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lamaGOET_full_release.sh
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lamaGOET_full_release.sh
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#!/bin/bash
Encoding=UTF-8
export LC_NUMERIC="en_US.UTF-8"
SPACEGROUP(){
SPACEGROUPARRAY=(
"1 = p 1 = p 1 "
"2 = p -1 = -p 1 "
"3:b = p 1 2 1 = p 2y "
"3:b = p 2 = p 2y "
"3:c = p 1 1 2 = p 2 "
"3:a = p 2 1 1 = p 2x "
"4:b = p 1 21 1 = p 2yb "
"4:b = p 1 21 1 = p 2y1 "
"4:b = p 21 = p 2yb "
"4:c = p 1 1 21 = p 2c "
"4:c = p 1 1 21 = p 21 "
"4:a = p 21 1 1 = p 2xa "
"4:a = p 21 1 1 = p 2x1 "
"5:b1 = c 1 2 1 = c 2y "
"5:b1 = c 2 = c 2y "
"5:b2 = a 1 2 1 = a 2y "
"5:b3 = i 1 2 1 = i 2y "
"5:c1 = a 1 1 2 = a 2 "
"5:c2 = b 1 1 2 = b 2 "
"5:c3 = i 1 1 2 = i 2 "
"5:a1 = b 2 1 1 = b 2x "
"5:a2 = c 2 1 1 = c 2x "
"5:a3 = i 2 1 1 = i 2x "
"6:b = p 1 m 1 = p -2y "
"6:b = p m = p -2y "
"6:c = p 1 1 m = p -2 "
"6:a = p m 1 1 = p -2x "
"7:b1 = p 1 c 1 = p -2yc "
"7:b1 = p c = p -2yc "
"7:b2 = p 1 n 1 = p -2yac "
"7:b2 = p n = p -2yac "
"7:b3 = p 1 a 1 = p -2ya "
"7:b3 = p a = p -2ya "
"7:c1 = p 1 1 a = p -2a "
"7:c2 = p 1 1 n = p -2ab "
"7:c3 = p 1 1 b = p -2b "
"7:a1 = p b 1 1 = p -2xb "
"7:a2 = p n 1 1 = p -2xbc "
"7:a3 = p c 1 1 = p -2xc "
"8:b1 = c 1 m 1 = c -2y "
"8:b1 = c m = c -2y "
"8:b2 = a 1 m 1 = a -2y "
"8:b3 = i 1 m 1 = i -2y "
"8:b3 = i m = i -2y "
"8:c1 = a 1 1 m = a -2 "
"8:c2 = b 1 1 m = b -2 "
"8:c3 = i 1 1 m = i -2 "
"8:a1 = b m 1 1 = b -2x "
"8:a2 = c m 1 1 = c -2x "
"8:a3 = i m 1 1 = i -2x "
"9:b1 = c 1 c 1 = c -2yc "
"9:b1 = c c = c -2yc "
"9:b2 = a 1 n 1 = a -2yab "
"9:b3 = i 1 a 1 = i -2ya "
"9:-b1 = a 1 a 1 = a -2ya "
"9:-b2 = c 1 n 1 = c -2yac "
"9:-b3 = i 1 c 1 = i -2yc "
"9:c1 = a 1 1 a = a -2a "
"9:c2 = b 1 1 n = b -2ab "
"9:c3 = i 1 1 b = i -2b "
"9:-c1 = b 1 1 b = b -2b "
"9:-c2 = a 1 1 n = a -2ab "
"9:-c3 = i 1 1 a = i -2a "
"9:a1 = b b 1 1 = b -2xb "
"9:a2 = c n 1 1 = c -2xac "
"9:a3 = i c 1 1 = i -2xc "
"9:-a1 = c c 1 1 = c -2xc "
"9:-a2 = b n 1 1 = b -2xab "
"9:-a3 = i b 1 1 = i -2xb "
"10:b = p 1 2/m 1 = -p 2y "
"10:b = p 2/m = -p 2y "
"10:c = p 1 1 2/m = -p 2 "
"10:a = p 2/m 1 1 = -p 2x "
"11:b = p 1 21/m 1 = -p 2yb "
"11:b = p 1 21/m 1 = -p 2y1 "
"11:b = p 21/m = -p 2yb "
"11:c = p 1 1 21/m = -p 2c "
"11:c = p 1 1 21/m = -p 21 "
"11:a = p 21/m 1 1 = -p 2xa "
"11:a = p 21/m 1 1 = -p 2x1 "
"12:b1 = c 1 2/m 1 = -c 2y "
"12:b1 = c 2/m = -c 2y "
"12:b2 = a 1 2/m 1 = -a 2y "
"12:b3 = i 1 2/m 1 = -i 2y "
"12:b3 = i 2/m = -i 2y "
"12:c1 = a 1 1 2/m = -a 2 "
"12:c2 = b 1 1 2/m = -b 2 "
"12:c3 = i 1 1 2/m = -i 2 "
"12:a1 = b 2/m 1 1 = -b 2x "
"12:a2 = c 2/m 1 1 = -c 2x "
"12:a3 = i 2/m 1 1 = -i 2x "
"13:b1 = p 1 2/c 1 = -p 2yc "
"13:b1 = p 2/c = -p 2yc "
"13:b2 = p 1 2/n 1 = -p 2yac "
"13:b2 = p 2/n = -p 2yac "
"13:b3 = p 1 2/a 1 = -p 2ya "
"13:b3 = p 2/a = -p 2ya "
"13:c1 = p 1 1 2/a = -p 2a "
"13:c2 = p 1 1 2/n = -p 2ab "
"13:c3 = p 1 1 2/b = -p 2b "
"13:a1 = p 2/b 1 1 = -p 2xb "
"13:a2 = p 2/n 1 1 = -p 2xbc "
"13:a3 = p 2/c 1 1 = -p 2xc "
"14:b1 = p 1 21/c 1 = -p 2ybc "
"14:b1 = p 21/c = -p 2ybc "
"14:b2 = p 1 21/n 1 = -p 2yn "
"14:b2 = p 21/n = -p 2yn "
"14:b3 = p 1 21/a 1 = -p 2yab "
"14:b3 = p 21/a = -p 2yab "
"14:c1 = p 1 1 21/a = -p 2ac "
"14:c2 = p 1 1 21/n = -p 2n "
"14:c3 = p 1 1 21/b = -p 2bc "
"14:a1 = p 21/b 1 1 = -p 2xab "
"14:a2 = p 21/n 1 1 = -p 2xn "
"14:a3 = p 21/c 1 1 = -p 2xac "
"15:b1 = c 1 2/c 1 = -c 2yc "
"15:b1 = c 2/c = -c 2yc "
"15:b2 = a 1 2/n 1 = -a 2yab "
"15:b3 = i 1 2/a 1 = -i 2ya "
"15:b3 = i 2/a = -i 2ya "
"15:-b1 = a 1 2/a 1 = -a 2ya "
"15:-b2 = c 1 2/n 1 = -c 2yac "
"15:-b2 = c 2/n = -c 2yac "
"15:-b3 = i 1 2/c 1 = -i 2yc "
"15:-b3 = i 2/c = -i 2yc "
"15:c1 = a 1 1 2/a = -a 2a "
"15:c2 = b 1 1 2/n = -b 2ab "
"15:c3 = i 1 1 2/b = -i 2b "
"15:-c1 = b 1 1 2/b = -b 2b "
"15:-c2 = a 1 1 2/n = -a 2ab "
"15:-c3 = i 1 1 2/a = -i 2a "
"15:a1 = b 2/b 1 1 = -b 2xb "
"15:a2 = c 2/n 1 1 = -c 2xac "
"15:a3 = i 2/c 1 1 = -i 2xc "
"15:-a1 = c 2/c 1 1 = -c 2xc "
"15:-a2 = b 2/n 1 1 = -b 2xab "
"15:-a3 = i 2/b 1 1 = -i 2xb "
"16 = p 2 2 2 = p 2 2 "
"17: = p 2 2 21 = p 2c 2 "
"17: = p 2 2 21 = p 21 2 "
"17:cab = p 21 2 2 = p 2a 2a "
