table with 4000 data points for LJ6.
Tabscale = 2000 points/nm
Generated table with 4000 data points for LJ12.
Tabscale = 2000 points/nm
Configuring nonbonded kernels...
Testing x86_64 SSE2 support... present.


Removing pbc first time
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
  0:  rest
There are: 2 Atoms
Max number of connections per atom is 1
Total number of connections is 2
Max number of graph edges per atom is 1
Total number of graph edges is 2
Initial temperature: 17884.7 K

Started mdrun on node 0 Tue Jun  2 13:38:03 2009

           Step           Time         Lambda
              0        0.00000        0.00000

   Energies (kJ/mol)
        G96Bond        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
    1.99416e+01    0.00000e+00    0.00000e+00    0.00000e+00    1.99416e+01
    Kinetic En.   Total Energy    Temperature Pressure (bar)
            nan            nan            nan            nan

           Step           Time         Lambda
              1        0.00010        0.00000

------------------------------------------------------------------------------------------------

MDRUN_MPI0.LOG
==============

symtab (56):
   symtab[0]="O"
   symtab[1]="OM"
   symtab[2]="OA"
   symtab[3]="OW"
   symtab[4]="N"
   symtab[5]="NT"
   symtab[6]="NL"
   symtab[7]="NR"
   symtab[8]="NZ"
   symtab[9]="NE"
   symtab[10]="C"
   symtab[11]="CH1"
   symtab[12]="CH2"
   symtab[13]="CH3"
   symtab[14]="CH4"
   symtab[15]="CR1"
   symtab[16]="HC"
   symtab[17]="H"
   symtab[18]="S"
   symtab[19]="CU1+"
   symtab[20]="CU2+"
   symtab[21]="FE"
   symtab[22]="ZN2+"
   symtab[23]="MG2+"
   symtab[24]="CA2+"
   symtab[25]="P"
   symtab[26]="AR"
   symtab[27]="F"
   symtab[28]="CL"
   symtab[29]="BR"
   symtab[30]="CMET"
   symtab[31]="OMET"
   symtab[32]="NA+"
   symtab[33]="CL-"
   symtab[34]="CCHL"
   symtab[35]="CLCHL"
   symtab[36]="HCHL"
   symtab[37]="SDMSO"
   symtab[38]="CDMSO"
   symtab[39]="ODMSO"
   symtab[40]="CCL4"
   symtab[41]="CLCL4"
   symtab[42]="SI"
   symtab[43]="MNH3"
   symtab[44]="OWT3"
   symtab[45]="OWT4"
   symtab[46]="MW"
   symtab[47]="DUM"
   symtab[48]="IW"
   symtab[49]="SX"
   symtab[50]="1S2"
   symtab[51]="SL"
   symtab[52]="SR"
   symtab[53]="Single Molecule of Sulfur"
   symtab[54]="System"
   symtab[55]="rest"
ffparams->atnr = 1, ntypes = 2
functype (2):
   functype[0]=26
   functype[1]=1
c6= 1.00000000e-03, c12= 1.00000000e-05
b0A= 4.16160e-02, cbA= 5.30000e+06, b0B= 4.16160e-02, cbB= 5.30000e+06
atoms:
   atom (2):
      atom[     0]={type=  0, typeB=  0, ptype=    Atom, m= 3.20600e+01, q= 0.00000e+00, mB= 3.20600e+01, qB= 0.00000e+00, resnr=    0, atomnumber= -1}
      atom[     1]={type=  0, typeB=  0, ptype=    Atom, m= 3.20600e+01, q= 0.00000e+00, mB= 3.20600e+01, qB= 0.00000e+00, resnr=    0, atomnumber= -1}
   atom (2):
      atom[0]={name="SL"}
      atom[1]={name="SR"}
   type (2):
      type[0]={name="SX",nameB="SX"}
      type[1]={name="SX",nameB="SX"}
   residue (1):
      residue[0]={name="1S2"}
cgs:
   nr=2
   cgs[0]={0..0}
   cgs[1]={1..1}
atomtypes:
   atomtype[  0]={radius= 0.00000e+00, volume= 0.00000e+00, surftens=-1.00000e+00, atomnumber=  -1)}
mols:
   nr=1
   mols[0]={0..1}
inputrec:
   integrator           = sd
   nsteps               = 10000
   init_step            = 0
   ns_type              = Simple
   nstlist              = 10
   ndelta               = 2
   nstcomm              = 1
   comm_mode            = Linear
   nstlog               = 1
   nstxout              = 1
   nstvout              = 1
   nstfout              = 1
   nstenergy            = 1
   nstxtcout            = 0
   init_t               = 0
   delta_t              = 0.0001
   xtcprec              = 1000
   nkx                  = 54
   nky                  = 54
   nkz                  = 54
   pme_order            = 4
   ewald_rtol           = 1e-05
   ewald_geometry       = 0
   epsilon_surface      = 0
   optimize_fft         = FALSE
   ePBC                 = xyz
   bPeriodicMols        = FALSE
   bContinuation        = FALSE
   bShakeSOR            = FALSE
   etc                  = No
   epc                  = No
   epctype              = Isotropic
   tau_p                = 1
   ref_p (3x3):
      ref_p[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      ref_p[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      ref_p[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   compress (3x3):
      compress[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      compress[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      compress[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   refcoord_scaling     = No
   posres_com (3):
      posres_com[0]= 0.00000e+00
      posres_com[1]= 0.00000e+00
      posres_com[2]= 0.00000e+00
   posres_comB (3):
      posres_comB[0]= 0.00000e+00
      posres_comB[1]= 0.00000e+00
      posres_comB[2]= 0.00000e+00
   andersen_seed        = 815131
   rlist                = 1
   rtpi                 = 0.05
   coulombtype          = PME
   rcoulomb_switch      = 0
   rcoulomb             = 1
   vdwtype              = Cut-off
   rvdw_switch          = 0
   rvdw                 = 1
   epsilon_r            = 1
   epsilon_rf           = 1
