made latte.in compatible with v1.1.1 and updated log files

This commit is contained in:
Steven J. Plimpton 2018-06-21 11:10:29 -06:00
parent 3e58ebea4f
commit cbfb751e92
13 changed files with 524 additions and 986 deletions

View File

@ -129,12 +129,14 @@ region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE :pre
so that you do not have to define (or discard) a temporary variable X. so that you do not have to define (or discard) a temporary variable X.
Additionally, the "immediate" expression may be followed by a colon, Additionally, the "immediate" variable expression may be followed by a
followed by a C-style format string, e.g. "%f" or "%.10g", which must be colon, followed by a C-style format string, e.g. ":%f" or ":%.10g".
appropriate for formatting a double-precision floating-point value. The The format string must be appropriate for a double-precision
format string will be used to output the result of the variable evaluation, floating-point value. The format string is used to output the result
so you do not have to define a temporary "format-style variable"_variable.html. of the variable expression evaluation. If a format string is not
This may be used for formatting print output: specified a high-precision "%.20g" is used as the default.
This can be useful for formatting print output to a desired precion:
print "Final energy per atom: $(pe/atoms:%10.3f) eV/atom" :pre print "Final energy per atom: $(pe/atoms:%10.3f) eV/atom" :pre

View File

@ -35,8 +35,11 @@ fix 5 all dt/reset 5 NULL 0.001 0.5 emax 30 units box :pre
[Description:] [Description:]
Reset the timestep size every N steps during a run, so that no atom Reset the timestep size every N steps during a run, so that no atom
moves further than Xmax, based on current atom velocities and forces, moves further than the specified {Xmax} distance, based on current
and (optionally) no atom's kinetic energy changes by more than Emax. atom velocities and forces. Optionally an additional criterion is
imposed by the {emax} keyword, so that no atom's kinetic energy
changes by more than the specified {Emax}.
This can be useful when starting from a configuration with overlapping This can be useful when starting from a configuration with overlapping
atoms, where forces will be large. Or it can be useful when running atoms, where forces will be large. Or it can be useful when running
an impact simulation where one or more high-energy atoms collide with an impact simulation where one or more high-energy atoms collide with
@ -52,9 +55,12 @@ current velocity and force. Since performing this calculation exactly
would require the solution to a quartic equation, a cheaper estimate would require the solution to a quartic equation, a cheaper estimate
is generated. The estimate is conservative in that the atom's is generated. The estimate is conservative in that the atom's
displacement is guaranteed not to exceed {Xmax}, though it may be displacement is guaranteed not to exceed {Xmax}, though it may be
smaller. Also, if the {Emax} value is given, for each atom, the smaller.
timestep is limited to a value that allows the atom's kinetic energy
to change by at most {Emax}. In addition if the {emax} keyword is used, the specified {Emax} value
is enforced as a limit on how much an atom's kinetic energy can
change. If the timestep required is even smaller than for the {Xmax}
displacement, then the smaller timestep is used.
Given this putative timestep for each atom, the minimum timestep value Given this putative timestep for each atom, the minimum timestep value
across all atoms is computed. Then the {Tmin} and {Tmax} bounds are across all atoms is computed. Then the {Tmin} and {Tmax} bounds are
@ -93,4 +99,5 @@ minimization"_minimize.html.
[Default:] [Default:]
The option defaults is units = lattice, and no kinetic energy change limit. The option defaults are units = lattice, and no emax kinetic energy
limit.

View File

@ -305,9 +305,15 @@ string parameter is quoted.
For the {format} style, an equal-style variable is specified along For the {format} style, an equal-style variable is specified along
with a C-style format string, e.g. "%f" or "%.10g", which must be with a C-style format string, e.g. "%f" or "%.10g", which must be
appropriate for formatting a double-precision floating-point value. appropriate for formatting a double-precision floating-point value.
This allows an equal-style variable to be formatted specifically for The default format is "%.15g". This variable style allows an
output as a string, e.g. by the "print"_print.html command, if the equal-style variable to be formatted precisely when it is evaluated.
default format "%.15g" has too much precision.
If you simply wish to print a variable value with desired precision to
the screen or logfile via the "print"_print.html or "fix
print"_fix_print.html commands, you can also do this by specifying an
"immediate" variable with a trailing colon and format string, as part
of the string argument of those commands. This is explained in
"Section 3.2"_Section_commands.html#cmd_2.
For the {getenv} style, a single string is assigned to the variable For the {getenv} style, a single string is assigned to the variable
which should be the name of an environment variable. When the which should be the name of an environment variable. When the

View File

@ -37,5 +37,6 @@ thermo_style custom step temp pe etotal press
# minimization # minimization
thermo 10 thermo 10
min_style fire
minimize 1.0e-9 1.0e-9 500 500 min_style fire
minimize 1.0e-4 1.0e-4 500 500

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@ -9,7 +9,7 @@ LATTE INPUT FILE
#General controls #General controls
CONTROL{ CONTROL{
XCONTROL= 1 xControl= 1
BASISTYPE= NONORTHO BASISTYPE= NONORTHO
PARAMPATH= "./TBparam" PARAMPATH= "./TBparam"
KBT= 0.0 KBT= 0.0
@ -31,4 +31,3 @@ CONTROL{
XBODISORDER= 5 XBODISORDER= 5
KON= 0 KON= 0
} }