"17:bca = p 2 21 2 = p 2 2b "
"18: = p 21 21 2 = p 2 2ab "
"18:cab = p 2 21 21 = p 2bc 2 "
"18:bca = p 21 2 21 = p 2ac 2ac "
"19 = p 21 21 21 = p 2ac 2ab "
"20: = c 2 2 21 = c 2c 2 "
"20: = c 2 2 21 = c 21 2 "
"20:cab = a 21 2 2 = a 2a 2a "
"20:cab = a 21 2 2 = a 2a 21 "
"20:bca = b 2 21 2 = b 2 2b "
"21: = c 2 2 2 = c 2 2 "
"21:cab = a 2 2 2 = a 2 2 "
"21:bca = b 2 2 2 = b 2 2 "
"22 = f 2 2 2 = f 2 2 "
"23 = i 2 2 2 = i 2 2 "
"24 = i 21 21 21 = i 2b 2c "
"25: = p m m 2 = p 2 -2 "
"25:cab = p 2 m m = p -2 2 "
"25:bca = p m 2 m = p -2 -2 "
"26: = p m c 21 = p 2c -2 "
"26: = p m c 21 = p 21 -2 "
"26:ba-c = p c m 21 = p 2c -2c "
"26:ba-c = p c m 21 = p 21 -2c "
"26:cab = p 21 m a = p -2a 2a "
"26:-cba = p 21 a m = p -2 2a "
"26:bca = p b 21 m = p -2 -2b "
"26:a-cb = p m 21 b = p -2b -2 "
"27: = p c c 2 = p 2 -2c "
"27:cab = p 2 a a = p -2a 2 "
"27:bca = p b 2 b = p -2b -2b "
"28: = p m a 2 = p 2 -2a "
"28: = p m a 2 = p 2 -21 "
"28:ba-c = p b m 2 = p 2 -2b "
"28:cab = p 2 m b = p -2b 2 "
"28:-cba = p 2 c m = p -2c 2 "
"28:-cba = p 2 c m = p -21 2 "
"28:bca = p c 2 m = p -2c -2c "
"28:a-cb = p m 2 a = p -2a -2a "
"29: = p c a 21 = p 2c -2ac "
"29:ba-c = p b c 21 = p 2c -2b "
"29:cab = p 21 a b = p -2b 2a "
"29:-cba = p 21 c a = p -2ac 2a "
"29:bca = p c 21 b = p -2bc -2c "
"29:a-cb = p b 21 a = p -2a -2ab "
"30: = p n c 2 = p 2 -2bc "
"30:ba-c = p c n 2 = p 2 -2ac "
"30:cab = p 2 n a = p -2ac 2 "
"30:-cba = p 2 a n = p -2ab 2 "
"30:bca = p b 2 n = p -2ab -2ab "
"30:a-cb = p n 2 b = p -2bc -2bc "
"31: = p m n 21 = p 2ac -2 "
"31:ba-c = p n m 21 = p 2bc -2bc "
"31:cab = p 21 m n = p -2ab 2ab "
"31:-cba = p 21 n m = p -2 2ac "
"31:bca = p n 21 m = p -2 -2bc "
"31:a-cb = p m 21 n = p -2ab -2 "
"32: = p b a 2 = p 2 -2ab "
"32:cab = p 2 c b = p -2bc 2 "
"32:bca = p c 2 a = p -2ac -2ac "
"33: = p n a 21 = p 2c -2n "
"33: = p n a 21 = p 21 -2n "
"33:ba-c = p b n 21 = p 2c -2ab "
"33:ba-c = p b n 21 = p 21 -2ab "
"33:cab = p 21 n b = p -2bc 2a "
"33:cab = p 21 n b = p -2bc 21 "
"33:-cba = p 21 c n = p -2n 2a "
"33:-cba = p 21 c n = p -2n 21 "
"33:bca = p c 21 n = p -2n -2ac "
"33:a-cb = p n 21 a = p -2ac -2n "
"34: = p n n 2 = p 2 -2n "
"34:cab = p 2 n n = p -2n 2 "
"34:bca = p n 2 n = p -2n -2n "
"35: = c m m 2 = c 2 -2 "
"35:cab = a 2 m m = a -2 2 "
"35:bca = b m 2 m = b -2 -2 "
"36: = c m c 21 = c 2c -2 "
"36: = c m c 21 = c 21 -2 "
"36:ba-c = c c m 21 = c 2c -2c "
"36:ba-c = c c m 21 = c 21 -2c "
"36:cab = a 21 m a = a -2a 2a "
"36:cab = a 21 m a = a -2a 21 "
"36:-cba = a 21 a m = a -2 2a "
"36:-cba = a 21 a m = a -2 21 "
"36:bca = b b 21 m = b -2 -2b "
"36:a-cb = b m 21 b = b -2b -2 "
"37: = c c c 2 = c 2 -2c "
"37:cab = a 2 a a = a -2a 2 "
"37:bca = b b 2 b = b -2b -2b "
"38: = a m m 2 = a 2 -2 "
"38:ba-c = b m m 2 = b 2 -2 "
"38:cab = b 2 m m = b -2 2 "
"38:-cba = c 2 m m = c -2 2 "
"38:bca = c m 2 m = c -2 -2 "
"38:a-cb = a m 2 m = a -2 -2 "
"39: = a b m 2 = a 2 -2c "
"39:ba-c = b m a 2 = b 2 -2a "
"39:cab = b 2 c m = b -2a 2 "
"39:-cba = c 2 m b = c -2a 2 "
"39:bca = c m 2 a = c -2a -2a "
"39:a-cb = a c 2 m = a -2c -2c "
"40: = a m a 2 = a 2 -2a "
"40:ba-c = b b m 2 = b 2 -2b "
"40:cab = b 2 m b = b -2b 2 "
"40:-cba = c 2 c m = c -2c 2 "
"40:bca = c c 2 m = c -2c -2c "
"40:a-cb = a m 2 a = a -2a -2a "
"41: = a b a 2 = a 2 -2ab "
"41:ba-c = b b a 2 = b 2 -2ab "
"41:cab = b 2 c b = b -2ab 2 "
"41:-cba = c 2 c b = c -2ac 2 "
"41:bca = c c 2 a = c -2ac -2ac "
"41:a-cb = a c 2 a = a -2ab -2ab "
"42: = f m m 2 = f 2 -2 "
"42:cab = f 2 m m = f -2 2 "
"42:bca = f m 2 m = f -2 -2 "
"43: = f d d 2 = f 2 -2d "
"43:cab = f 2 d d = f -2d 2 "
"43:bca = f d 2 d = f -2d -2d "
"44: = i m m 2 = i 2 -2 "
"44:cab = i 2 m m = i -2 2 "
"44:bca = i m 2 m = i -2 -2 "
"45: = i b a 2 = i 2 -2c "
"45:cab = i 2 c b = i -2a 2 "
"45:bca = i c 2 a = i -2b -2b "
"46: = i m a 2 = i 2 -2a "
"46:ba-c = i b m 2 = i 2 -2b "
"46:cab = i 2 m b = i -2b 2 "
"46:-cba = i 2 c m = i -2c 2 "
"46:bca = i c 2 m = i -2c -2c "
"46:a-cb = i m 2 a = i -2a -2a "
"47 = p m m m = -p 2 2 "
"48:1 = p n n n:1 = p 2 2 -1n "
"48:2 = p n n n:2 = -p 2ab 2bc "
"49: = p c c m = -p 2 2c "
"49:cab = p m a a = -p 2a 2 "
