ATC version 2.0, date: Sep1
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10709 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
rjones
@ -1,43 +1,51 @@
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LAMMPS (27 Aug 2013)
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LAMMPS (30 Aug 2013)
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log schrodinger-poisson2d_Jconstraint.log
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#variable iter equal 2 # need two for potential to affect density
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variable iter1 equal 4 # NOTE <<<<
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variable iter2 equal 25 # NOTE <<<<
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variable r equal 1
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variable nx equal 12 # 30 40 10
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variable mx equal 4 # 4 2
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#variable ny equal ${nx}
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variable ny equal 12 # 30 40
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variable my equal 8 # 12 6
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variable nz equal 1
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variable hx equal 1.0
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variable hy equal ${hx}*${nx}/${ny}
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variable hy equal 1*${nx}/${ny}
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variable hy equal 1*12/${ny}
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variable hy equal 1*12/12
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variable l equal -${hx}*${nx}
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variable l equal -1*${nx}
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variable l equal -1*12
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variable u equal ${hx}*${nx}
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variable u equal 1*${nx}
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variable u equal 1*12
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# physical parameters ===========================
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variable T equal 300
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variable n0 equal 0.00007
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variable J0 equal 40.0
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variable Vs equal 1.0
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# geometric parameters ===========================
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#variable Vg equal 1.0
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variable iter1 equal 4
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variable iter2 equal 25
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variable r equal 10 # run
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variable nx equal 12 # elements in x
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variable ny equal 12 # elements in y
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variable nz equal 1 # elements in z
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variable mx equal 4 # wire elements in x
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variable my equal 3 # wire elements in y
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variable n1 equal floor(${nx}/4) # number of elements in lower vaccuum
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variable n1 equal floor(12/4)
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variable n2 equal 3*${n1} # number of elements in lower vaccuum + wire
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variable n2 equal 3*3
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variable hx equal 1.0 # mesh size in x
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variable hy equal ${hx} # mesh size in y
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variable hy equal 1
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variable l equal -${hx}*${nx} # box lower bound
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variable l equal -1*${nx}
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variable l equal -1*12
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variable u equal ${hx}*${nx} # box upper bound
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variable u equal 1*${nx}
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variable u equal 1*12
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variable w equal ${hy}*${my}
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variable w equal 1*${my}
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variable w equal 1*8
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variable w equal 1*3
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variable q equal ${hx}*${mx}
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variable q equal 1*${mx}
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variable q equal 1*4
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variable y equal ${nx}+1-${mx}
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variable y equal 12+1-${mx}
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variable y equal 12+1-4
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variable T equal 300
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variable S equal 1
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variable n0 equal 0.00007
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variable J0 equal 40.0 # 100.0 40.0
