[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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