problem about example Gly_NH.dat |
- Date: 2014/12/10 23:37
- Name: Wang Yuanqing
<yuanqing.wang@riken.jp>
- Dear Ozaki-san,
Hi. I tried to obtain the resutls you gave in the work directory (Gly_NH.dat) as a excercise. However, I found my calculation result is a little differernt from your result shown in Figures in page 64 in the manuual. I am not sure where the difference is from and how it will effect my future MD calculation. Basically, I made no change to the input. The input and output will be pasted below as a reference.
INPUT
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#
# File Name
#
System.CurrrentDirectory /home/openMX/openmx3.7/work/test8/ # default=./
System.Name gly_NH
level.of.stdout 1 # default=1 (1-3)
level.of.fileout 0 # default=1 (1-3)
DATA.PATH /home/wyg1234/openMX/openmx3.7/DFT_DATA13
#
# Definition of Atomic Species
#
Species.Number 4
<Definition.of.Atomic.Species
H H5.0-s1 H_CA13
C C5.0-s1p1 C_CA13
N N5.0-s1p1 N_CA13
O O5.0-s1p1 O_CA13
Definition.of.Atomic.Species>
#
# Atoms
#
Atoms.Number 10
Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU
<Atoms.SpeciesAndCoordinates
1 C -0.555017 -0.051675 0.354086 2.0 2.0
2 C 0.815000 -0.465853 -0.137825 2.0 2.0
3 O 0.868601 -1.679578 -0.731357 3.0 3.0
4 N -0.896974 1.284812 -0.176738 2.8 2.2
5 H -1.335795 -0.760116 0.008336 0.5 0.5
6 H -0.547565 -0.109411 1.464499 0.5 0.5
7 O 1.870955 0.133646 -0.045947 3.3 2.7
8 H 1.758633 -1.867358 -1.013112 0.5 0.5
9 H -1.778440 1.565012 0.196758 0.5 0.5
10 H -0.199398 1.950523 0.081299 0.5 0.5
Atoms.SpeciesAndCoordinates>
Atoms.UnitVectors.Unit Ang # Ang|AU
#<Atoms.UnitVectors
# 10.0 0.0 0.0
# 0.0 10.0 0.0
# 0.0 0.0 12.0
#Atoms.UnitVectors>
#
# SCF or Electronic System
#
scf.XcType LDA # LDA|LSDA-CA|LSDA-PW
scf.SpinPolarization off # On|Off
scf.ElectronicTemperature 300.0 # default=300 (K)
scf.energycutoff 150 # default=150 (Ry)
scf.maxIter 60 # default=40
scf.EigenvalueSolver cluster # Recursion|Cluster|Band
scf.Kgrid 1 1 1 # means 4x4x4
scf.Mixing.Type rmm-diis # Simple|Rmm-Diis|Gr-Pulay
scf.Init.Mixing.Weight 0.10 # default=0.30
scf.Min.Mixing.Weight 0.001 # default=0.001
scf.Max.Mixing.Weight 0.200 # default=0.40
scf.Mixing.History 7 # default=5
scf.Mixing.StartPulay 5 # default=6
scf.criterion 1.0e-7 # default=1.0e-6 (Hartree)
scf.Electric.Field 0.0 0.0 0.0 # default=0 0 0 (GV/m)
scf.system.charge -1.0
scf.ProExpn.VNA on
#
# MD or Geometry Optimization
#
MD.Type NVT_NH # Nomd|Constant_Energy_MD|Opt
# Constraint_Opt|DIIS2|Constraint_DIIS2
MD.maxIter 700 # default=1
MD.TimeStep 0.2 # default=0.5 (fs)
MD.Opt.criterion 1.0e-11 # default=1.0e-4 (Hartree/bohr)
MD.Opt.DIIS_Mixing 0.1 # default=0.5
<MD.TempControl
4
1 1000.0
100 1000.0
400 700.0
700 600.0
MD.TempControl>
NH.Mass.HeatBath 30
---------------------------------------------------------------------------
OUTPUT in *.md file
-------------------------------------------------------------------------------
time= 0.000 (fs) Energy= -56.61832 (Hartree) Temperature= 1000.000 (Given Temp.= 1000.000)