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variable Vs equal 1.0
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#variable Vg equal 1.0 # 10.0 0.0
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variable y equal ${nx}+1-${mx}
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variable y equal 12+1-${mx}
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variable y equal 12+1-4
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variable w1 equal (-$w-$l)/($u-$l)
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variable w1 equal (-3-$l)/($u-$l)
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variable w1 equal (-3--12)/($u-$l)
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variable w1 equal (-3--12)/(12-$l)
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variable w1 equal (-3--12)/(12--12)
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variable w2 equal 1-${w1}
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variable w2 equal 1-0.375
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variable tol equal 0.01
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#################################################
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#================================================
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atom_style atomic
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timestep 0.001
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boundary f f f
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@ -53,8 +61,7 @@ Created orthogonal box = (-19.0488 -19.0488 0) to (19.0488 19.0488 1.5874)
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2 by 2 by 1 MPI processor grid
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mass * 12.01
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atom_modify sort 0 1
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# ID group atc PhysicsType ParameterFile
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fix AtC all atc drift_diffusion-schrodinger-slice SiVacuum_ddm_schrodinger.mat
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fix AtC all atc drift_diffusion-schrodinger-slice SiVacuum_ddm_schrodinger.mat
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Constructing ATC transfer (drift_diffusion-schrodinger-slice) with parameter file SiVacuum_ddm_schrodinger.mat
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ATC: version 2.0
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ATC: peratom PE compute created with ID: 3
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@ -66,6 +73,7 @@ Constructing ATC transfer (drift_diffusion-schrodinger-slice) with parameter fil
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ATC: creating drift_diffusion extrinsic model
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ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e
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ATC: WARNING: material units metal do not match lammps
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[pharsalus:03148] *** Process received signal ***
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ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e
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ATC: WARNING: material units metal do not match lammps
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ATC: 2 materials defined from SiVacuum_ddm_schrodinger.mat
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@ -74,138 +82,82 @@ Constructing ATC transfer (drift_diffusion-schrodinger-slice) with parameter fil
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ATC: WARNING: must use a unit system where: [Energy/force] = [Length] and [charge] = e
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ATC: WARNING: material units metal do not match lammps
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ATC: 2 materials defined from SiVacuum_ddm_schrodinger.mat
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# ID part keywords nx ny nz region
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fix_modify AtC mesh create ${nx} ${ny} ${nz} BOX f f p
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fix_modify AtC mesh create 12 ${ny} ${nz} BOX f f p
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fix_modify AtC mesh create 12 12 ${nz} BOX f f p
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fix_modify AtC mesh create 12 12 1 BOX f f p
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ATC: created uniform mesh with 338 nodes, 169 unique nodes, and 144 elements
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# surfaces & regions
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variable a equal $l-${tol}
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variable a equal -12-${tol}
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variable a equal -12-0.010000000000000000208
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variable b equal $l+$q+${tol}
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variable b equal -12+$q+${tol}
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variable b equal -12+4+${tol}
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variable b equal -12+4+0.010000000000000000208
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variable c equal -$w-${tol}
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variable c equal -8-${tol}
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variable c equal -8-0.010000000000000000208
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variable d equal $w+${tol}
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variable d equal 8+${tol}