"49:bca = p b m b = -p 2b 2b "
"50:1 = p b a n:1 = p 2 2 -1ab "
"50:2 = p b a n:2 = -p 2ab 2b "
"50:1cab = p n c b:1 = p 2 2 -1bc "
"50:2cab = p n c b:2 = -p 2b 2bc "
"50:1bca = p c n a:1 = p 2 2 -1ac "
"50:2bca = p c n a:2 = -p 2a 2c "
"51: = p m m a = -p 2a 2a "
"51:ba-c = p m m b = -p 2b 2 "
"51:cab = p b m m = -p 2 2b "
"51:-cba = p c m m = -p 2c 2c "
"51:bca = p m c m = -p 2c 2 "
"51:a-cb = p m a m = -p 2 2a "
"52: = p n n a = -p 2a 2bc "
"52:ba-c = p n n b = -p 2b 2n "
"52:cab = p b n n = -p 2n 2b "
"52:-cba = p c n n = -p 2ab 2c "
"52:bca = p n c n = -p 2ab 2n "
"52:a-cb = p n a n = -p 2n 2bc "
"53: = p m n a = -p 2ac 2 "
"53:ba-c = p n m b = -p 2bc 2bc "
"53:cab = p b m n = -p 2ab 2ab "
"53:-cba = p c n m = -p 2 2ac "
"53:bca = p n c m = -p 2 2bc "
"53:a-cb = p m a n = -p 2ab 2 "
"54: = p c c a = -p 2a 2ac "
"54:ba-c = p c c b = -p 2b 2c "
"54:cab = p b a a = -p 2a 2b "
"54:-cba = p c a a = -p 2ac 2c "
"54:bca = p b c b = -p 2bc 2b "
"54:a-cb = p b a b = -p 2b 2ab "
"55: = p b a m = -p 2 2ab "
"55:cab = p m c b = -p 2bc 2 "
"55:bca = p c m a = -p 2ac 2ac "
"56: = p c c n = -p 2ab 2ac "
"56:cab = p n a a = -p 2ac 2bc "
"56:bca = p b n b = -p 2bc 2ab "
"57: = p b c m = -p 2c 2b "
"57:ba-c = p c a m = -p 2c 2ac "
"57:cab = p m c a = -p 2ac 2a "
"57:-cba = p m a b = -p 2b 2a "
"57:bca = p b m a = -p 2a 2ab "
"57:a-cb = p c m b = -p 2bc 2c "
"58: = p n n m = -p 2 2n "
"58:cab = p m n n = -p 2n 2 "
"58:bca = p n m n = -p 2n 2n "
"59:1 = p m m n:1 = p 2 2ab -1ab "
"59:2 = p m m n:2 = -p 2ab 2a "
"59:1cab = p n m m:1 = p 2bc 2 -1bc "
"59:2cab = p n m m:2 = -p 2c 2bc "
"59:1bca = p m n m:1 = p 2ac 2ac -1ac "
"59:2bca = p m n m:2 = -p 2c 2a "
"60: = p b c n = -p 2n 2ab "
"60:ba-c = p c a n = -p 2n 2c "
"60:cab = p n c a = -p 2a 2n "
"60:-cba = p n a b = -p 2bc 2n "
"60:bca = p b n a = -p 2ac 2b "
"60:a-cb = p c n b = -p 2b 2ac "
"61: = p b c a = -p 2ac 2ab "
"61:ba-c = p c a b = -p 2bc 2ac "
"62: = p n m a = -p 2ac 2n "
"62:ba-c = p m n b = -p 2bc 2a "
"62:cab = p b n m = -p 2c 2ab "
"62:-cba = p c m n = -p 2n 2ac "
"62:bca = p m c n = -p 2n 2a "
"62:a-cb = p n a m = -p 2c 2n "
"63: = c m c m = -c 2c 2 "
"63:ba-c = c c m m = -c 2c 2c "
"63:cab = a m m a = -a 2a 2a "
"63:-cba = a m a m = -a 2 2a "
"63:bca = b b m m = -b 2 2b "
"63:a-cb = b m m b = -b 2b 2 "
"64: = c m c a = -c 2ac 2 "
"64:ba-c = c c m b = -c 2ac 2ac "
"64:cab = a b m a = -a 2ab 2ab "
"64:-cba = a c a m = -a 2 2ab "
"64:bca = b b c m = -b 2 2ab "
"64:a-cb = b m a b = -b 2ab 2 "
"65: = c m m m = -c 2 2 "
"65:cab = a m m m = -a 2 2 "
"65:bca = b m m m = -b 2 2 "
"66: = c c c m = -c 2 2c "
"66:cab = a m a a = -a 2a 2 "
"66:bca = b b m b = -b 2b 2b "
"67: = c m m a = -c 2a 2 "
"67:ba-c = c m m b = -c 2a 2a "
"67:cab = a b m m = -a 2b 2b "
"67:-cba = a c m m = -a 2 2c "
"67:bca = b m c m = -b 2 2a "
"67:a-cb = b m a m = -b 2a 2 "
"68:1 = c c c a:1 = c 2 2 -1ac "
"68:2 = c c c a:2 = -c 2a 2ac "
"68:1ba-c = c c c b:1 = c 2 2 -1ac "
"68:2ba-c = c c c b:2 = -c 2a 2c "
"68:1cab = a b a a:1 = a 2 2 -1ab "
"68:2cab = a b a a:2 = -a 2a 2c "
"68:1-cba = a c a a:1 = a 2 2 -1ab "
"68:2-cba = a c a a:2 = -a 2ab 2b "
"68:1bca = b b c b:1 = b 2 2 -1ab "
"68:2bca = b b c b:2 = -b 2ab 2b "
"68:1a-cb = b b a b:1 = b 2 2 -1ab "
"68:2a-cb = b b a b:2 = -b 2b 2ab "
"69 = f m m m = -f 2 2 "
"70:1 = f d d d:1 = f 2 2 -1d "
"70:2 = f d d d:2 = -f 2uv 2vw "
"71 = i m m m = -i 2 2 "
"72: = i b a m = -i 2 2c "
"72:cab = i m c b = -i 2a 2 "
"72:bca = i c m a = -i 2b 2b "
"73: = i b c a = -i 2b 2c "
"73:ba-c = i c a b = -i 2a 2b "
"74: = i m m a = -i 2b 2 "
"74:ba-c = i m m b = -i 2a 2a "
"74:cab = i b m m = -i 2c 2c "
"74:-cba = i c m m = -i 2 2b "
"74:bca = i m c m = -i 2 2a "
"74:a-cb = i m a m = -i 2c 2 "
"75 = p 4 = p 4 "
"76: = p 41 = p 4w "
"76: = p 41 = p 41 "
"77: = p 42 = p 4c "
"77: = p 42 = p 42 "
"78: = p 43 = p 4cw "
"78: = p 43 = p 43 "
"79 = i 4 = i 4 "
"80 = i 41 = i 4bw "
"81 = p -4 = p -4 "
"82 = i -4 = i -4 "
"83 = p 4/m = -p 4 "
"84: = p 42/m = -p 4c "
"84: = p 42/m = -p 42 "
"85:1 = p 4/n:1 = p 4ab -1ab "
"85:2 = p 4/n:2 = -p 4a "
"86:1 = p 42/n:1 = p 4n -1n "
"86:2 = p 42/n:2 = -p 4bc "
"87 = i 4/m = -i 4 "
"88:1 = i 41/a:1 = i 4bw -1bw "