   tabext               = 1
   implicit_solvent     = No
   gb_algorithm         = Still
   gb_epsilon_solvent   = 80
   nstgbradii           = 1
   rgbradii             = 2
   gb_saltconc          = 0
   gb_obc_alpha         = 1
   gb_obc_beta          = 0.8
   gb_obc_gamma         = 4.85
   sa_surface_tension   = 2.092
   DispCorr             = No
   free_energy          = no
   init_lambda          = 0
   sc_alpha             = 0
   sc_power             = 0
   sc_sigma             = 0.3
   delta_lambda         = 0
   nwall                = 0
   wall_type            = 9-3
   wall_atomtype[0]     = -1
   wall_atomtype[1]     = -1
   wall_density[0]      = 0
   wall_density[1]      = 0
   wall_ewald_zfac      = 3
   pull                 = no
   disre                = No
   disre_weighting      = Conservative
   disre_mixed          = FALSE
   dr_fc                = 1000
   dr_tau               = 0
   nstdisreout          = 100
   orires_fc            = 0
   orires_tau           = 0
   nstorireout          = 100
   dihre-fc             = 1000
   em_stepsize          = 0.01
   em_tol               = 10
   niter                = 20
   fc_stepsize          = 0
   nstcgsteep           = 1000
   nbfgscorr            = 10
   ConstAlg             = Lincs
   shake_tol            = 0.0001
   lincs_order          = 4
   lincs_warnangle      = 30
   lincs_iter           = 1
   bd_fric              = 0
   ld_seed              = 1993
   cos_accel            = 0
   deform (3x3):
      deform[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      deform[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      deform[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   userint1             = 0
   userint2             = 0
   userint3             = 0
   userint4             = 0
   userreal1            = 0
   userreal2            = 0
   userreal3            = 0
   userreal4            = 0
grpopts:
   nrdf:         1.5         1.5
   ref_t:           0           0
   tau_t:           0           1
anneal:          No          No
ann_npoints:           0           0
   acc:	           0           0           0
   nfreeze:           N           N           N
   energygrp_flags[  0]: 0 0
   energygrp_flags[  1]: 0 0
   efield-x:
      n = 0
   efield-xt:
      n = 0
   efield-y:
      n = 0
   efield-yt:
      n = 0
   efield-z:
      n = 0
   efield-zt:
      n = 0
   bQMMM                = FALSE
   QMconstraints        = 0
   QMMMscheme           = 0
   scalefactor          = 1
qm_opts:
   ngQM                 = 0
Setting up tables
Setting up tables
Setting up tables
Going to determine what solvent types we have.
bHaveVdW (1):
   bHaveVdW[0]=1
graph part[] nchanged=1, bMultiPart=0
graph part[] nchanged=0, bMultiPart=0
graph:  graph
nnodes: 2
nbound: 2
start:  0
end:    1
 atom shiftx shifty shiftz C nedg    e1    e2 etc.
    1      0      0      0      1     2
    2      0      0      0      1     1
Creating PME data structures.
Installing signal handler for SIGTERM
Installing signal handler for SIGUSR1
SD const tc-grp 0: b nan  c inf  d -inf
SD const tc-grp 1: b 2.08344e-18  c 8.33302e-14  d -2.5e-09
graph part[] nchanged=1, bMultiPart=0
graph part[] nchanged=0, bMultiPart=0
graph:  graph
nnodes: 2
nbound: 2
start:  0
end:    1
 atom shiftx shifty shiftz C nedg    e1    e2 etc.
    1      0      0      0      1     2
    2      0      0      0      1     1
cgcm (2x3):
   cgcm[    0]={ 3.19756e+00,  3.20532e+00,  3.18725e+00}
   cgcm[    1]={ 3.03044e+00,  3.21568e+00,  3.08875e+00}
Initiating neighbourlist type 48 for Atom interactions,
with 2 SR, 0 LR atoms.
reallocating neigborlist il_code=48, maxnri=8
Initiating neighbourlist type 48 for Atom interactions,
with 2 SR, 0 LR atoms.
reallocating neigborlist il_code=48, maxnri=0
Initiating neighbourlist type 0 for Atom interactions,
with 2 SR, 0 LR atoms.
reallocating neigborlist il_code=0, maxnri=8
Initiating neighbourlist type 0 for Atom interactions,
with 2 SR, 0 LR atoms.
reallocating neigborlist il_code=0, maxnri=0
Initiating neighbourlist type 43 for Atom interactions,
with 2 SR, 0 LR atoms.
reallocating neigborlist il_code=43, maxnri=8
Initiating neighbourlist type 43 for Atom interactions,
with 2 SR, 0 LR atoms.
reallocating neigborlist il_code=43, maxnri=0
Initiating neighbourlist type 48 for Water interactions,
with 0 SR, 0 LR atoms.
reallocating neigborlist il_code=48, maxnri=0
Initiating neighbourlist type 48 for Water interactions,
with 0 SR, 0 LR atoms.
reallocating neigborlist il_code=48, maxnri=0
Initiating neighbourlist type 43 for Water interactions,
with 0 SR, 0 LR atoms.
reallocating neigborlist il_code=43, maxnri=0
Initiating neighbourlist type 43 for Water interactions,
with 0 SR, 0 LR atoms.
reallocating neigborlist il_code=43, maxnri=0
Initiating neighbourlist type 48 for Water-Water interactions,
with 0 SR, 0 LR atoms.
reallocating neigborlist il_code=48, maxnri=0
Initiating neighbourlist type 48 for Water-Water interactions,
with 0 SR, 0 LR atoms.
reallocating neigborlist il_code=48, maxnri=0
Initiating neighbourlist type 43 for Water-Water interactions,
with 0 SR, 0 LR atoms.
reallocating neigborlist il_code=43, maxnri=0
Initiating neighbourlist type 43 for Water-Water interactions,