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variable d equal 8+0.010000000000000000208
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variable e equal $l+$q-${tol}
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variable e equal -12+$q-${tol}
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variable e equal -12+4-${tol}
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variable e equal -12+4-0.010000000000000000208
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fix_modify AtC mesh create_nodeset bot -INF INF $a $b -INF INF
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fix_modify AtC mesh create_nodeset bot -INF INF -12.009999999999999787 $b -INF INF
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fix_modify AtC mesh create_nodeset bot -INF INF -12.009999999999999787 -7.9900000000000002132 -INF INF
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ATC: created nodeset bot with 39 nodes
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fix_modify AtC mesh create_nodeset lbc $a $b -INF INF -INF INF
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fix_modify AtC mesh create_nodeset lbc -12.009999999999999787 $b -INF INF -INF INF
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fix_modify AtC mesh create_nodeset lbc -12.009999999999999787 -7.9900000000000002132 -INF INF -INF INF
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ATC: created nodeset lbc with 39 nodes
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variable a equal $u-$q-${tol}
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variable a equal 12-$q-${tol}
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variable a equal 12-4-${tol}
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variable a equal 12-4-0.010000000000000000208
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variable b equal $u+${tol}
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variable b equal 12+${tol}
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variable b equal 12+0.010000000000000000208
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variable e equal $u-$q+${tol}
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variable e equal 12-$q+${tol}
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variable e equal 12-4+${tol}
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variable e equal 12-4+0.010000000000000000208
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fix_modify AtC mesh create_nodeset top -INF INF $a $b -INF INF
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fix_modify AtC mesh create_nodeset top -INF INF 7.9900000000000002132 $b -INF INF
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fix_modify AtC mesh create_nodeset top -INF INF 7.9900000000000002132 12.009999999999999787 -INF INF
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ATC: created nodeset top with 39 nodes
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fix_modify AtC mesh create_nodeset rbc $a $b -INF INF -INF INF
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fix_modify AtC mesh create_nodeset rbc 7.9900000000000002132 $b -INF INF -INF INF
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fix_modify AtC mesh create_nodeset rbc 7.9900000000000002132 12.009999999999999787 -INF INF -INF INF
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ATC: created nodeset rbc with 39 nodes
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variable a equal -$w-${tol}
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variable a equal -8-${tol}
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variable a equal -8-0.010000000000000000208
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variable b equal $w+${tol}
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variable b equal 8+${tol}
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variable b equal 8+0.010000000000000000208
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variable c equal $l+$q-${tol}
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variable c equal -12+$q-${tol}
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variable c equal -12+4-${tol}
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variable c equal -12+4-0.010000000000000000208
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variable d equal $u-$q+${tol}
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variable d equal 12-$q+${tol}
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variable d equal 12-4+${tol}
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variable d equal 12-4+0.010000000000000000208
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fix_modify AtC mesh create_elementset wire $c $d $a $b -INF INF
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fix_modify AtC mesh create_elementset wire -8.0099999999999997868 $d $a $b -INF INF
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fix_modify AtC mesh create_elementset wire -8.0099999999999997868 8.0099999999999997868 $a $b -INF INF
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fix_modify AtC mesh create_elementset wire -8.0099999999999997868 8.0099999999999997868 -8.0099999999999997868 $b -INF INF
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fix_modify AtC mesh create_elementset wire -8.0099999999999997868 8.0099999999999997868 -8.0099999999999997868 8.0099999999999997868 -INF INF
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ATC: created elementset wire with 64 elements
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fix_modify AtC mesh create_nodeset wire $c $d $a $b -INF INF