time= 0.200 (fs) Energy= -56.61728 (Hartree) Temperature= 983.269 (Given Temp.= 1000.000)
time= 0.400 (fs) Energy= -56.61841 (Hartree) Temperature= 984.449 (Given Temp.= 1000.000)
time= 0.600 (fs) Energy= -56.62151 (Hartree) Temperature= 1029.637 (Given Temp.= 1000.000)
time= 0.800 (fs) Energy= -56.62623 (Hartree) Temperature= 1112.941 (Given Temp.= 1000.000)
time= 1.000 (fs) Energy= -56.63213 (Hartree) Temperature= 1225.915 (Given Temp.= 1000.000)
time= 1.200 (fs) Energy= -56.63873 (Hartree) Temperature= 1358.657 (Given Temp.= 1000.000)
time= 1.400 (fs) Energy= -56.64557 (Hartree) Temperature= 1500.981 (Given Temp.= 1000.000)
time= 1.600 (fs) Energy= -56.65223 (Hartree) Temperature= 1643.500 (Given Temp.= 1000.000)
time= 1.800 (fs) Energy= -56.65839 (Hartree) Temperature= 1778.351 (Given Temp.= 1000.000)
time= 2.000 (fs) Energy= -56.66382 (Hartree) Temperature= 1899.590 (Given Temp.= 1000.000)
time= 2.200 (fs) Energy= -56.66837 (Hartree) Temperature= 2003.273 (Given Temp.= 1000.000)
time= 2.400 (fs) Energy= -56.67200 (Hartree) Temperature= 2087.290 (Given Temp.= 1000.000)
time= 2.600 (fs) Energy= -56.67471 (Hartree) Temperature= 2151.086 (Given Temp.= 1000.000)
time= 2.800 (fs) Energy= -56.67655 (Hartree) Temperature= 2195.256 (Given Temp.= 1000.000)
time= 3.000 (fs) Energy= -56.67760 (Hartree) Temperature= 2221.298 (Given Temp.= 1000.000)
time= 3.200 (fs) Energy= -56.67797 (Hartree) Temperature= 2231.250 (Given Temp.= 1000.000)
time= 3.400 (fs) Energy= -56.67778 (Hartree) Temperature= 2227.431 (Given Temp.= 1000.000)
time= 3.600 (fs) Energy= -56.67714 (Hartree) Temperature= 2212.317 (Given Temp.= 1000.000)
time= 3.800 (fs) Energy= -56.67615 (Hartree) Temperature= 2188.330 (Given Temp.= 1000.000)
time= 4.000 (fs) Energy= -56.67493 (Hartree) Temperature= 2157.779 (Given Temp.= 1000.000)
time= 4.200 (fs) Energy= -56.67358 (Hartree) Temperature= 2122.853 (Given Temp.= 1000.000)
time= 4.400 (fs) Energy= -56.67217 (Hartree) Temperature= 2085.545 (Given Temp.= 1000.000)
time= 4.600 (fs) Energy= -56.67080 (Hartree) Temperature= 2047.758 (Given Temp.= 1000.000)
time= 4.800 (fs) Energy= -56.66955 (Hartree) Temperature= 2011.142 (Given Temp.= 1000.000)
time= 5.000 (fs) Energy= -56.66847 (Hartree) Temperature= 1977.216 (Given Temp.= 1000.000)
time= 5.200 (fs) Energy= -56.66762 (Hartree) Temperature= 1947.346 (Given Temp.= 1000.000)
time= 5.400 (fs) Energy= -56.66707 (Hartree) Temperature= 1922.753 (Given Temp.= 1000.000)
time= 5.600 (fs) Energy= -56.66686 (Hartree) Temperature= 1904.478 (Given Temp.= 1000.000)
time= 5.800 (fs) Energy= -56.66702 (Hartree) Temperature= 1893.435 (Given Temp.= 1000.000)
time= 6.000 (fs) Energy= -56.66760 (Hartree) Temperature= 1890.325 (Given Temp.= 1000.000)
time= 6.200 (fs) Energy= -56.66861 (Hartree) Temperature= 1895.689 (Given Temp.= 1000.000)
time= 6.400 (fs) Energy= -56.67007 (Hartree) Temperature= 1909.895 (Given Temp.= 1000.000)
time= 6.600 (fs) Energy= -56.67198 (Hartree) Temperature= 1933.060 (Given Temp.= 1000.000)
time= 6.800 (fs) Energy= -56.67434 (Hartree) Temperature= 1965.120 (Given Temp.= 1000.000)