View File

@ -1,406 +0,0 @@
The log file for latte_lib
CONTROL{ }
WARNING: variable JobName= is missing. I will use a default value instead ...
WARNING: variable PARAMPATH= is missing. I will use a default value instead ...
WARNING: variable DEBUGON= is missing. I will use a default value instead ...
WARNING: variable FERMIM= is missing. I will use a default value instead ...
WARNING: variable CGORLIB= is missing. I will use a default value instead ...
WARNING: variable NORECS= is missing. I will use a default value instead ...
WARNING: variable VDWON= is missing. I will use a default value instead ...
WARNING: variable ORDERNMOL= is missing. I will use a default value instead ...
WARNING: variable LCNON= is missing. I will use a default value instead ...
WARNING: variable LCNITER= is missing. I will use a default value instead ...
WARNING: variable MDON= is missing. I will use a default value instead ...
WARNING: variable PBCON= is missing. I will use a default value instead ...
WARNING: variable RESTART= is missing. I will use a default value instead ...
WARNING: variable NGPU= is missing. I will use a default value instead ...
WARNING: variable COMPFORCE= is missing. I will use a default value instead ...
WARNING: variable DOSFIT= is missing. I will use a default value instead ...
WARNING: variable INTS2FIT= is missing. I will use a default value instead ...
WARNING: variable NFITSTEP= is missing. I will use a default value instead ...
WARNING: variable QFIT= is missing. I will use a default value instead ...
WARNING: variable PPFITON= is missing. I will use a default value instead ...
WARNING: variable ALLFITON= is missing. I will use a default value instead ...
WARNING: variable PPSTEP= is missing. I will use a default value instead ...
WARNING: variable BISTEP= is missing. I will use a default value instead ...
WARNING: variable PP2FIT= is missing. I will use a default value instead ...
WARNING: variable BINT2FIT= is missing. I will use a default value instead ...
WARNING: variable PPNMOL= is missing. I will use a default value instead ...
WARNING: variable PPNGEOM= is missing. I will use a default value instead ...
WARNING: variable PARREP= is missing. I will use a default value instead ...
WARNING: variable VERBOSE= is missing. I will use a default value instead ...
WARNING: variable MIXER= is missing. I will use a default value instead ...
WARNING: variable RESTARTLIB= is missing. I will use a default value instead ...
WARNING: variable CGTOL= is missing. I will use a default value instead ...
WARNING: variable ELEC_ETOL= is missing. I will use a default value instead ...
WARNING: variable COULACC= is missing. I will use a default value instead ...
WARNING: variable COULCUT= is missing. I will use a default value instead ...
WARNING: variable COULR1= is missing. I will use a default value instead ...
WARNING: variable CHTOL= is missing. I will use a default value instead ...
WARNING: variable BETA= is missing. I will use a default value instead ...
WARNING: variable MCSIGMA= is missing. I will use a default value instead ...
WARNING: variable PPBETA= is missing. I will use a default value instead ...
WARNING: variable PPSIGMA= is missing. I will use a default value instead ...
WARNING: variable ER= is missing. I will use a default value instead ...
WARNING: variable INITIALIZED= is missing. I will use a default value instead ...
############### Parameters used for this run ################
CONTROL{
xControl= 1
DEBUGON= 0
FERMIM= 6
CGORLIB= 1
NORECS= 1
ENTROPYKIND= 1
PPOTON= 1
VDWON= 0
SPINON= 0
ELECTRO= 1
ELECMETH= 0
MAXSCF= 450
MINSP2ITER= 22
FULLQCONV= 1
QITER= 3
ORDERNMOL= 0
SPARSEON= 1
THRESHOLDON= 1
FILLINSTOP= 100
BLKSZ= 4
MSPARSE= 1500
LCNON= 0
LCNITER= 4
RELAX= 0
MAXITER= 100000
MDON= 1
PBCON= 1
RESTART= 0
CHARGE= 0
XBO= 1
XBODISON= 1
XBODISORDER= 5
NGPU= 2
KON= 0
COMPFORCE= 1
DOSFIT= 0
INTS2FIT= 1
NFITSTEP= 5000
QFIT= 0
PPFITON= 0
ALLFITON= 0
PPSTEP= 500
BISTEP= 500