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fix_modify AtC mesh create_nodeset wire -8.0099999999999997868 $d $a $b -INF INF
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fix_modify AtC mesh create_nodeset wire -8.0099999999999997868 8.0099999999999997868 $a $b -INF INF
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fix_modify AtC mesh create_nodeset wire -8.0099999999999997868 8.0099999999999997868 -8.0099999999999997868 $b -INF INF
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fix_modify AtC mesh create_nodeset wire -8.0099999999999997868 8.0099999999999997868 -8.0099999999999997868 8.0099999999999997868 -INF INF
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ATC: created nodeset wire with 81 nodes
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variable e equal $c+2*${tol}
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variable e equal -8.0099999999999997868+2*${tol}
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variable e equal -8.0099999999999997868+2*0.010000000000000000208
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variable f equal $c+${tol}
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variable f equal -8.0099999999999997868+${tol}
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variable f equal -8.0099999999999997868+0.010000000000000000208
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fix_modify AtC mesh create_nodeset lwire $c $e $a $b -INF INF
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fix_modify AtC mesh create_nodeset lwire -8.0099999999999997868 $e $a $b -INF INF
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fix_modify AtC mesh create_nodeset lwire -8.0099999999999997868 -7.9900000000000002132 $a $b -INF INF
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fix_modify AtC mesh create_nodeset lwire -8.0099999999999997868 -7.9900000000000002132 -8.0099999999999997868 $b -INF INF
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fix_modify AtC mesh create_nodeset lwire -8.0099999999999997868 -7.9900000000000002132 -8.0099999999999997868 8.0099999999999997868 -INF INF
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ATC: created nodeset lwire with 9 nodes
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fix_modify AtC mesh create_faceset lwire $f INF $a $b -INF INF
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fix_modify AtC mesh create_faceset lwire -8 INF $a $b -INF INF
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fix_modify AtC mesh create_faceset lwire -8 INF -8.0099999999999997868 $b -INF INF
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fix_modify AtC mesh create_faceset lwire -8 INF -8.0099999999999997868 8.0099999999999997868 -INF INF
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ATC: created faceset lwire with 8 faces
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variable e equal $d-2*${tol}
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variable e equal 8.0099999999999997868-2*${tol}
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variable e equal 8.0099999999999997868-2*0.010000000000000000208
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variable f equal $d-${tol}
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variable f equal 8.0099999999999997868-${tol}
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variable f equal 8.0099999999999997868-0.010000000000000000208
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fix_modify AtC mesh create_nodeset rwire $e $d $a $b -INF INF
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fix_modify AtC mesh create_nodeset rwire 7.9900000000000002132 $d $a $b -INF INF
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fix_modify AtC mesh create_nodeset rwire 7.9900000000000002132 8.0099999999999997868 $a $b -INF INF
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fix_modify AtC mesh create_nodeset rwire 7.9900000000000002132 8.0099999999999997868 -8.0099999999999997868 $b -INF INF
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fix_modify AtC mesh create_nodeset rwire 7.9900000000000002132 8.0099999999999997868 -8.0099999999999997868 8.0099999999999997868 -INF INF
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ATC: created nodeset rwire with 9 nodes
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fix_modify AtC mesh create_faceset rwire -INF $f $a $b -INF INF
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fix_modify AtC mesh create_faceset rwire -INF 8 $a $b -INF INF
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fix_modify AtC mesh create_faceset rwire -INF 8 -8.0099999999999997868 $b -INF INF
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fix_modify AtC mesh create_faceset rwire -INF 8 -8.0099999999999997868 8.0099999999999997868 -INF INF
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ATC: created faceset rwire with 8 faces
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variable e equal $a+2*${tol}
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variable e equal -8.0099999999999997868+2*${tol}
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variable e equal -8.0099999999999997868+2*0.010000000000000000208
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fix_modify AtC mesh create_nodeset bwire $c $d $a $e -INF INF
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fix_modify AtC mesh create_nodeset bwire -8.0099999999999997868 $d $a $e -INF INF
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fix_modify AtC mesh create_nodeset bwire -8.0099999999999997868 8.0099999999999997868 $a $e -INF INF
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fix_modify AtC mesh create_nodeset bwire -8.0099999999999997868 8.0099999999999997868 -8.0099999999999997868 $e -INF INF