time= 7.000 (fs) Energy= -56.67713 (Hartree) Temperature= 2005.739 (Given Temp.= 1000.000)
time= 7.200 (fs) Energy= -56.68032 (Hartree) Temperature= 2054.390 (Given Temp.= 1000.000)
time= 7.400 (fs) Energy= -56.68388 (Hartree) Temperature= 2110.299 (Given Temp.= 1000.000)
time= 7.600 (fs) Energy= -56.68775 (Hartree) Temperature= 2172.404 (Given Temp.= 1000.000)
time= 7.800 (fs) Energy= -56.69187 (Hartree) Temperature= 2239.414 (Given Temp.= 1000.000)
time= 8.000 (fs) Energy= -56.69616 (Hartree) Temperature= 2309.701 (Given Temp.= 1000.000)
time= 8.200 (fs) Energy= -56.70054 (Hartree) Temperature= 2381.448 (Given Temp.= 1000.000)
time= 8.400 (fs) Energy= -56.70489 (Hartree) Temperature= 2452.523 (Given Temp.= 1000.000)
time= 8.600 (fs) Energy= -56.70911 (Hartree) Temperature= 2520.515 (Given Temp.= 1000.000)
time= 8.800 (fs) Energy= -56.71306 (Hartree) Temperature= 2582.827 (Given Temp.= 1000.000)
time= 9.000 (fs) Energy= -56.71662 (Hartree) Temperature= 2636.680 (Given Temp.= 1000.000)
time= 9.200 (fs) Energy= -56.71965 (Hartree) Temperature= 2679.346 (Given Temp.= 1000.000)
time= 9.400 (fs) Energy= -56.72203 (Hartree) Temperature= 2708.103 (Given Temp.= 1000.000)
time= 9.600 (fs) Energy= -56.72364 (Hartree) Temperature= 2720.546 (Given Temp.= 1000.000)
time= 9.800 (fs) Energy= -56.72440 (Hartree) Temperature= 2714.694 (Given Temp.= 1000.000)
time= 10.000 (fs) Energy= -56.72425 (Hartree) Temperature= 2689.365 (Given Temp.= 1000.000)
time= 10.200 (fs) Energy= -56.72321 (Hartree) Temperature= 2644.338 (Given Temp.= 1000.000)
time= 10.400 (fs) Energy= -56.72134 (Hartree) Temperature= 2580.579 (Given Temp.= 1000.000)
time= 10.600 (fs) Energy= -56.71877 (Hartree) Temperature= 2500.445 (Given Temp.= 1000.000)
time= 10.800 (fs) Energy= -56.71570 (Hartree) Temperature= 2407.681 (Given Temp.= 1000.000)
time= 11.000 (fs) Energy= -56.71237 (Hartree) Temperature= 2307.349 (Given Temp.= 1000.000)
time= 11.200 (fs) Energy= -56.70910 (Hartree) Temperature= 2205.529 (Given Temp.= 1000.000)
time= 11.400 (fs) Energy= -56.70618 (Hartree) Temperature= 2108.721 (Given Temp.= 1000.000)
time= 11.600 (fs) Energy= -56.70390 (Hartree) Temperature= 2023.207 (Given Temp.= 1000.000)
time= 11.800 (fs) Energy= -56.70247 (Hartree) Temperature= 1954.315 (Given Temp.= 1000.000)
time= 12.000 (fs) Energy= -56.70204 (Hartree) Temperature= 1905.593 (Given Temp.= 1000.000)
time= 12.200 (fs) Energy= -56.70261 (Hartree) Temperature= 1878.286 (Given Temp.= 1000.000)
time= 12.400 (fs) Energy= -56.70407 (Hartree) Temperature= 1871.147 (Given Temp.= 1000.000)
time= 12.600 (fs) Energy= -56.70623 (Hartree) Temperature= 1880.622 (Given Temp.= 1000.000)
time= 12.800 (fs) Energy= -56.70882 (Hartree) Temperature= 1901.398 (Given Temp.= 1000.000)
time= 13.000 (fs) Energy= -56.71153 (Hartree) Temperature= 1927.143 (Given Temp.= 1000.000)
time= 13.200 (fs) Energy= -56.71406 (Hartree) Temperature= 1951.387 (Given Temp.= 1000.000)
time= 13.400 (fs) Energy= -56.71616 (Hartree) Temperature= 1968.304 (Given Temp.= 1000.000)