"88:2 = i 41/a:2 = -i 4ad "
"89 = p 4 2 2 = p 4 2 "
"90 = p 4 21 2 = p 4ab 2ab "
"91: = p 41 2 2 = p 4w 2c "
"91: = p 41 2 2 = p 41 2c "
"92 = p 41 21 2 = p 4abw 2nw "
"93: = p 42 2 2 = p 4c 2 "
"93: = p 42 2 2 = p 42 2 "
"94 = p 42 21 2 = p 4n 2n "
"95: = p 43 2 2 = p 4cw 2c "
"95: = p 43 2 2 = p 43 2c "
"96 = p 43 21 2 = p 4nw 2abw "
"97 = i 4 2 2 = i 4 2 "
"98 = i 41 2 2 = i 4bw 2bw "
"99 = p 4 m m = p 4 -2 "
"100 = p 4 b m = p 4 -2ab "
"101: = p 42 c m = p 4c -2c "
"101: = p 42 c m = p 42 -2c "
"102 = p 42 n m = p 4n -2n "
"103 = p 4 c c = p 4 -2c "
"104 = p 4 n c = p 4 -2n "
"105: = p 42 m c = p 4c -2 "
"105: = p 42 m c = p 42 -2 "
"106: = p 42 b c = p 4c -2ab "
"106: = p 42 b c = p 42 -2ab "
"107 = i 4 m m = i 4 -2 "
"108 = i 4 c m = i 4 -2c "
"109 = i 41 m d = i 4bw -2 "
"110 = i 41 c d = i 4bw -2c "
"111 = p -4 2 m = p -4 2 "
"112 = p -4 2 c = p -4 2c "
"113 = p -4 21 m = p -4 2ab "
"114 = p -4 21 c = p -4 2n "
"115 = p -4 m 2 = p -4 -2 "
"116 = p -4 c 2 = p -4 -2c "
"117 = p -4 b 2 = p -4 -2ab "
"118 = p -4 n 2 = p -4 -2n "
"119 = i -4 m 2 = i -4 -2 "
"120 = i -4 c 2 = i -4 -2c "
"121 = i -4 2 m = i -4 2 "
"122 = i -4 2 d = i -4 2bw "
"123 = p 4/m m m = -p 4 2 "
"124 = p 4/m c c = -p 4 2c "
"125:1 = p 4/n b m:1 = p 4 2 -1ab "
"125:2 = p 4/n b m:2 = -p 4a 2b "
"126:1 = p 4/n n c:1 = p 4 2 -1n "
"126:2 = p 4/n n c:2 = -p 4a 2bc "
"127 = p 4/m b m = -p 4 2ab "
"128 = p 4/m n c = -p 4 2n "
"129:1 = p 4/n m m:1 = p 4ab 2ab -1ab "
"129:2 = p 4/n m m:2 = -p 4a 2a "
"130:1 = p 4/n c c:1 = p 4ab 2n -1ab "
"130:2 = p 4/n c c:2 = -p 4a 2ac "
"131 = p 42/m m c = -p 4c 2 "
"132 = p 42/m c m = -p 4c 2c "
"133:1 = p 42/n b c:1 = p 4n 2c -1n "
"133:2 = p 42/n b c:2 = -p 4ac 2b "
"134:1 = p 42/n n m:1 = p 4n 2 -1n "
"134:2 = p 42/n n m:2 = -p 4ac 2bc "
"135: = p 42/m b c = -p 4c 2ab "
"135: = p 42/m b c = -p 42 2ab "
"136 = p 42/m n m = -p 4n 2n "
"137:1 = p 42/n m c:1 = p 4n 2n -1n "
"137:2 = p 42/n m c:2 = -p 4ac 2a "
"138:1 = p 42/n c m:1 = p 4n 2ab -1n "
"138:2 = p 42/n c m:2 = -p 4ac 2ac "
"139 = i 4/m m m = -i 4 2 "
"140 = i 4/m c m = -i 4 2c "
"141:1 = i 41/a m d:1 = i 4bw 2bw -1bw "
"141:2 = i 41/a m d:2 = -i 4bd 2 "
"142:1 = i 41/a c d:1 = i 4bw 2aw -1bw "
"142:2 = i 41/a c d:2 = -i 4bd 2c "
"143 = p 3 = p 3 "
"144 = p 31 = p 31 "
"145 = p 32 = p 32 "
"146:h = r 3:h = r 3 "
"146:r = r 3:r = p 3* "
"147 = p -3 = -p 3 "
"148:h = r -3:h = -r 3 "
"148:r = r -3:r = -p 3* "
"149 = p 3 1 2 = p 3 2 "
"150 = p 3 2 1 = p 3 2"" "
"151 = p 31 1 2 = p 31 2 (0 0 4) "
"152 = p 31 2 1 = p 31 2"" "
"153 = p 32 1 2 = p 32 2 (0 0 2) "
"154 = p 32 2 1 = p 32 2"" "
"155:h = r 3 2:h = r 3 2"" "
"155:r = r 3 2:r = p 3* 2 "
"156 = p 3 m 1 = p 3 -2"" "
"157 = p 3 1 m = p 3 -2 "
"158 = p 3 c 1 = p 3 -2""c "
"159 = p 3 1 c = p 3 -2c "
"160:h = r 3 m:h = r 3 -2"" "
"160:r = r 3 m:r = p 3* -2 "
"161:h = r 3 c:h = r 3 -2""c "
"161:r = r 3 c:r = p 3* -2n "
"162 = p -3 1 m = -p 3 2 "
"163 = p -3 1 c = -p 3 2c "
"164 = p -3 m 1 = -p 3 2"" "
"165 = p -3 c 1 = -p 3 2""c "
"166:h = r -3 m:h = -r 3 2"" "
"166:r = r -3 m:r = -p 3* 2 "
"167:h = r -3 c:h = -r 3 2""c "
"167:r = r -3 c:r = -p 3* 2n "
"168 = p 6 = p 6 "
"169 = p 61 = p 61 "
"170 = p 65 = p 65 "
"171 = p 62 = p 62 "
"172 = p 64 = p 64 "
"173: = p 63 = p 6c "
"173: = p 63 = p 63 "
"174 = p -6 = p -6 "
"175 = p 6/m = -p 6 "
"176: = p 63/m = -p 6c "
"176: = p 63/m = -p 63 "
"177 = p 6 2 2 = p 6 2 "
"178 = p 61 2 2 = p 61 2 (0 0 5) "
"179 = p 65 2 2 = p 65 2 (0 0 1) "
"180 = p 62 2 2 = p 62 2 (0 0 4) "
"181 = p 64 2 2 = p 64 2 (0 0 2) "
"182: = p 63 2 2 = p 6c 2c "
"182: = p 63 2 2 = p 63 2c "
"183 = p 6 m m = p 6 -2 "
"184 = p 6 c c = p 6 -2c "
"185: = p 63 c m = p 6c -2 "
"185: = p 63 c m = p 63 -2 "
"186: = p 63 m c = p 6c -2c "
"186: = p 63 m c = p 63 -2c "
"187 = p -6 m 2 = p -6 2 "
"188 = p -6 c 2 = p -6c 2 "
"189 = p -6 2 m = p -6 -2 "
"190 = p -6 2 c = p -6c -2c "
"191 = p 6/m m m = -p 6 2 "
"192 = p 6/m c c = -p 6 2c "
"193: = p 63/m c m = -p 6c 2 "
"193: = p 63/m c m = -p 63 2 "
"194: = p 63/m m c = -p 6c 2c "
"194: = p 63/m m c = -p 63 2c "
"195 = p 2 3 = p 2 2 3 "
"196 = f 2 3 = f 2 2 3 "
"197 = i 2 3 = i 2 2 3 "