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fix_modify AtC mesh create_nodeset bwire -8.0099999999999997868 8.0099999999999997868 -8.0099999999999997868 -7.9900000000000002132 -INF INF
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ATC: created nodeset bwire with 9 nodes
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variable e equal $b-2*${tol}
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variable e equal 8.0099999999999997868-2*${tol}
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variable e equal 8.0099999999999997868-2*0.010000000000000000208
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fix_modify AtC mesh create_nodeset twire $c $d $e $b -INF INF
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fix_modify AtC mesh create_nodeset twire -8.0099999999999997868 $d $e $b -INF INF
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fix_modify AtC mesh create_nodeset twire -8.0099999999999997868 8.0099999999999997868 $e $b -INF INF
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fix_modify AtC mesh create_nodeset twire -8.0099999999999997868 8.0099999999999997868 7.9900000000000002132 $b -INF INF
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fix_modify AtC mesh create_nodeset twire -8.0099999999999997868 8.0099999999999997868 7.9900000000000002132 8.0099999999999997868 -INF INF
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ATC: created nodeset twire with 9 nodes
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# new material
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fix_modify AtC material wire Si
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# simplify
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fix_modify AtC extrinsic one_dimensional x wire $y
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fix_modify AtC extrinsic one_dimensional x wire 9
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ERROR: Illegal fix_modify command (../fix.cpp:104)
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fix_modify AtC mesh create ${nx} ${ny} ${nz} BOX f f p dy position-number-density 0 0 4.0 ${w1} ${n1} 1. ${w2} ${n2} 1. 1 ${ny} 4.0
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fix_modify AtC mesh create 12 ${ny} ${nz} BOX f f p dy position-number-density 0 0 4.0 ${w1} ${n1} 1. ${w2} ${n2} 1. 1 ${ny} 4.0
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fix_modify AtC mesh create 12 12 ${nz} BOX f f p dy position-number-density 0 0 4.0 ${w1} ${n1} 1. ${w2} ${n2} 1. 1 ${ny} 4.0
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fix_modify AtC mesh create 12 12 1 BOX f f p dy position-number-density 0 0 4.0 ${w1} ${n1} 1. ${w2} ${n2} 1. 1 ${ny} 4.0
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fix_modify AtC mesh create 12 12 1 BOX f f p dy position-number-density 0 0 4.0 0.375 ${n1} 1. ${w2} ${n2} 1. 1 ${ny} 4.0
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fix_modify AtC mesh create 12 12 1 BOX f f p dy position-number-density 0 0 4.0 0.375 3 1. ${w2} ${n2} 1. 1 ${ny} 4.0
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fix_modify AtC mesh create 12 12 1 BOX f f p dy position-number-density 0 0 4.0 0.375 3 1. 0.625 ${n2} 1. 1 ${ny} 4.0
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fix_modify AtC mesh create 12 12 1 BOX f f p dy position-number-density 0 0 4.0 0.375 3 1. 0.625 9 1. 1 ${ny} 4.0
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fix_modify AtC mesh create 12 12 1 BOX f f p dy position-number-density 0 0 4.0 0.375 3 1. 0.625 9 1. 1 12 4.0
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[pharsalus:03148] Signal: Segmentation fault (11)
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[pharsalus:03148] Signal code: Address not mapped (1)
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[pharsalus:03148] Failing at address: (nil)
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[pharsalus:03149] *** Process received signal ***
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[pharsalus:03149] Signal: Segmentation fault (11)
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[pharsalus:03149] Signal code: Address not mapped (1)
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[pharsalus:03149] Failing at address: (nil)
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[pharsalus:03151] *** Process received signal ***
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[pharsalus:03150] *** Process received signal ***
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[pharsalus:03150] Signal: Segmentation fault (11)
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[pharsalus:03150] Signal code: Address not mapped (1)
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[pharsalus:03150] Failing at address: (nil)
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[pharsalus:03151] Signal: Segmentation fault (11)
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[pharsalus:03151] Signal code: Address not mapped (1)
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[pharsalus:03151] Failing at address: (nil)
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[pharsalus:03148] [ 0] /lib64/libpthread.so.0() [0x3e7ce0f500]
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[pharsalus:03148] [ 1] ../../../lmp_openmpi(_ZN3ATC9FE_Engine6modifyEiPPc+0x9d7) [0xae409f]
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[pharsalus:03148] [ 2] ../../../lmp_openmpi(_ZN3ATC10ATC_Method6modifyEiPPc+0x5e) [0xa9f036]
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[pharsalus:03148] [ 3] ../../../lmp_openmpi(_ZN3ATC12ATC_Coupling6modifyEiPPc+0x1c37) [0xbb3b0d]
