python动力学_一维分子动力学模拟python代码.pdf

1 #!/usr/bin/env python3

2

3 # Molecular dynamics in 1D

4

5 # import needed modules

6 import random

7 import math

8 import sys

9

10 # the main loop function

11 def main ( md):

12 time = 0.0 # initialise time

13

14 # open coordinate output files

15 cfile = open ( "coords.xyz" , "w" )

16 # open temperature output file

17 tfile = open ( "temperature.dat" , "w" )

18 tfile . write ( "# time temperature\n" )

19 # open energy output file

20 efile = open ( "energy.dat" , "w" )

21 efile . write ( "# time energy\n" )

22

23 # main MD loop

24 for t in range ( md. tsteps ):

25 print ( "# Time = " , round ( time , 2 ), " Steps = " , t , "

" ) # python3

26 en = md. force () # calculate forces

27 md. integrate ( t , en ) # integrate equations of motion

28 # print current coordinates to file

29 md. printcoords ( time , cfile )

30 # print current temperature to file

31 tfile . write ( str ( round ( time , 2))+ " " +str ( md. temp )+ "\n" )

32 # print current energy to file

33 efile . write ( str ( round ( time , 2))+ " " +str ( md. etot )+ "\n" )

34

35 time += md. dt # increase time by dt

36

37 md. statistics ( tfile , efile ) # calculate averages, SD, etc

38

39 # close output files

40 cfile . close ()

41 tfile . close ()

42 efile . close ()

43

44 class MD(