"198 = p 21 3 = p 2ac 2ab 3 "
"199 = i 21 3 = i 2b 2c 3 "
"200 = p m -3 = -p 2 2 3 "
"201:1 = p n -3:1 = p 2 2 3 -1n "
"201:2 = p n -3:2 = -p 2ab 2bc 3 "
"202 = f m -3 = -f 2 2 3 "
"203:1 = f d -3:1 = f 2 2 3 -1d "
"203:2 = f d -3:2 = -f 2uv 2vw 3 "
"204 = i m -3 = -i 2 2 3 "
"205 = p a -3 = -p 2ac 2ab 3 "
"206 = i a -3 = -i 2b 2c 3 "
"207 = p 4 3 2 = p 4 2 3 "
"208 = p 42 3 2 = p 4n 2 3 "
"209 = f 4 3 2 = f 4 2 3 "
"210 = f 41 3 2 = f 4d 2 3 "
"211 = i 4 3 2 = i 4 2 3 "
"212 = p 43 3 2 = p 4acd 2ab 3 "
"213 = p 41 3 2 = p 4bd 2ab 3 "
"214 = i 41 3 2 = i 4bd 2c 3 "
"215 = p -4 3 m = p -4 2 3 "
"216 = f -4 3 m = f -4 2 3 "
"217 = i -4 3 m = i -4 2 3 "
"218 = p -4 3 n = p -4n 2 3 "
"219 = f -4 3 c = f -4a 2 3 "
"220 = i -4 3 d = i -4bd 2c 3 "
"221 = p m -3 m = -p 4 2 3 "
"222:1 = p n -3 n:1 = p 4 2 3 -1n "
"222:2 = p n -3 n:2 = -p 4a 2bc 3 "
"223 = p m -3 n = -p 4n 2 3 "
"224:1 = p n -3 m:1 = p 4n 2 3 -1n "
"224:2 = p n -3 m:2 = -p 4bc 2bc 3 "
"225 = f m -3 m = -f 4 2 3 "
"226 = f m -3 c = -f 4a 2 3 "
"227:1 = f d -3 m:1 = f 4d 2 3 -1d "
"227:2 = f d -3 m:2 = -f 4vw 2vw 3 "
"228:1 = f d -3 c:1 = f 4d 2 3 -1ad "
"228:2 = f d -3 c:2 = -f 4ud 2vw 3 "
"229 = i m -3 m = -i 4 2 3 "
"230 = i a -3 d = -i 4bd 2c 3 ")
zenity --forms --title="Crystal data" --text="Enter the unit cell parameters and space group:" \
--add-entry="a= " \
--add-entry="b= " \
--add-entry="c= " \
--add-entry="alpha= " \
--add-entry="beta = " \
--add-entry="gamma= " > crystal_data.txt
zenity --entry --title "Window title" --text "${SPACEGROUPARRAY[@]}" --text "Select the space group (number = IT symbol = Hall Symbol):" > spacegroup.txt
}
GAMESS_ELMODB_OLD_PDB(){
I=$[ $I + 1 ]
PDB=$( echo $CIF | awk -F "/" '{print $NF}' )
echo "title" > $JOBNAME.gamess.inp
echo "prova $JOBNAME - $BASISSETG - closed shell SCF" >> $JOBNAME.gamess.inp
echo "charge $CHARGE " >> $JOBNAME.gamess.inp
if [ "$MULTIPLICITY" != "1" ]; then
echo "multiplicity $MULTIPLICITY" >> $JOBNAME.gamess.inp
fi
echo "adapt off" >> $JOBNAME.gamess.inp
echo "nosym" >> $JOBNAME.gamess.inp
echo "geometry angstrom" >> $JOBNAME.gamess.inp
if [ "$I" = "1" ]; then
awk '$1 ~ /ATOM/ {printf "%f\t %f\t %f\t %s\t %s\n", $6, $7, $8, "carga", $3}' $CIF > atoms
else
awk 'NR > 2 {printf "%f\t %f\t %f\t %s\t %s\n", $2, $3, $4, "carga", $1}' $JOBNAME.xyz > atoms
fi
awk '{print $5}' atoms | gawk 'BEGIN { FS = "" } {print $1}' | awk '{ if ($1 == "N") print "7.0"; else if ($1 == "H") print "1.0"; else if ($1 == "O") print "8.0"; else if ($1 == "C") print "6.0"; else if ($1 == "S") print "16.0"; }' > atoms_Z
awk '{print $5}' atoms | gawk 'BEGIN { FS = "" } {print $1}' > atoms_names
awk 'FNR==NR{a[NR]=$1;next}{$4=a[FNR]}1' atoms_Z atoms > full
cp full atoms
awk 'FNR==NR{a[NR]=$1;next}{$5=a[FNR]}1' atoms_names atoms > full
awk '{printf "%f\t %f\t %f\t %s\t %s\n", $1, $2, $3, $4, $5}' full >> $JOBNAME.gamess.inp
rm atoms
rm atoms_Z
rm full
rm atoms_names
echo "end" >> $JOBNAME.gamess.inp
case "6-31g(d,p)" in
$BASISSETG ) echo "basis 6-31G**" >> $JOBNAME.gamess.inp;;
*) case "6-311g(d,p)" in
$BASISSETG ) echo "basis 6-311G**" >> $JOBNAME.gamess.inp;;
*) echo "basis $BASISSETG" >> $JOBNAME.gamess.inp;;
esac;;
esac
echo "runtype scf" >> $JOBNAME.gamess.inp
echo "scftype rhf" >> $JOBNAME.gamess.inp
echo "enter " >> $JOBNAME.gamess.inp
echo "Calculating overlap integrals with gamessus, cycle number $I"
$GAMESS < $JOBNAME.gamess.inp > $JOBNAME.gamess.out
echo "Gamess cycle number $I ended"
mkdir $I.$SCFCALCPROG.cycle.$JOBNAME
cp $JOBNAME.gamess.inp $I.$SCFCALCPROG.cycle.$JOBNAME/$I.$JOBNAME.gamess.inp
cp $JOBNAME.gamess.out $I.$SCFCALCPROG.cycle.$JOBNAME/$I.$JOBNAME.gamess.out
cp sao $I.$SCFCALCPROG.cycle.$JOBNAME/$I.sao
rm ed*
rm gamess_input*
if ! grep -q 'OVERLAP INTEGRALS WRITTEN ON FILE sao' "$JOBNAME.gamess.out"; then
echo "ERROR: Calculation of overlap integrals with gamessus finished with error, please check the $I.th gamess.out file for more details" | tee -a $JOBNAME.lst
unset MAIN_DIALOG
exit 0
else
echo "Calculation of overlap integrals with gamess done, writing elmodb input files"
if [[ ! -f "$( echo $SCFCALC_BIN | awk -F "/" '{print $NF}' )" ]]; then
cp $SCFCALC_BIN .