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[pharsalus:03148] [ 4] ../../../lmp_openmpi(_ZN3ATC18ATC_CouplingEnergy6modifyEiPPc+0x30f) [0xa7c631]
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[pharsalus:03148] [ 5] ../../../lmp_openmpi(_ZN9LAMMPS_NS6FixATC12modify_paramEiPPc+0x1d) [0x696fad]
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[pharsalus:03148] [ 6] ../../../lmp_openmpi(_ZN9LAMMPS_NS3Fix13modify_paramsEiPPc+0xb9) [0x691659]
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[pharsalus:03148] [ 7] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input15execute_commandEv+0xcab) [0x79fe8b]
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[pharsalus:03148] [ 8] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input4fileEv+0x63c) [0x7a196c]
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[pharsalus:03148] [ 9] ../../../lmp_openmpi(main+0x49) [0x7af929]
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[pharsalus:03148] [10] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3e7c21ecdd]
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[pharsalus:03148] [11] ../../../lmp_openmpi() [0x53b429]
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[pharsalus:03148] *** End of error message ***
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[pharsalus:03149] [ 0] /lib64/libpthread.so.0() [0x3e7ce0f500]
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[pharsalus:03150] [ 0] /lib64/libpthread.so.0() [0x3e7ce0f500]
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[pharsalus:03150] [ 1] ../../../lmp_openmpi(_ZN3ATC9FE_Engine6modifyEiPPc+0x9d7) [0xae409f]
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[pharsalus:03150] [ 2] ../../../lmp_openmpi(_ZN3ATC10ATC_Method6modifyEiPPc+0x5e) [0xa9f036]
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[pharsalus:03150] [ 3] ../../../lmp_openmpi(_ZN3ATC12ATC_Coupling6modifyEiPPc+0x1c37) [0xbb3b0d]
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[pharsalus:03150] [ 4] ../../../lmp_openmpi(_ZN3ATC18ATC_CouplingEnergy6modifyEiPPc+0x30f) [0xa7c631]
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[pharsalus:03150] [ 5] ../../../lmp_openmpi(_ZN9LAMMPS_NS6FixATC12modify_paramEiPPc+0x1d) [0x696fad]
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[pharsalus:03150] [ 6] ../../../lmp_openmpi(_ZN9LAMMPS_NS3Fix13modify_paramsEiPPc+0xb9) [0x691659]
|
||||
[pharsalus:03150] [ 7] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input15execute_commandEv+0xcab) [0x79fe8b]
|
||||
[pharsalus:03150] [ 8] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input4fileEv+0x63c) [0x7a196c]
|
||||
[pharsalus:03150] [ 9] ../../../lmp_openmpi(main+0x49) [0x7af929]
|
||||
[pharsalus:03150] [10] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3e7c21ecdd]
|
||||
[pharsalus:03150] [11] ../../../lmp_openmpi() [0x53b429]
|
||||
[pharsalus:03150] *** End of error message ***
|
||||
[pharsalus:03151] [ 0] /lib64/libpthread.so.0() [0x3e7ce0f500]
|
||||
[pharsalus:03149] [ 1] ../../../lmp_openmpi(_ZN3ATC9FE_Engine6modifyEiPPc+0x9d7) [0xae409f]
|
||||
[pharsalus:03149] [ 2] ../../../lmp_openmpi(_ZN3ATC10ATC_Method6modifyEiPPc+0x5e) [0xa9f036]
|
||||
[pharsalus:03149] [ 3] ../../../lmp_openmpi(_ZN3ATC12ATC_Coupling6modifyEiPPc+0x1c37) [0xbb3b0d]
|
||||
[pharsalus:03149] [ 4] ../../../lmp_openmpi(_ZN3ATC18ATC_CouplingEnergy6modifyEiPPc+0x30f) [0xa7c631]
|
||||
[pharsalus:03149] [ 5] ../../../lmp_openmpi(_ZN9LAMMPS_NS6FixATC12modify_paramEiPPc+0x1d) [0x696fad]
|
||||
[pharsalus:03149] [ 6] ../../../lmp_openmpi(_ZN9LAMMPS_NS3Fix13modify_paramsEiPPc+0xb9) [0x691659]
|
||||
[pharsalus:03149] [ 7] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input15execute_commandEv+0xcab) [0x79fe8b]
|
||||
[pharsalus:03149] [ 8] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input4fileEv+0x63c) [0x7a196c]
|
||||
[pharsalus:03149] [ 9] ../../../lmp_openmpi(main+0x49) [0x7af929]
|
||||
[pharsalus:03149] [10] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3e7c21ecdd]
|
||||
[pharsalus:03149] [11] ../../../lmp_openmpi() [0x53b429]
|
||||
[pharsalus:03149] *** End of error message ***
|
||||
[pharsalus:03151] [ 1] ../../../lmp_openmpi(_ZN3ATC9FE_Engine6modifyEiPPc+0x9d7) [0xae409f]
|
||||
[pharsalus:03151] [ 2] ../../../lmp_openmpi(_ZN3ATC10ATC_Method6modifyEiPPc+0x5e) [0xa9f036]
|
||||
[pharsalus:03151] [ 3] ../../../lmp_openmpi(_ZN3ATC12ATC_Coupling6modifyEiPPc+0x1c37) [0xbb3b0d]
|
||||
[pharsalus:03151] [ 4] ../../../lmp_openmpi(_ZN3ATC18ATC_CouplingEnergy6modifyEiPPc+0x30f) [0xa7c631]
|
||||
[pharsalus:03151] [ 5] ../../../lmp_openmpi(_ZN9LAMMPS_NS6FixATC12modify_paramEiPPc+0x1d) [0x696fad]
|
||||
[pharsalus:03151] [ 6] ../../../lmp_openmpi(_ZN9LAMMPS_NS3Fix13modify_paramsEiPPc+0xb9) [0x691659]
|
||||
[pharsalus:03151] [ 7] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input15execute_commandEv+0xcab) [0x79fe8b]
|
||||
[pharsalus:03151] [ 8] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input4fileEv+0x63c) [0x7a196c]
|
||||
[pharsalus:03151] [ 9] ../../../lmp_openmpi(main+0x49) [0x7af929]
|
||||
[pharsalus:03151] [10] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3e7c21ecdd]
|
||||
[pharsalus:03151] [11] ../../../lmp_openmpi() [0x53b429]
|
||||
[pharsalus:03151] *** End of error message ***
|
||||
--------------------------------------------------------------------------
|
||||
mpirun noticed that process rank 1 with PID 3149 on node pharsalus exited on signal 11 (Segmentation fault).
|
||||
--------------------------------------------------------------------------
|
||||
|
||||
Reference in New Issue
Block a user