with 0 SR, 0 LR atoms.
reallocating neigborlist il_code=43, maxnri=0
nsearch = 3
fshift after SR (45x3):
   fshift after SR[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[    3]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[    4]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[    5]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[    6]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[    7]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[    8]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[    9]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   10]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   11]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   12]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   13]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   14]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   15]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   16]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   17]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   18]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   19]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   20]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   21]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   22]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   23]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   24]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   25]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   26]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   27]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   28]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   29]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   30]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   31]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   32]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   33]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   34]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   35]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   36]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   37]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   38]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   39]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   40]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   41]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   42]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   43]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   44]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
dipcorr =    0.000     0.000     0.000
mutot   =    0.000     0.000     0.000
Long Range corrections for Ewald interactions:
start=0,natoms=2
q2sum = 0, Vself=0
Long Range correction: Vexcl=0
Total charge correction: Vcharge=0
PME: nnodes = 1, nodeid = 0
Grid = 0x3869b30
Node=      0, pme local particles=     2
PME mesh energy: 0
Vlr = 0, Vcorr = 0, Vlr_corr = 0
vir_el_recip after corr (3x3):
   vir_el_recip after corr[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   vir_el_recip after corr[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   vir_el_recip after corr[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
fshift after LR Corrections (45x3):
   fshift after LR Corrections[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after LR Corrections[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after LR Corrections[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after LR Corrections[    3]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after LR Corrections[    4]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after LR Corrections[    5]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after LR Corrections[    6]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after LR Corrections[    7]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after LR Corrections[    8]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after LR Corrections[    9]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after LR Corrections[   10]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after LR Corrections[   11]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after LR Corrections[   12]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after LR Corrections[   13]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after LR Corrections[   14]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after LR Corrections[   15]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after LR Corrections[   16]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after LR Corrections[   17]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after LR Corrections[   18]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after LR Corrections[   19]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after LR Corrections[   20]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after LR Corrections[   21]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after LR Corrections[   22]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after LR Corrections[   