PP2FIT= 2
BINT2FIT= 6
PPNMOL= 10
PPNGEOM= 200
PARREP= 0
VERBOSE= 0
MIXER= 0
RESTARTLIB= 0
CGTOL= 9.9999999747524271E-007
KBT= 0.0000000000000000
SPINTOL= 1.0000000000000000E-004
ELEC_ETOL= 1.0000000474974513E-003
ELEC_QTOL= 1.0000000000000000E-008
COULACC= 9.9999999747524271E-007
COULCUT= -500.00000000000000
COULR1= 500.00000000000000
BREAKTOL= 9.9999999999999995E-007
QMIX= 0.25000000000000000
SPINMIX= 0.25000000000000000
MDMIX= 0.25000000000000000
NUMTHRESH= 9.9999999999999995E-007
CHTOL= 9.9999997764825821E-003
SKIN= 1.0000000000000000
RLXFTOL= 9.9999999999999995E-008
BETA= 1000.0000000000000
MCSIGMA= 0.20000000298023224
PPBETA= 1000.0000000000000
PPSIGMA= 9.9999997764825821E-003
ER= 1.0000000000000000
JobName=MyJob
BASISTYPE=NONORTHO
SP2CONV=REL
RELAXTYPE=SD
PARAMPATH=./TBparam
COORDSFILE=./coords.dat
INITIALIZED= F
}
./TBparam/electrons.dat
MDCONTROL{ }
WARNING: variable RNDIST= is missing. I will use a default value instead ...
WARNING: variable SEEDINIT= is missing. I will use a default value instead ...
WARNING: variable NPTTYPE= is missing. I will use a default value instead ...
WARNING: variable UDNEIGH= is missing. I will use a default value instead ...
WARNING: variable DUMPFREQ= is missing. I will use a default value instead ...
WARNING: variable RSFREQ= is missing. I will use a default value instead ...
WARNING: variable WRTFREQ= is missing. I will use a default value instead ...
WARNING: variable TOINITTEMP5= is missing. I will use a default value instead ...
WARNING: variable THERMPER= is missing. I will use a default value instead ...
WARNING: variable THERMRUN= is missing. I will use a default value instead ...
WARNING: variable NVTON= is missing. I will use a default value instead ...
WARNING: variable NPTON= is missing. I will use a default value instead ...
WARNING: variable AVEPER= is missing. I will use a default value instead ...
WARNING: variable SEED= is missing. I will use a default value instead ...
WARNING: variable SHOCKON= is missing. I will use a default value instead ...
WARNING: variable SHOCKSTART= is missing. I will use a default value instead ...
WARNING: variable SHOCKDIR= is missing. I will use a default value instead ...
WARNING: variable MDADAPT= is missing. I will use a default value instead ...
WARNING: variable GETHUG= is missing. I will use a default value instead ...
WARNING: variable RSLEVEL= is missing. I will use a default value instead ...
WARNING: variable DT= is missing. I will use a default value instead ...
WARNING: variable TEMPERATURE= is missing. I will use a default value instead ...
WARNING: variable FRICTION= is missing. I will use a default value instead ...
WARNING: variable PTARGET= is missing. I will use a default value instead ...
WARNING: variable UPARTICLE= is missing. I will use a default value instead ...
WARNING: variable USHOCK= is missing. I will use a default value instead ...
WARNING: variable C0= is missing. I will use a default value instead ...
WARNING: variable E0= is missing. I will use a default value instead ...
WARNING: variable V0= is missing. I will use a default value instead ...
WARNING: variable P0= is missing. I will use a default value instead ...
WARNING: variable DUMMY= is missing. I will use a default value instead ...
############### Parameters used for this run ################
MDCONTROL{
MAXITER= -1
UDNEIGH= 1
DUMPFREQ= 250
RSFREQ= 500
WRTFREQ= 25
TOINITTEMP5= 1
THERMPER= 500
THERMRUN= 50000
NVTON= 0
NPTON= 0
AVEPER= 1000
SEED= 54
SHOCKON= 0
SHOCKSTART= 100000
SHOCKDIR= 1
MDADAPT= 0
GETHUG= 0
RSLEVEL= 0
DT= 0.25000000000000000
TEMPERATURE= 300.00000000000000
FRICTION= 1000.0000000000000
PTARGET= 0.0000000000000000
UPARTICLE= 500.00000000000000
USHOCK= -4590.0000000000000
C0= 1300.0000000000000
E0= -795.72497558593750
V0= 896.98486328125000
P0= 8.3149001002311707E-002
RNDIST=GAUSSIAN
SEEDINIT=UNIFORM
NPTTYPE=ISO
DUMMY= F
}
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View File