fi
if [ "$I" = "1" ]; then
BASISSETDIR=$( echo "$(dirname $BASISSETDIR)/" )
ELMOLIB=$( echo "$(dirname $ELMOLIB)/" )
#this is correct but until the elmo problem is solved I will keep it commented
# if [[ "$INITADP" == "true" ]];then
# echo " "'$INPUT_METHOD'" job_title='$JOBNAME' basis_set='$BASISSETG' cif=.true. iprint_level=1 ncpus=$NUMPROC alloc_mem=$MEM bset_path='$BASISSETDIR' lib_path='$ELMOLIB' nci=.true. "'$END'" " > $JOBNAME.elmodb.inp
# else
echo " "'$INPUT_METHOD'" job_title='$JOBNAME' basis_set='$BASISSETG' iprint_level=1 ncpus=$NUMPROC alloc_mem=$MEM bset_path='$BASISSETDIR' lib_path='$ELMOLIB' nci=.true. "'$END'" " > $JOBNAME.elmodb.inp
# fi
# if [[ "$INITADP" == "true" ]];then
# echo " "'$INPUT_STRUCTURE'" pdb_file='$PDB' cif_file='$INITADPFILE' ntail=$NTAIL max_atail=$ATAIL max_frtail=$FRTAIL nssbond=$NSSBOND "'$END'" " >> $JOBNAME.elmodb.inp
# else
echo " "'$INPUT_STRUCTURE'" pdb_file='$PDB' ntail=$NTAIL max_atail=$ATAIL max_frtail=$FRTAIL nssbond=$NSSBOND "'$END'" " >> $JOBNAME.elmodb.inp
# fi
if [[ "$NTAIL" != "0" ]]; then
echo "$MANUALRESIDUE" >> $JOBNAME.elmodb.inp
fi
if [[ "$NSSBOND" != "0" ]]; then
echo "$SSBONDATOMS" >> $JOBNAME.elmodb.inp
fi
else
#there is a problem with the conversion from fractional to cartesian inside the elmodb program, saving example files in the aga folder 4cut and changing back to always use the xyz. The elmo cannot read the cartesian cif
# echo " "'$INPUT_METHOD'" job_title='$JOBNAME' basis_set='$BASISSETG' cif=.true. iprint_level=1 ncpus=$NUMPROC alloc_mem=$MEM bset_path='$BASISSETDIR' lib_path='$ELMOLIB' nci=.true. comp_sao=.false. "'$END'" " > $JOBNAME.elmodb.inp
echo " "'$INPUT_METHOD'" job_title='$JOBNAME' basis_set='$BASISSETG' xyz=.true. iprint_level=1 ncpus=$NUMPROC alloc_mem=$MEM bset_path='$BASISSETDIR' lib_path='$ELMOLIB' nci=.true. comp_sao=.false. "'$END'" " > $JOBNAME.elmodb.inp
echo " "'$INPUT_STRUCTURE'" pdb_file='$PDB' xyz_file='$JOBNAME.xyz' ntail=$NTAIL nssbond=$NSSBOND "'$END'" " >> $JOBNAME.elmodb.inp
if [[ "$NTAIL" != "0" ]]; then
echo "$MANUALRESIDUE" >> $JOBNAME.elmodb.inp
fi
if [[ "$NSSBOND" != "0" ]]; then
echo "$SSBONDATOMS" >> $JOBNAME.elmodb.inp
fi
fi
echo "Running elmodb"
./$( echo $SCFCALC_BIN | awk -F "/" '{print $NF}' ) < $JOBNAME.elmodb.inp > $JOBNAME.elmodb.out
if ! grep -q 'CONGRATULATIONS: THE ELMO-TRANSFERs ENDED GRACEFULLY!!!' "$JOBNAME.elmodb.out"; then
echo "ERROR: elmodb finished with error, please check the $I.th elmodb.out file for more details" | tee -a $JOBNAME.lst
unset MAIN_DIALOG
exit 0
else
echo "elmodb job finish correctly."
cp $JOBNAME.elmodb.out $I.$SCFCALCPROG.cycle.$JOBNAME/$I.$JOBNAME.elmodb.out
cp $JOBNAME.elmodb.inp $I.$SCFCALCPROG.cycle.$JOBNAME/$I.$JOBNAME.elmodb.inp
cp $JOBNAME.fchk $I.$SCFCALCPROG.cycle.$JOBNAME/$I.$JOBNAME.elmodb.fchk
if [ "$I" != "1" ]; then
cp $JOBNAME.xyz $I.$SCFCALCPROG.cycle.$JOBNAME/$I.$JOBNAME.xyz
fi
fi
fi
}
ELMODB(){
I=$[ $I + 1 ]
if [[ ! -f "$( echo $SCFCALC_BIN | awk -F "/" '{print $NF}' )" ]]; then
cp $SCFCALC_BIN .