23]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after LR Corrections[   24]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after LR Corrections[   25]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after LR Corrections[   26]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after LR Corrections[   27]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after LR Corrections[   28]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after LR Corrections[   29]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after LR Corrections[   30]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after LR Corrections[   31]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after LR Corrections[   32]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after LR Corrections[   33]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after LR Corrections[   34]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after LR Corrections[   35]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after LR Corrections[   36]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after LR Corrections[   37]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after LR Corrections[   38]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after LR Corrections[   39]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after LR Corrections[   40]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after LR Corrections[   41]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after LR Corrections[   42]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after LR Corrections[   43]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after LR Corrections[   44]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
 Outer nonbonded loop                3.
 Calc Weights                        6.
 Spread Q Bspline                  128.
 Gather F Bspline                  128.
 3D-FFT                        5437124.
 Solve PME                       81648.
 NS-Pairs                            3.
 Reset In Box                        2.
 Shift-X                             2.
 CG-CoM                              2.
 Bonds                               1.
 Calc-Ekin                           2.
fshift after bondeds (45x3):
   fshift after bondeds[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after bondeds[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after bondeds[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after bondeds[    3]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after bondeds[    4]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after bondeds[    5]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after bondeds[    6]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after bondeds[    7]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after bondeds[    8]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after bondeds[    9]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after bondeds[   10]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after bondeds[   11]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after bondeds[   12]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after bondeds[   13]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after bondeds[   14]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after bondeds[   15]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after bondeds[   16]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after bondeds[   17]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after bondeds[   18]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after bondeds[   19]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after bondeds[   20]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after bondeds[   21]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after bondeds[   22]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after bondeds[   23]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after bondeds[   24]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after bondeds[   25]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after bondeds[   26]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after bondeds[   27]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after bondeds[   28]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after bondeds[   29]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after bondeds[   30]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after bondeds[   31]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after bondeds[   32]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after bondeds[   33]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after bondeds[   34]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after bondeds[   35]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after bondeds[   36]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after bondeds[   37]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after bondeds[   38]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after bondeds[   39]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after bondeds[   40]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after bondeds[   41]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after bondeds[   42]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after bondeds[   43]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after bondeds[   44]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