@ -1,406 +0,0 @@
The log file for latte_lib
CONTROL{ }
WARNING: variable JobName= is missing. I will use a default value instead ...
WARNING: variable PARAMPATH= is missing. I will use a default value instead ...
WARNING: variable DEBUGON= is missing. I will use a default value instead ...
WARNING: variable FERMIM= is missing. I will use a default value instead ...
WARNING: variable CGORLIB= is missing. I will use a default value instead ...
WARNING: variable NORECS= is missing. I will use a default value instead ...
WARNING: variable VDWON= is missing. I will use a default value instead ...
WARNING: variable ORDERNMOL= is missing. I will use a default value instead ...
WARNING: variable LCNON= is missing. I will use a default value instead ...
WARNING: variable LCNITER= is missing. I will use a default value instead ...
WARNING: variable MDON= is missing. I will use a default value instead ...
WARNING: variable PBCON= is missing. I will use a default value instead ...
WARNING: variable RESTART= is missing. I will use a default value instead ...
WARNING: variable NGPU= is missing. I will use a default value instead ...
WARNING: variable COMPFORCE= is missing. I will use a default value instead ...
WARNING: variable DOSFIT= is missing. I will use a default value instead ...
WARNING: variable INTS2FIT= is missing. I will use a default value instead ...
WARNING: variable NFITSTEP= is missing. I will use a default value instead ...
WARNING: variable QFIT= is missing. I will use a default value instead ...
WARNING: variable PPFITON= is missing. I will use a default value instead ...
WARNING: variable ALLFITON= is missing. I will use a default value instead ...
WARNING: variable PPSTEP= is missing. I will use a default value instead ...
WARNING: variable BISTEP= is missing. I will use a default value instead ...
WARNING: variable PP2FIT= is missing. I will use a default value instead ...
WARNING: variable BINT2FIT= is missing. I will use a default value instead ...
WARNING: variable PPNMOL= is missing. I will use a default value instead ...
WARNING: variable PPNGEOM= is missing. I will use a default value instead ...
WARNING: variable PARREP= is missing. I will use a default value instead ...
WARNING: variable VERBOSE= is missing. I will use a default value instead ...
WARNING: variable MIXER= is missing. I will use a default value instead ...
WARNING: variable RESTARTLIB= is missing. I will use a default value instead ...
WARNING: variable CGTOL= is missing. I will use a default value instead ...
WARNING: variable ELEC_ETOL= is missing. I will use a default value instead ...
WARNING: variable COULACC= is missing. I will use a default value instead ...
WARNING: variable COULCUT= is missing. I will use a default value instead ...
WARNING: variable COULR1= is missing. I will use a default value instead ...
WARNING: variable CHTOL= is missing. I will use a default value instead ...
WARNING: variable BETA= is missing. I will use a default value instead ...
WARNING: variable MCSIGMA= is missing. I will use a default value instead ...
WARNING: variable PPBETA= is missing. I will use a default value instead ...
WARNING: variable PPSIGMA= is missing. I will use a default value instead ...
WARNING: variable ER= is missing. I will use a default value instead ...
WARNING: variable INITIALIZED= is missing. I will use a default value instead ...
############### Parameters used for this run ################
CONTROL{
xControl= 1
DEBUGON= 0
FERMIM= 6
CGORLIB= 1
NORECS= 1
ENTROPYKIND= 1
PPOTON= 1
VDWON= 0
SPINON= 0
ELECTRO= 1
ELECMETH= 0
MAXSCF= 450
MINSP2ITER= 22
FULLQCONV= 1
QITER= 3
ORDERNMOL= 0
SPARSEON= 1
THRESHOLDON= 1
FILLINSTOP= 100
BLKSZ= 4
MSPARSE= 1500
LCNON= 0
LCNITER= 4
RELAX= 0
MAXITER= 100000
MDON= 1
PBCON= 1
RESTART= 0
CHARGE= 0
XBO= 1
XBODISON= 1
XBODISORDER= 5
NGPU= 2
KON= 0
COMPFORCE= 1
DOSFIT= 0
INTS2FIT= 1
NFITSTEP= 5000
QFIT= 0
PPFITON= 0
ALLFITON= 0
PPSTEP= 500
BISTEP= 500
PP2FIT= 2
BINT2FIT= 6
PPNMOL= 10
PPNGEOM= 200
PARREP= 0
VERBOSE= 0
MIXER= 0
RESTARTLIB= 0
CGTOL= 9.9999999747524271E-007
KBT= 0.0000000000000000
SPINTOL= 1.0000000000000000E-004
ELEC_ETOL= 1.0000000474974513E-003
ELEC_QTOL= 1.0000000000000000E-008
COULACC= 9.9999999747524271E-007
COULCUT= -500.00000000000000
COULR1= 500.00000000000000
BREAKTOL= 9.9999999999999995E-007
QMIX= 0.25000000000000000
SPINMIX= 0.25000000000000000
MDMIX= 0.25000000000000000
NUMTHRESH= 9.9999999999999995E-007
CHTOL= 9.9999997764825821E-003
SKIN= 1.0000000000000000
RLXFTOL= 9.9999999999999995E-008
BETA= 1000.0000000000000
MCSIGMA= 0.20000000298023224
PPBETA= 1000.0000000000000
PPSIGMA= 9.9999997764825821E-003
ER= 1.0000000000000000
JobName=MyJob
BASISTYPE=NONORTHO
SP2CONV=REL
RELAXTYPE=SD
PARAMPATH=./TBparam
COORDSFILE=./coords.dat
INITIALIZED= F
}
./TBparam/electrons.dat
MDCONTROL{ }
WARNING: variable RNDIST= is missing. I will use a default value instead ...
WARNING: variable SEEDINIT= is missing. I will use a default value instead ...
WARNING: variable NPTTYPE= is missing. I will use a default value instead ...
WARNING: variable UDNEIGH= is missing. I will use a default value instead ...
WARNING: variable DUMPFREQ= is missing. I will use a default value instead ...
WARNING: variable RSFREQ= is missing. I will use a default value instead ...
WARNING: variable WRTFREQ= is missing. I will use a default value instead ...
WARNING: variable TOINITTEMP5= is missing. I will use a default value instead ...
WARNING: variable THERMPER= is missing. I will use a default value instead ...
WARNING: variable THERMRUN= is missing. I will use a default value instead ...
WARNING: variable NVTON= is missing. I will use a default value instead ...
WARNING: variable NPTON= is missing. I will use a default value instead ...
WARNING: variable AVEPER= is missing. I will use a default value instead ...
WARNING: variable SEED= is missing. I will use a default value instead ...
WARNING: variable SHOCKON= is missing. I will use a default value instead ...
WARNING: variable SHOCKSTART= is missing. I will use a default value instead ...
WARNING: variable SHOCKDIR= is missing. I will use a default value instead ...
WARNING: variable MDADAPT= is missing. I will use a default value instead ...
WARNING: variable GETHUG= is missing. I will use a default value instead ...
WARNING: variable RSLEVEL= is missing. I will use a default value instead ...
WARNING: variable DT= is missing. I will use a default value instead ...
WARNING: variable TEMPERATURE= is missing. I will use a default value instead ...