fi
if [ "$I" = "1" ]; then
BASISSETDIR=$( echo "$(dirname $BASISSETDIR)/" )
ELMOLIB=$( echo "$(dirname $ELMOLIB)/" )
#this is correct but until the elmo problem is solved I will keep it commented
# if [[ "$INITADP" == "true" ]];then
# echo " "'$INPUT_METHOD'" job_title='$JOBNAME' basis_set='$BASISSETG' cif=.true. iprint_level=1 ncpus=$NUMPROC alloc_mem=$MEM bset_path='$BASISSETDIR' lib_path='$ELMOLIB' nci=.true. "'$END'" " > $JOBNAME.elmodb.inp
# else
echo " "'$INPUT_METHOD'" job_title='$JOBNAME' basis_set='$BASISSETG' iprint_level=1 ncpus=$NUMPROC alloc_mem=$MEM bset_path='$BASISSETDIR' lib_path='$ELMOLIB' nci=.true. "'$END'" " > $JOBNAME.elmodb.inp
# fi
# if [[ "$INITADP" == "true" ]];then
# echo " "'$INPUT_STRUCTURE'" pdb_file='$PDB' cif_file='$INITADPFILE' ntail=$NTAIL max_atail=$ATAIL max_frtail=$FRTAIL nssbond=$NSSBOND "'$END'" " >> $JOBNAME.elmodb.inp
# else
echo " "'$INPUT_STRUCTURE'" pdb_file='$PDB' ntail=$NTAIL max_atail=$ATAIL max_frtail=$FRTAIL nssbond=$NSSBOND "'$END'" " >> $JOBNAME.elmodb.inp
# fi
if [[ "$NTAIL" != "0" ]]; then
echo "$MANUALRESIDUE" >> $JOBNAME.elmodb.inp
fi
if [[ "$NSSBOND" != "0" ]]; then
echo "$SSBONDATOMS" >> $JOBNAME.elmodb.inp
fi
else
#there is a problem with the conversion from fractional to cartesian inside the elmodb program, saving example files in the aga folder 4cut and changing back to always use the xyz. The elmo cannot read the cartesian cif
# echo " "'$INPUT_METHOD'" job_title='$JOBNAME' basis_set='$BASISSETG' cif=.true. iprint_level=1 ncpus=$NUMPROC alloc_mem=$MEM bset_path='$BASISSETDIR' lib_path='$ELMOLIB' nci=.true. "'$END'" " > $JOBNAME.elmodb.inp
echo " "'$INPUT_METHOD'" job_title='$JOBNAME' basis_set='$BASISSETG' xyz=.true. iprint_level=1 ncpus=$NUMPROC alloc_mem=$MEM bset_path='$BASISSETDIR' lib_path='$ELMOLIB' nci=.true. "'$END'" " > $JOBNAME.elmodb.inp
if [[ "$NTAIL" != "0" ]]; then
# echo " "'$INPUT_STRUCTURE'" pdb_file='$PDB' cif_file='$JOBNAME.fractional.cif1' ntail=$NTAIL max_atail=$ATAIL max_frtail=$FRTAIL nssbond=$NSSBOND "'$END'" " >> $JOBNAME.elmodb.inp
echo " "'$INPUT_STRUCTURE'" pdb_file='$PDB' xyz_file='$JOBNAME.xyz' ntail=$NTAIL max_atail=$ATAIL max_frtail=$FRTAIL nssbond=$NSSBOND "'$END'" " >> $JOBNAME.elmodb.inp
echo "$MANUALRESIDUE" >> $JOBNAME.elmodb.inp
else
# echo " "'$INPUT_STRUCTURE'" pdb_file='$PDB' cif_file='$JOBNAME.fractional.cif1' nssbond=$NSSBOND "'$END'" " >>
echo " "'$INPUT_STRUCTURE'" pdb_file='$PDB' xyz_file='$JOBNAME.xyz' nssbond=$NSSBOND "'$END'" " >> $JOBNAME.elmodb.inp
fi
if [[ "$NSSBOND" != "0" ]]; then
echo "$SSBONDATOMS" >> $JOBNAME.elmodb.inp
fi
fi
./$( echo $SCFCALC_BIN | awk -F "/" '{print $NF}' ) < $JOBNAME.elmodb.inp > $JOBNAME.elmodb.out
if ! grep -q 'CONGRATULATIONS: THE ELMO-TRANSFERs ENDED GRACEFULLY!!!' "$JOBNAME.elmodb.out"; then
echo "ERROR: elmodb finished with error, please check the $I.th elmodb.out file for more details" | tee -a $JOBNAME.lst
unset MAIN_DIALOG
exit 0
else
mkdir $I.$SCFCALCPROG.cycle.$JOBNAME
cp $JOBNAME.elmodb.out $I.$SCFCALCPROG.cycle.$JOBNAME/$I.$JOBNAME.elmodb.out
cp $JOBNAME.elmodb.inp $I.$SCFCALCPROG.cycle.$JOBNAME/$I.$JOBNAME.elmodb.inp
cp $JOBNAME.fchk $I.$SCFCALCPROG.cycle.$JOBNAME/$I.$JOBNAME.elmodb.fchk
if [ "$I" != "1" ]; then
cp $JOBNAME.xyz $I.$SCFCALCPROG.cycle.$JOBNAME/$I.$JOBNAME.xyz
fi
fi
}
TONTO_TO_ORCA(){
I=$[ $I + 1 ]
echo "Extracting XYZ for Orca cycle number $I"
if [ "$METHOD" = "rks" ]; then
echo "! blyp $BASISSETG" > $JOBNAME.inp
else
if [ "$METHOD" = "uks" ]; then
echo "! ublyp $BASISSETG" > $JOBNAME.inp
else
echo "! $METHOD $BASISSETG" > $JOBNAME.inp
fi
fi
echo "" >> $JOBNAME.inp
echo "%output" >> $JOBNAME.inp
echo " PrintLevel=Normal" >> $JOBNAME.inp
echo " Print[ P_Basis ] 2" >> $JOBNAME.inp
echo " Print[ P_GuessOrb ] 1" >> $JOBNAME.inp
echo " Print[ P_MOs ] 1" >> $JOBNAME.inp
echo " Print[ P_Density ] 1" >> $JOBNAME.inp
echo " Print[ P_SpinDensity ] 1" >> $JOBNAME.inp
echo "end" >> $JOBNAME.inp
echo "" >> $JOBNAME.inp
echo "* xyz $CHARGE $MULTIPLICITY" >> $JOBNAME.inp
awk 'NR>2' $JOBNAME.xyz >> $JOBNAME.inp
if [ "$SCCHARGES" = "true" ]; then
awk '{a[NR]=$0}{b=12}/^------------------------------------------------------------------------/{c=NR}END{for(d=b;d<=c-1;++d)print a[d]}' gaussian-point-charges | awk '{printf "%s\t %s\t %s\t %s\t \n", "Q\t" $2, $3, $4, $1 }' >> $JOBNAME.inp
fi
echo "*" >> $JOBNAME.inp
echo "Running Orca, cycle number $I"
$SCFCALC_BIN $JOBNAME.inp > $JOBNAME.log
echo "Orca cycle number $I ended"
if ! grep -q '****ORCA TERMINATED NORMALLY****' "$JOBNAME.out"; then
echo "ERROR: Orca job finished with error, please check the $I.th out file for more details" | tee -a $JOBNAME.lst
unset MAIN_DIALOG
exit 0
fi
echo "Generation molden file for Orca cycle number $I"
orca_2mkl $JOBNAME -molden
echo "Orca cycle number $I, final energy is: $ENERGIA, RMSD is: $RMSD "
mkdir $I.$SCFCALCPROG.cycle.$JOBNAME
cp $JOBNAME.inp $I.$SCFCALCPROG.cycle.$JOBNAME/$I.$JOBNAME.inp
cp $JOBNAME.molden.input $I.$SCFCALCPROG.cycle.$JOBNAME/$I.$JOBNAME.molden.input
cp $JOBNAME.log $I.$SCFCALCPROG.cycle.$JOBNAME/$I.$JOBNAME.log
}
TONTO_HEADER(){
echo "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!" > stdin
