1from numpy import genfromtxt, fromstring, reshape, zeros, sum as nsum 

2 

3from urllib import request as urllibr 

4from urllib import error as urlerror 

5 

6from mango.io import read_data, separater 

7from mango.constants import c 

8 

9 

10def initpos(lj_num, sigma, location=None, boxsize=0, xyz=False): 

11 """ 

12 Get the positions of particles. 

13 

14 Also can collect magnetisations and momentums 

15 

16 Can be user specified with location or downloaded using urllj 

17 

18 Downloaded positions from standard LJ stable structures 

19 

20 An (extended) xyz file can be specified the last frame in the file 

21 will be used 

22 

23 Parameters 

24 ---------- 

25 lj_num: int 

26 Number of molecules 

27 sigma: float 

28 distance between particle centres 

29 location: string 

30 location of file to load 

31 boxsize: float 

32 periodic boxsize (only required for 2 particle periodic systems) 

33 

34 """ 

35 if isinstance(location, str): 

36 molecules, response, xyz = posfile(location, sigma) 

37 elif lj_num == 1: 

38 response = zeros(3) 

39 elif lj_num == 2: 

40 response = twoparticlesinabox(boxsize, sigma) 

41 elif lj_num > 150: 

42 c.Error("{}{}{}".format("F This is only setup for under 150 particles\n", 

43 "for larger systems please specify a position file.\n", 

44 "Larger structures may be available at http://doye.chem.ox.ac.uk/jon/structures/LJ/")) 

45 else: 

46 # TODO proper sigma conversion 

47 response = urllj(lj_num) * sigma[:, None] 

48 

49 return separater(response), xyz 

50 

51 

52def twoparticlesinabox(boxsize, sigma): 

53 """ 

54 Set location of 2 particles. 

55 

56 put two particles next to each other 

57 """ 

58 response = zeros((2, 3)) 

59 avdist = nsum(sigma) / 2 

60 if boxsize >= nsum(sigma): 

61 response[0, :] = [-avdist / 2, 0, 0] 

62 response[1, :] = [avdist / 2, 0, 0] 

63 else: 

64 response[0, :] = [-boxsize / 8, 0, 0] 

65 response[1, :] = [boxsize / 8, 0, 0] 

66 return response 

67 

68 

69def posfile(location, sigma, xyz=False, com=0): 

70 """ 

71 Open position file. 

72 

73 Reads first two lines to check 

74 if xyz open xyz otherwise read as unscaled coordinates 

75 """ 

76 lines = [] 

77 try: 

78 with open(location, "r") as file: 

79 for n, l in enumerate(file): 79 ↛ 89line 79 didn't jump to line 89, because the loop on line 79 didn't complete

80 if l.startswith(("#", "\n")): 

81 com += 1 

82 elif n < (2 + com): 

83 lines += [l.split()] 

84 else: 

85 break 

86 except OSError: 

87 c.Error(f"F Unable to find location file '{location}'") 

88 

89 if len(lines[0]) != len(lines[1]): 

90 # TODO more secure xyz check (check lines[0][0] is int?) 

91 molecules, response = read_data(location.rsplit(".", 1)[0], "xyz").xyzread() 

92 response = response[-1] 

93 xyz = True 

94 else: 

95 # TODO Currently this doesn't check if the file is prescaled. XYZ is the safe option in this case 

96 # TODO Catch errors here from genfromtxt 

97 response = genfromtxt(location) * sigma[:, None] 

98 molecules = None 

99 

100 return molecules, response, xyz 

101 

102 

103def urllj(lj_num, url="http://doye.chem.ox.ac.uk/jon/structures/LJ/points/{}"): 

104 """ 

105 Download lj configuration. 

106 

107 Default url is http://doye.chem.ox.ac.uk/jon/structures/LJ/ 

108 

109 Parameters 

110 ---------- 

111 lj_num: int 

112 Number of molecules 

113 url: str 

114 url with formatting {} for lj_num 

115 

116 """ 

117 try: 

118 url = url.format(lj_num) 

119 response = urllibr.urlopen(url).read().decode('utf-8') 

120 response = fromstring(" ".join(response.split("\n")), sep=" ") 

121 response = reshape(response, (lj_num, 3)) 

122 except urlerror.HTTPError: 

123 c.Error("F Not found online for {} molecules".format(lj_num)) 

124 except urlerror.URLError: 

125 c.Error("F Internet Connection Error, Particle locations cannot be downloaded") 

126 else: 

127 return response 

128 

129 

130if __name__ == '__main__': 

131 pass