WARNING: variable FRICTION= is missing. I will use a default value instead ...
WARNING: variable PTARGET= is missing. I will use a default value instead ...
WARNING: variable UPARTICLE= is missing. I will use a default value instead ...
WARNING: variable USHOCK= is missing. I will use a default value instead ...
WARNING: variable C0= is missing. I will use a default value instead ...
WARNING: variable E0= is missing. I will use a default value instead ...
WARNING: variable V0= is missing. I will use a default value instead ...
WARNING: variable P0= is missing. I will use a default value instead ...
WARNING: variable DUMMY= is missing. I will use a default value instead ...
############### Parameters used for this run ################
MDCONTROL{
MAXITER= -1
UDNEIGH= 1
DUMPFREQ= 250
RSFREQ= 500
WRTFREQ= 25
TOINITTEMP5= 1
THERMPER= 500
THERMRUN= 50000
NVTON= 0
NPTON= 0
AVEPER= 1000
SEED= 54
SHOCKON= 0
SHOCKSTART= 100000
SHOCKDIR= 1
MDADAPT= 0
GETHUG= 0
RSLEVEL= 0
DT= 0.25000000000000000
TEMPERATURE= 300.00000000000000
FRICTION= 1000.0000000000000
PTARGET= 0.0000000000000000
UPARTICLE= 500.00000000000000
USHOCK= -4590.0000000000000
C0= 1300.0000000000000
E0= -795.72497558593750
V0= 896.98486328125000
P0= 8.3149001002311707E-002
RNDIST=GAUSSIAN
SEEDINIT=UNIFORM
NPTTYPE=ISO
DUMMY= F
}
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LIBCALLS 64
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -116.89550228683500 12.167344616151606 0.0000000000000000 3.1339818740985033
LIBCALLS 65
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -116.14487351718614 11.479908971904207 0.0000000000000000 3.1610748652786995
LIBCALLS 66
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -115.43917601644073 10.856755674815151 0.0000000000000000 3.1869042214936911
LIBCALLS 67
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -114.79630542914917 10.307930318909381 0.0000000000000000 3.2107896540741994
LIBCALLS 68
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -114.23118520942130 9.8399835349372715 0.0000000000000000 3.2322754400486997
LIBCALLS 69
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -113.75645667348935 9.4568320682906393 0.0000000000000000 3.2508686207040949
LIBCALLS 70
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -113.38220191758144 9.1605931457952803 0.0000000000000000 3.2662052636761625
LIBCALLS 71
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -113.11651461323785 8.9523172650382463 0.0000000000000000 3.2778578161416640
LIBCALLS 72
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -112.96490300473705 8.8325758589074610 0.0000000000000000 3.2856373346184280
LIBCALLS 73
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -112.93101384064629 8.8018792766284140 0.0000000000000000 3.2893376450243901
LIBCALLS 74
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -113.01657988020818 8.8609123616606951 0.0000000000000000 3.2887786713823335
LIBCALLS 75
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -113.22122702505257 9.0105808374276855 0.0000000000000000 3.2838806809960044
LIBCALLS 76
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -113.54255812607462 9.2518619694254909 0.0000000000000000 3.2746170980725564
LIBCALLS 77
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -113.97595003796289 9.5854566564348804 0.0000000000000000 3.2610495238703536
LIBCALLS 78
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -114.51445216471619 10.011242264155852 0.0000000000000000 3.2433103887056101
LIBCALLS 79
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -115.14835871057100 10.527538366743359 0.0000000000000000 3.2217018278255036
LIBCALLS 80
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -115.86512618816471 11.130220642932718 0.0000000000000000 3.1966546818138903
LIBCALLS 81
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -116.64916580084807 11.811746817430592 0.0000000000000000 3.1687509169099037
LIBCALLS 82
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -117.48162972769103 12.560201275368994 0.0000000000000000 3.1387793445426220
LIBCALLS 83
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -118.34080112521505 13.358507776606700 0.0000000000000000 3.1076005013428842
LIBCALLS 84
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -119.20206255799097 14.183999576696523 0.0000000000000000 3.0762625451098367
LIBCALLS 85
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -120.03875955947012 15.008549885925623 0.0000000000000000 3.0458557745855401
LIBCALLS 86
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -120.82281065648482 15.799445052997022 0.0000000000000000 3.0175902569508040
LIBCALLS 87
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -121.52638053902615 16.521105731022047 0.0000000000000000 2.9925661691795984
LIBCALLS 88
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -122.12297505178334 17.137613862262167 0.0000000000000000 2.9718740800190462
LIBCALLS 89
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -122.58954501498538 17.615819283155187 0.0000000000000000 2.9563457612376758
LIBCALLS 90
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -122.90768650775293 17.928615619513138 0.0000000000000000 2.9466637669908935
LIBCALLS 91
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -123.06510359278838 18.057846294334183 0.0000000000000000 2.9432773288779130
LIBCALLS 92
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -123.05653995529889 17.996310208253615 0.0000000000000000 2.9463730237128352
LIBCALLS 93
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -122.88443709725219 17.748486968230267 0.0000000000000000 2.9557418006906766
LIBCALLS 94
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -122.55804625906457 17.329857520510558 0.0000000000000000 2.9710497340098647
LIBCALLS 95
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -122.09316916859144 16.764989519228550 0.0000000000000000 2.9916333369114647
LIBCALLS 96
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -121.51050736457847 16.084787212290774 0.0000000000000000 3.0167038701280053
LIBCALLS 97
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -120.83475656442954 15.323405512114466 0.0000000000000000 3.0451593241515909
LIBCALLS 98
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -120.09218577985371 14.515310319889227 0.0000000000000000 3.0759929793994090
LIBCALLS 99
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -119.30969482099719 13.692843612811791 0.0000000000000000 3.1081426979179545
LIBCALLS 100
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -118.51358261827596 12.884492109393644 0.0000000000000000 3.1405428597121636