echo "!!! !!!" >> stdin
echo "!!! This stdin was written with lamaGOET !!!" >> stdin
echo "!!! !!!" >> stdin
echo "!!! script written by Lorraine Andrade Malaspina !!!" >> stdin
echo "!!! contact: [email protected] !!!" >> stdin
echo "!!! !!!" >> stdin
echo "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!" >> stdin
echo "{ " >> stdin
echo "" >> stdin
echo " keyword_echo_on" >> stdin
echo "" >> stdin
}
READ_ELMO_FCHK(){
echo " name= $JOBNAME" >> stdin
echo "" >> stdin
echo " read_g09_fchk_file $JOBNAME.fchk" >> stdin
echo "" >> stdin
}
READ_GAUSSIAN_FCHK(){
echo " name= $JOBNAME" >> stdin
echo "" >> stdin
echo " read_g09_fchk_file $I.$SCFCALCPROG.cycle.$JOBNAME/$I.$JOBNAME.fchk" >> stdin
echo "" >> stdin
}
READ_ORCA_FCHK(){
echo " name= $JOBNAME" >> stdin
echo "" >> stdin
echo " read_molden_file $I.$SCFCALCPROG.cycle.$JOBNAME/$I.$JOBNAME.molden.input" >> stdin
echo "" >> stdin
}
DEFINE_JOB_NAME(){
echo " name= $JOBNAME" >> stdin
echo "" >> stdin
}
CHANGE_JOB_NAME(){
echo " name= $JOBNAME.XCW" >> stdin
echo "" >> stdin
}
PROCESS_CIF(){
echo " ! Process the CIF" >> stdin
echo " CIF= {" >> stdin
if [ $J = 0 ]; then
if [[ "$COMPLETECIF" == "true" && "$SCFCALCPROG" != "Tonto" ]]; then
echo " file_name= $J.tonto_cycle.$JOBNAME/$J.$JOBNAME.cartesian.cif2" >> stdin
else
echo " file_name= $CIF" >> stdin
fi
if [ "$XHALONG" = "true" ]; then
if [[ ! -z "$BHBOND" ]]; then
echo " BH_bond_length= $BHBOND angstrom" >> stdin
fi
if [[ ! -z "$CHBOND" ]]; then
echo " CH_bond_length= $CHBOND angstrom" >> stdin
fi
if [[ ! -z "$NHBOND" ]]; then
echo " NH_bond_length= $NHBOND angstrom" >> stdin
fi
if [[ ! -z "$OHBOND" ]]; then
echo " OH_bond_length= $OHBOND angstrom" >> stdin
fi
fi
else
echo " file_name= $J.tonto_cycle.$JOBNAME/$J.$JOBNAME.cartesian.cif2" >> stdin
fi
echo " }" >> stdin
echo "" >> stdin
echo " process_CIF" >> stdin
echo "" >> stdin
}
TONTO_BASIS_SET(){
echo " basis_directory= $BASISSETDIR" >> stdin
echo " basis_name= $BASISSETT" >> stdin
echo "" >> stdin
}
DISPERSION_COEF(){
echo " dispersion_coefficients= {" >> stdin
echo " $(cat DISP_inst.txt)" >> stdin
echo " }" >> stdin
echo "" >> stdin
}
CHARGE_MULT(){
echo " charge= $CHARGE" >> stdin
echo " multiplicity= $MULTIPLICITY" >> stdin
echo "" >> stdin
}
TONTO_IAM_BLOCK(){
echo ""
echo " crystal= { " >> stdin
if [[ "$SCFCALCPROG" = "elmodb" && "$INITADP" == "false" ]]; then
echo " REDIRECT tonto.cell" >> stdin
fi
echo " xray_data= { " >> stdin
echo " optimise_extinction= false" >> stdin
echo " correct_dispersion= $DISP" >> stdin
echo " wavelength= $WAVE Angstrom" >> stdin
if [ "$REFANHARM" == "true" ]; then
if [[ "$THIRDORD" == "false" && "$FOURTHORD" == "true" ]]; then
echo " refine_4th_order_only= true " >> stdin
echo " refine_4th_order_for_atoms= { $ANHARMATOMS } " >> stdin
elif [[ "$THIRDORD" == "true" && "$FOURTHORD" == "true" ]]; then
echo " refine_4th_order_for_atoms= { $ANHARMATOMS } " >> stdin
elif [[ "$THIRDORD" == "true" && "$FOURTHORD" == "false" ]]; then
echo " refine_3rd_order_for_atoms= { $ANHARMATOMS } " >> stdin
else
echo "ERROR: Please select at least one of the anharmonic terms to refine" | tee -a $JOBNAME.lst
unset MAIN_DIALOG
exit 0
fi
fi
echo " REDIRECT $HKL" >> stdin
echo " f_sigma_cutoff= $FCUT" >> stdin
echo " tol_for_shift_on_esd= $CONVTOL" >> stdin
echo " refine_H_U_iso= yes" >> stdin
echo "" >> stdin
echo " show_fit_output= true" >> stdin
echo " show_fit_results= true" >> stdin
echo "" >> stdin
echo " } " >> stdin
echo " } " >> stdin
echo "" >> stdin
echo " ! Geometry " >> stdin
echo " put" >> stdin
echo "" >> stdin
echo " IAM_refinement" >> stdin
echo "" >> stdin
}
CRYSTAL_BLOCK(){
echo "" >> stdin
echo " crystal= { " >> stdin
if [[ "$SCFCALCPROG" == "elmodb" && $J == 0 && "$INITADP" == "false" ]]; then
echo " REDIRECT tonto.cell" >> stdin
fi
if [[ "$SCFCALCPROG" == "optgaussian" ]]; then
echo " REDIRECT tonto.cell" >> stdin
fi
if [[ "$SCFCALCPROG" != "optgaussian" ]]; then
echo " xray_data= { " >> stdin
echo " thermal_smearing_model= hirshfeld" >> stdin
echo " partition_model= mulliken" >> stdin
if [[ "$PLOT_TONTO" == "false" ]]; then
echo " optimise_extinction= false" >> stdin
echo " correct_dispersion= $DISP" >> stdin
echo " optimise_scale_factor= true" >> stdin
fi
echo " wavelength= $WAVE Angstrom" >> stdin
if [[ "$REFANHARM" == "true" && "$PLOT_TONTO" == "false" ]]; then
if [[ "$THIRDORD" == "false" && "$FOURTHORD" == "true" ]]; then
echo " refine_4th_order_only= true " >> stdin
echo " refine_4th_order_for_atoms= { $ANHARMATOMS } " >> stdin
elif [[ "$THIRDORD" == "true" && "$FOURTHORD" == "true" ]]; then
echo " refine_4th_order_for_atoms= { $ANHARMATOMS } " >> stdin
elif [[ "$THIRDORD" == "true" && "$FOURTHORD" == "false" ]]; then
echo " refine_3rd_order_for_atoms= { $ANHARMATOMS } " >> stdin
else
echo "ERROR: Please select at least one of the anharmonic terms to refine" | tee -a $JOBNAME.lst
unset MAIN_DIALOG
exit 0
fi
fi
echo " REDIRECT $HKL" >> stdin
echo " f_sigma_cutoff= $FCUT" >> stdin
if [[ "$PLOT_TONTO" == "false" ]]; then
echo " tol_for_shift_on_esd= $CONVTOL" >> stdin
echo " refine_H_U_iso= $HADP" >> stdin
if [[ "$SCFCALCPROG" = "Tonto" && "$IAMTONTO" = "true" ]]; then
echo "" >> stdin