time= 13.600 (fs) Energy= -56.71764 (Hartree) Temperature= 1973.267 (Given Temp.= 1000.000)
time= 13.800 (fs) Energy= -56.71838 (Hartree) Temperature= 1963.277 (Given Temp.= 1000.000)
time= 14.000 (fs) Energy= -56.71835 (Hartree) Temperature= 1936.977 (Given Temp.= 1000.000)
time= 14.200 (fs) Energy= -56.71757 (Hartree) Temperature= 1894.688 (Given Temp.= 1000.000)
time= 14.400 (fs) Energy= -56.71615 (Hartree) Temperature= 1838.136 (Given Temp.= 1000.000)
time= 14.600 (fs) Energy= -56.71422 (Hartree) Temperature= 1770.065 (Given Temp.= 1000.000)
time= 14.800 (fs) Energy= -56.71195 (Hartree) Temperature= 1694.005 (Given Temp.= 1000.000)
time= 15.000 (fs) Energy= -56.70951 (Hartree) Temperature= 1613.656 (Given Temp.= 1000.000)
time= 15.200 (fs) Energy= -56.70705 (Hartree) Temperature= 1532.667 (Given Temp.= 1000.000)
time= 15.400 (fs) Energy= -56.70472 (Hartree) Temperature= 1454.260 (Given Temp.= 1000.000)
time= 15.600 (fs) Energy= -56.70262 (Hartree) Temperature= 1380.913 (Given Temp.= 1000.000)
time= 15.800 (fs) Energy= -56.70080 (Hartree) Temperature= 1314.264 (Given Temp.= 1000.000)
time= 16.000 (fs) Energy= -56.69930 (Hartree) Temperature= 1255.144 (Given Temp.= 1000.000)
time= 16.200 (fs) Energy= -56.69811 (Hartree) Temperature= 1203.580 (Given Temp.= 1000.000)
time= 16.400 (fs) Energy= -56.69719 (Hartree) Temperature= 1159.038 (Given Temp.= 1000.000)
time= 16.600 (fs) Energy= -56.69650 (Hartree) Temperature= 1120.580 (Given Temp.= 1000.000)
time= 16.800 (fs) Energy= -56.69599 (Hartree) Temperature= 1087.106 (Given Temp.= 1000.000)
time= 17.000 (fs) Energy= -56.69562 (Hartree) Temperature= 1057.542 (Given Temp.= 1000.000)
time= 17.200 (fs) Energy= -56.69535 (Hartree) Temperature= 1030.912 (Given Temp.= 1000.000)
time= 17.400 (fs) Energy= -56.69514 (Hartree) Temperature= 1006.502 (Given Temp.= 1000.000)
time= 17.600 (fs) Energy= -56.69500 (Hartree) Temperature= 983.851 (Given Temp.= 1000.000)
time= 17.800 (fs) Energy= -56.69491 (Hartree) Temperature= 962.765 (Given Temp.= 1000.000)
time= 18.000 (fs) Energy= -56.69488 (Hartree) Temperature= 943.272 (Given Temp.= 1000.000)
time= 18.200 (fs) Energy= -56.69492 (Hartree) Temperature= 925.557 (Given Temp.= 1000.000)
time= 18.400 (fs) Energy= -56.69506 (Hartree) Temperature= 909.898 (Given Temp.= 1000.000)
time= 18.600 (fs) Energy= -56.69530 (Hartree) Temperature= 896.630 (Given Temp.= 1000.000)
time= 18.800 (fs) Energy= -56.69566 (Hartree) Temperature= 886.063 (Given Temp.= 1000.000)
time= 19.000 (fs) Energy= -56.69617 (Hartree) Temperature= 878.471 (Given Temp.= 1000.000)
time= 19.200 (fs) Energy= -56.69682 (Hartree) Temperature= 874.031 (Given Temp.= 1000.000)
time= 19.400 (fs) Energy= -56.69762 (Hartree) Temperature= 872.809 (Given Temp.= 1000.000)
time= 19.600 (fs) Energy= -56.69857 (Hartree) Temperature= 874.783 (Given Temp.= 1000.000)
time= 19.800 (fs) Energy= -56.69966 (Hartree) Temperature= 879.788 (Given Temp.= 1000.000)
....
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Best,
Yuanqing Wang
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Re: problem about example Gly_NH.dat