View File

@ -1,152 +0,0 @@
LAMMPS (1 Sep 2017)
# simple water model with LATTE
units metal
atom_style full
atom_modify sort 0 0.0 # turn off sorting of the coordinates
read_data data.water
orthogonal box = (0 0 0) to (6.267 6.267 6.267)
1 by 1 by 1 MPI processor grid
reading atoms ...
24 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
# replicate system if requested
variable x index 1
variable y index 1
variable z index 1
variable nrep equal v_x*v_y*v_z
if "${nrep} > 1" then "replicate $x $y $z"
# initialize system
velocity all create 0.0 87287 loop geom
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
timestep 0.00025
fix 1 all nve
fix 2 all latte NULL
fix_modify 2 energy yes
thermo_style custom step temp pe etotal press
# minimization
thermo 10
min_style fire
minimize 1.0e-9 1.0e-9 500 500
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.629 | 5.629 | 5.629 Mbytes
Step Temp PotEng TotEng Press
0 0 -104.95614 -104.95614 48229.712
10 349.44219 -105.50971 -104.47083 62149.591
20 1253.6752 -107.00898 -103.28182 116444.44
30 134.63588 -107.56184 -107.16157 59854.143
40 2.4043703 -108.15301 -108.14586 32685.77
50 162.13426 -108.40551 -107.92349 62104.273
60 134.03149 -108.70118 -108.30271 49400.525
70 64.159014 -108.78034 -108.5896 37243.303
80 240.49926 -109.10766 -108.39266 42158.884
90 0.60467192 -109.61818 -109.61639 14107.515
100 1.4691163 -109.65556 -109.65119 21596.775
110 30.500628 -109.69267 -109.602 16104.639
120 120.62379 -109.83749 -109.47888 9474.971
130 8.4742975 -109.99986 -109.97467 10104.102
140 3.4732679 -110.01209 -110.00176 11990.442
150 24.749482 -110.04313 -109.96955 10851.569
160 4.1106505 -110.13288 -110.12066 8257.3969
170 0.0065628716 -110.18061 -110.18059 7876.8748
180 2.0542078 -110.1837 -110.17759 7996.0533
190 20.134782 -110.21071 -110.15085 7556.1811
200 2.3397267 -110.3244 -110.31745 3767.062
210 4.3544709 -110.34438 -110.33143 4889.145
220 1.1872367 -110.37457 -110.37104 4162.6543
230 2.2798399 -110.38081 -110.37403 4321.0943
240 11.835907 -110.39611 -110.36092 4187.5757
250 0.13741849 -110.41453 -110.41412 3720.7527
260 4.2283185 -110.42036 -110.40779 3743.3494
270 0.47243724 -110.44349 -110.44208 3172.1866
280 0.06090137 -110.45428 -110.4541 3065.9348
290 5.3413962 -110.46285 -110.44697 3121.2924
300 8.2032986 -110.48519 -110.4608 2705.5001
310 2.0783529 -110.48807 -110.48189 2740.7989
320 16.629185 -110.51002 -110.46058 2581.7434
330 0.19723065 -110.53444 -110.53385 1942.0228
340 6.2758334 -110.54361 -110.52495 1924.0965
350 1.4539052 -110.59108 -110.58676 -449.41056
360 0.0514233 -110.60143 -110.60128 1284.8259
370 1.7240145 -110.60394 -110.59881 1468.0004
380 13.28516 -110.62337 -110.58387 1573.4714
390 1.2247432 -110.63525 -110.63161 1113.4557
400 0.3946985 -110.63694 -110.63576 1083.0801
410 2.9831433 -110.641 -110.63213 1112.419
420 0.068550589 -110.66029 -110.66009 897.09211
430 0.83976182 -110.66259 -110.66009 918.69832
440 4.4760907 -110.66844 -110.65513 915.24435
450 1.2841241 -110.67482 -110.671 953.30422
460 2.5707455 -110.68509 -110.67745 775.21273
470 0.99721544 -110.68646 -110.6835 812.74984
480 6.8379261 -110.69468 -110.67435 787.9705
490 0.18134438 -110.69628 -110.69574 675.52792
500 2.0946523 -110.69918 -110.69295 696.82065
Loop time of 31.775 on 1 procs for 500 steps with 24 atoms
884.8% CPU use with 1 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
-104.95614332 -110.698546127 -110.699182193
Force two-norm initial, final = 19.119 0.234621
Force max component initial, final = 11.7759 0.0903198
Final line search alpha, max atom move = 0 0
Iterations, force evaluations = 500 500
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00016952 | 0.00016952 | 0.00016952 | 0.0 | 0.00
Bond | 2.8372e-05 | 2.8372e-05 | 2.8372e-05 | 0.0 | 0.00
Neigh | 3.0994e-05 | 3.0994e-05 | 3.0994e-05 | 0.0 | 0.00
Comm | 0.00060034 | 0.00060034 | 0.00060034 | 0.0 | 0.00
Output | 0.00057817 | 0.00057817 | 0.00057817 | 0.0 | 0.00
Modify | 31.771 | 31.771 | 31.771 | 0.0 | 99.99
Other | | 0.002469 | | | 0.01
Nlocal: 24 ave 24 max 24 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 71 ave 71 max 71 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 27 ave 27 max 27 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 27
Ave neighs/atom = 1.125
Ave special neighs/atom = 0
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:31