vir_part (3x3):
   vir_part[    0]={-2.87122e+02,  1.78161e+01, -1.69215e+02}
   vir_part[    1]={ 1.78161e+01, -1.10550e+00,  1.04999e+01}
   vir_part[    2]={-1.69215e+02,  1.04999e+01, -9.97267e+01}
fsr (2x3):
   fsr[    0]={ 3.43615e+03, -2.13216e+02,  2.02509e+03}
   fsr[    1]={-3.43615e+03,  2.13216e+02, -2.02509e+03}
flr (2x3):
   flr[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   flr[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
vir_force (3x3):
   vir_force[    0]={-2.87122e+02,  1.78161e+01, -1.69215e+02}
   vir_force[    1]={ 1.78161e+01, -1.10550e+00,  1.04999e+01}
   vir_force[    2]={-1.69215e+02,  1.04999e+01, -9.97267e+01}
dekin (3x3):
   dekin[    0]={         nan,          nan,          nan}
   dekin[    1]={         nan,          nan,          nan}
   dekin[    2]={         nan,          nan,          nan}
 ekin (3x3):
    ekin[    0]={ 1.59093e+02, -1.82889e+01,  9.92030e+01}
    ekin[    1]={-1.82889e+01,  2.10244e+00, -1.14041e+01}
    ekin[    2]={ 9.92030e+01, -1.14041e+01,  6.18584e+01}
dekin = nan, ekin = 223.054  vcm = (     nan      nan      nan)
mv = (     nan      nan      nan)
PC: pres (3x3):
   PC: pres[    0]={         nan,          nan,          nan}
   PC: pres[    1]={         nan,          nan,          nan}
   PC: pres[    2]={         nan,          nan,          nan}
PC: ekin (3x3):
   PC: ekin[    0]={         nan,          nan,          nan}
   PC: ekin[    1]={         nan,          nan,          nan}
   PC: ekin[    2]={         nan,          nan,          nan}
PC: vir  (3x3):
   PC: vir [    0]={-2.87122e+02,  1.78161e+01, -1.69215e+02}
   PC: vir [    1]={ 1.78161e+01, -1.10550e+00,  1.04999e+01}
   PC: vir [    2]={-1.69215e+02,  1.04999e+01, -9.97267e+01}
PC: box  (3x3):
   PC: box [    0]={ 6.37511e+00,  0.00000e+00,  0.00000e+00}
   PC: box [    1]={ 0.00000e+00,  6.37511e+00,  0.00000e+00}
   PC: box [    2]={ 0.00000e+00,  0.00000e+00,  6.37511e+00}
fshift after SR (45x3):
   fshift after SR[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[    3]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[    4]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[    5]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[    6]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[    7]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[    8]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[    9]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   10]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   11]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   12]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   13]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   14]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   15]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   16]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   17]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   18]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   19]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   20]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   21]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   22]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   23]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   24]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   25]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   26]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   27]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   28]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   29]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   30]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   31]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   32]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   33]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   34]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   35]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   36]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   37]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   38]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   39]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   40]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   41]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   42]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   43]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   fshift after SR[   44]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
dipcorr =    0.000     0.000     0.000
mutot   =      nan       nan       nan
Long Range corrections for Ewald interactions:
start=0,natoms=2
q2sum = 0, Vself=0
Long Range correction: Vexcl=0
Total charge correction: Vcharge=0
PME: nnodes = 1, nodeid = 0
Grid = 0x3869b30
Node=      0, pme local particles=     2


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