View File

@ -0,0 +1,170 @@
LAMMPS (11 May 2018)
# Simple water model with LATTE
units metal
atom_style full
atom_modify sort 0 0.0 # turn off sorting of the coordinates
read_data data.graphene.boxrel
triclinic box = (0 0 0) to (10 8 20) with tilt (4.89859e-16 1.22465e-15 1.22465e-15)
1 by 1 by 1 MPI processor grid
reading atoms ...
32 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
# replicate system if requested
variable x index 1
variable y index 1
variable z index 1
variable nrep equal v_x*v_y*v_z
if "${nrep} > 1" then "replicate $x $y $z"
# initialize system
velocity all create 0.0 87287 loop geom
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
timestep 0.00025
fix 1 all box/relax iso 0.0 vmax 0.001
fix 2 all latte NULL
fix_modify 2 energy yes
thermo_style custom etotal
# minimization
thermo 1
fix 3 all print 1 "Total Energy ="
min_style cg
min_modify dmax 0.1
min_modify line quadratic
minimize 1.0e-4 1.0e-4 10000 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 11 9 20
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/newton/tri
stencil: half/bin/3d/newton/tri
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.779 | 6.779 | 6.779 Mbytes
TotEng
-247.46002
-247.67224
-247.87937
-248.08148
-248.27865
-248.47096
-248.65851
-248.84137
-249.01964
-249.19342
-249.36281
-249.52791
-249.68883
-249.8457
-249.99865
-250.1478
-250.29332
-250.43535
-250.57409
-250.70972
-250.84247
-250.97258
-251.10035
-251.2261
-251.35021
-251.47314
-251.59543
-251.71776
-251.84096
-251.9661
-252.09459
-252.22833
-252.37003
-252.52371
-252.69578
-252.89752
-253.15197
-253.52044
-254.31418
-255.6175
-256.8162
-258.1227
-259.38401
-260.74831
-262.03991
-263.5463
-264.70486
-267.69144
-267.88682
-269.03519
-270.60187
-270.65382
-270.74279
-271.55883
-271.81248
-271.87529
-273.01494
-273.23948
-273.28719
-273.35272
-273.41591
-273.46274
-273.54755
-273.58318
-273.73111
-273.75754
Loop time of 39.4155 on 1 procs for 65 steps with 32 atoms
1582.4% CPU use with 1 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-247.460020579 -273.731112592 -273.757543461
Force two-norm initial, final = 201.608 9.43485
Force max component initial, final = 188.924 2.41297
Final line search alpha, max atom move = 0.000223273 0.00053875
Iterations, force evaluations = 65 65
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00012159 | 0.00012159 | 0.00012159 | 0.0 | 0.00
Bond | 5.1975e-05 | 5.1975e-05 | 5.1975e-05 | 0.0 | 0.00
Neigh | 4.1962e-05 | 4.1962e-05 | 4.1962e-05 | 0.0 | 0.00
Comm | 0.00026107 | 0.00026107 | 0.00026107 | 0.0 | 0.00
Output | 0.0013342 | 0.0013342 | 0.0013342 | 0.0 | 0.00
Modify | 39.412 | 39.412 | 39.412 | 0.0 | 99.99
Other | | 0.00127 | | | 0.00
Nlocal: 32 ave 32 max 32 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 100 ave 100 max 100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 48 ave 48 max 48 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 48
Ave neighs/atom = 1.5
Ave special neighs/atom = 0
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:40

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@ -0,0 +1,103 @@
LAMMPS (11 May 2018)
# simple sucrose model with LATTE
units metal
atom_style full
atom_modify sort 0 0.0 # turn off sorting of the coordinates
read_data data.sucrose
orthogonal box = (0 0 0) to (17.203 18.009 21.643)
1 by 1 by 1 MPI processor grid
reading atoms ...
45 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
# replicate system if requested
variable x index 1
variable y index 1
variable z index 1
variable nrep equal v_x*v_y*v_z
if "${nrep} > 1" then "replicate $x $y $z"
# initialize system
velocity all create 0.0 87287 loop geom
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
timestep 0.00025
fix 1 all nve
fix 2 all latte NULL
fix_modify 2 energy yes
thermo_style custom step temp pe etotal press
# dynamics
thermo 10
run 100
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 18 19 22
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 0.5064 | 0.5064 | 0.5064 Mbytes
Step Temp PotEng TotEng Press
0 0 -251.26617 -251.26617 16.617234
10 0.025263709 -251.26631 -251.26617 8.0576708
20 0.034232467 -251.26636 -251.26617 1.6673442
30 0.059079556 -251.2665 -251.26617 11.058458
40 0.055499766 -251.26648 -251.26617 14.837775
50 0.058499509 -251.2665 -251.26617 6.7183113
60 0.071094535 -251.26657 -251.26617 6.6133687
70 0.084309439 -251.26665 -251.26617 12.372721
80 0.1089929 -251.26679 -251.26617 8.8355516
90 0.11378257 -251.26681 -251.26617 5.1177922
100 0.13003966 -251.26691 -251.26617 8.2431185
Loop time of 27.8386 on 1 procs for 100 steps with 45 atoms
Performance: 0.078 ns/day, 309.318 hours/ns, 3.592 timesteps/s
1799.6% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 8.3685e-05 | 8.3685e-05 | 8.3685e-05 | 0.0 | 0.00
Bond | 7.4148e-05 | 7.4148e-05 | 7.4148e-05 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00016689 | 0.00016689 | 0.00016689 | 0.0 | 0.00
Output | 0.00032401 | 0.00032401 | 0.00032401 | 0.0 | 0.00
Modify | 27.837 | 27.837 | 27.837 | 0.0 |100.00
Other | | 0.0005403 | | | 0.00
Nlocal: 45 ave 45 max 45 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 59 ave 59 max 59 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 59
Ave neighs/atom = 1.31111
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:28

View File

@ -0,0 +1,103 @@
LAMMPS (11 May 2018)
# simple water model with LATTE
units metal
atom_style full
atom_modify sort 0 0.0 # turn off sorting of the coordinates
read_data data.water
orthogonal box = (0 0 0) to (6.267 6.267 6.267)
1 by 1 by 1 MPI processor grid
reading atoms ...
24 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
# replicate system if requested
variable x index 1
variable y index 1
variable z index 1
variable nrep equal v_x*v_y*v_z
if "${nrep} > 1" then "replicate $x $y $z"
# initialize system
velocity all create 0.0 87287 loop geom
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
timestep 0.00025
fix 1 all nve
fix 2 all latte NULL
fix_modify 2 energy yes
thermo_style custom step temp pe etotal press
# dynamics
thermo 10
run 100
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.629 | 5.629 | 5.629 Mbytes
Step Temp PotEng TotEng Press
0 0 -104.95594 -104.95594 48236.006
10 336.5303 -105.96026 -104.95976 97997.303
20 529.06385 -106.53021 -104.95731 131520.49
30 753.62616 -107.1995 -104.95898 49297.371
40 716.6565 -107.08802 -104.95741 28307.272
50 824.04417 -107.40822 -104.95835 102167.48
60 933.56056 -107.73478 -104.95932 92508.792
70 851.18518 -107.48766 -104.95711 13993.28
80 999.80265 -107.93146 -104.95906 36700.417
90 998.77707 -107.92569 -104.95634 107233.7
100 1281.4446 -108.76961 -104.95989 49703.193
Loop time of 10.6388 on 1 procs for 100 steps with 24 atoms
Performance: 0.203 ns/day, 118.209 hours/ns, 9.400 timesteps/s
6459.7% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.6771e-05 | 7.6771e-05 | 7.6771e-05 | 0.0 | 0.00
Bond | 7.5817e-05 | 7.5817e-05 | 7.5817e-05 | 0.0 | 0.00
Neigh | 4.6015e-05 | 4.6015e-05 | 4.6015e-05 | 0.0 | 0.00
Comm | 0.00031829 | 0.00031829 | 0.00031829 | 0.0 | 0.00
Output | 0.00032401 | 0.00032401 | 0.00032401 | 0.0 | 0.00
Modify | 10.637 | 10.637 | 10.637 | 0.0 | 99.99
Other | | 0.00052 | | | 0.00
Nlocal: 24 ave 24 max 24 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 77 ave 77 max 77 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 31 ave 31 max 31 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 31
Ave neighs/atom = 1.29167
Ave special neighs/atom = 0
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:10

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@ -0,0 +1,108 @@
LAMMPS (11 May 2018)
# simple water model with LATTE
units metal
atom_style full
atom_modify sort 0 0.0 # turn off sorting of the coordinates
read_data data.water
orthogonal box = (0 0 0) to (6.267 6.267 6.267)
1 by 1 by 1 MPI processor grid
reading atoms ...
24 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
# replicate system if requested
variable x index 1
variable y index 1
variable z index 1
variable nrep equal v_x*v_y*v_z
if "${nrep} > 1" then "replicate $x $y $z"
# initialize system
velocity all create 0.0 87287 loop geom
pair_style zero 1.0
pair_coeff * *
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
timestep 0.00025
fix 1 all nve
fix 2 all latte NULL
fix_modify 2 energy yes
thermo_style custom step temp pe etotal press
# minimization
thermo 10
min_style fire
minimize 1.0e-4 1.0e-4 500 500
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2
ghost atom cutoff = 2
binsize = 1, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.629 | 5.629 | 5.629 Mbytes
Step Temp PotEng TotEng Press
0 0 -104.95594 -104.95594 48236.006
10 349.4534 -105.50948 -104.47056 62157.729
20 1253.6636 -107.00863 -103.28151 116456.71
30 134.64051 -107.56155 -107.16127 59864.196
40 2.4044989 -108.1527 -108.14556 32695.648
47 137.26885 -108.30413 -107.89603 60177.442
Loop time of 6.42677 on 1 procs for 47 steps with 24 atoms
6481.9% CPU use with 1 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-104.955944301 -108.302982895 -108.304126127
Force two-norm initial, final = 19.119 3.44609
Force max component initial, final = 11.7758 1.3408
Final line search alpha, max atom move = 0 0
Iterations, force evaluations = 47 47
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.6253e-05 | 4.6253e-05 | 4.6253e-05 | 0.0 | 0.00
Bond | 3.1948e-05 | 3.1948e-05 | 3.1948e-05 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00014353 | 0.00014353 | 0.00014353 | 0.0 | 0.00
Output | 0.00012302 | 0.00012302 | 0.00012302 | 0.0 | 0.00
Modify | 6.426 | 6.426 | 6.426 | 0.0 | 99.99
Other | | 0.0004699 | | | 0.01
Nlocal: 24 ave 24 max 24 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 71 ave 71 max 71 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 37 ave 37 max 37 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 37
Ave neighs/atom = 1.54167
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:06

View File

@ -497,7 +497,7 @@ void Input::substitute(char *&str, char *&str2, int &max, int &max2, int flag)
beyond = ptr + strlen(var) + 3; beyond = ptr + strlen(var) + 3;
value = variable->retrieve(var); value = variable->retrieve(var);
// immediate variable between parenthesis, e.g. $(1/2) // immediate variable between parenthesis, e.g. $(1/3) or $(1/3:%.6g)
} else if (*(ptr+1) == '(') { } else if (*(ptr+1) == '(') {
var = ptr+2; var = ptr+2;
@ -516,17 +516,20 @@ void Input::substitute(char *&str, char *&str2, int &max, int &max2, int flag)
if (var[i] == '\0') error->one(FLERR,"Invalid immediate variable"); if (var[i] == '\0') error->one(FLERR,"Invalid immediate variable");
var[i] = '\0'; var[i] = '\0';
beyond = ptr + strlen(var) + 3; beyond = ptr + strlen(var) + 3;
// check if an inline format specifier was given
// check if an inline format specifier was appended with a colon
char fmtstr[64] = "%.20g"; char fmtstr[64] = "%.20g";
char *fmtflag; char *fmtflag;
if ((fmtflag=strrchr(var, ':')) && (fmtflag[1]=='%')) { if ((fmtflag=strrchr(var, ':')) && (fmtflag[1]=='%')) {
strncpy(fmtstr,&fmtflag[1],sizeof(fmtstr)-1); strncpy(fmtstr,&fmtflag[1],sizeof(fmtstr)-1);
*fmtflag='\0'; *fmtflag='\0';
} }
sprintf(immediate,fmtstr,variable->compute_equal(var)); sprintf(immediate,fmtstr,variable->compute_equal(var));
value = immediate; value = immediate;
// single character variable name, e.g. $a // single character variable name, e.g. $a
} else { } else {
var = ptr; var = ptr;