diff --git a/Ref/Inputs_G1/Al.xyz b/Ref/Inputs_G1/Al.xyz new file mode 100644 index 0000000..58f470f --- /dev/null +++ b/Ref/Inputs_G1/Al.xyz @@ -0,0 +1,2 @@ +0,2 +Al diff --git a/Ref/Inputs_G1/B.xyz b/Ref/Inputs_G1/B.xyz new file mode 100644 index 0000000..25c2c68 --- /dev/null +++ b/Ref/Inputs_G1/B.xyz @@ -0,0 +1,2 @@ +0,2 +B diff --git a/Ref/Inputs_G1/Be.xyz b/Ref/Inputs_G1/Be.xyz new file mode 100644 index 0000000..2f075c2 --- /dev/null +++ b/Ref/Inputs_G1/Be.xyz @@ -0,0 +1,2 @@ +0,1 +Be diff --git a/Ref/Inputs_G1/BeH.xyz b/Ref/Inputs_G1/BeH.xyz new file mode 100644 index 0000000..4ff32ad --- /dev/null +++ b/Ref/Inputs_G1/BeH.xyz @@ -0,0 +1,5 @@ +0,2 +Be +H,1,RBEH + +RBEH=1.34380733 diff --git a/Ref/Inputs_G1/C.xyz b/Ref/Inputs_G1/C.xyz new file mode 100644 index 0000000..0094d54 --- /dev/null +++ b/Ref/Inputs_G1/C.xyz @@ -0,0 +1,2 @@ +0,3 +C diff --git a/Ref/Inputs_G1/C2H2 b/Ref/Inputs_G1/C2H2 new file mode 100644 index 0000000..e8d6d4b --- /dev/null +++ b/Ref/Inputs_G1/C2H2 @@ -0,0 +1,9 @@ +C +C 1 CC +X 2 1. 1 90. +H 2 CH 3 90. 1 180. 0 +X 1 1. 2 90. 3 180. 0 +H 1 CH 5 90. 2 180. 0 + +CC=1.1989086 +CH=1.06216907 diff --git a/Ref/Inputs_G1/C2H2.xyz b/Ref/Inputs_G1/C2H2.xyz new file mode 100644 index 0000000..b46143f --- /dev/null +++ b/Ref/Inputs_G1/C2H2.xyz @@ -0,0 +1,10 @@ +0,1 +C +C,1,CC +X,2,1.,1,90. +H,2,CH,3,90.,1,180.,0 +X,1,1.,2,90.,3,180.,0 +H,1,CH,5,90.,2,180.,0 + +CC=1.1989086 +CH=1.06216907 diff --git a/Ref/Inputs_G1/C2H4.xyz b/Ref/Inputs_G1/C2H4.xyz new file mode 100644 index 0000000..6afa849 --- /dev/null +++ b/Ref/Inputs_G1/C2H4.xyz @@ -0,0 +1,11 @@ +0,1 +C +C,1,RCC +H,1,RCH,2,HCC +H,1,RCH,2,HCC,3,180.,0 +H,2,RCH,1,HCC,3,0.,0 +H,2,RCH,1,HCC,3,180.,0 + +RCC=1.32718886 +RCH=1.08577456 +HCC=121.95017938 diff --git a/Ref/Inputs_G1/C2H6.xyz b/Ref/Inputs_G1/C2H6.xyz new file mode 100644 index 0000000..b89f27b --- /dev/null +++ b/Ref/Inputs_G1/C2H6.xyz @@ -0,0 +1,13 @@ +0,1 +C +C,1,AA +H,1,AH,2,HAA +H,1,AH,2,HAA,3,120.,0 +H,1,AH,2,HAA,3,-120.,0 +H,2,AH,1,HAA,3,180.,0 +H,2,AH,1,HAA,6,120.,0 +H,2,AH,1,HAA,6,-120.,0 + +AA=1.53003633 +AH=1.09484731 +HAA=111.3741399 diff --git a/Ref/Inputs_G1/CH.xyz b/Ref/Inputs_G1/CH.xyz new file mode 100644 index 0000000..b3509f2 --- /dev/null +++ b/Ref/Inputs_G1/CH.xyz @@ -0,0 +1,5 @@ +0,2 +C +H,1,RCH + +RCH=1.13062603 diff --git a/Ref/Inputs_G1/CH2_1A1.xyz b/Ref/Inputs_G1/CH2_1A1.xyz new file mode 100644 index 0000000..45723ac --- /dev/null +++ b/Ref/Inputs_G1/CH2_1A1.xyz @@ -0,0 +1,7 @@ +0,1 +C +H,1,CH +H,1,CH,2,HCH + +CH=1.11792921 +HCH=99.85526193 diff --git a/Ref/Inputs_G1/CH2_3B1.xyz b/Ref/Inputs_G1/CH2_3B1.xyz new file mode 100644 index 0000000..f95a40a --- /dev/null +++ b/Ref/Inputs_G1/CH2_3B1.xyz @@ -0,0 +1,7 @@ +0,3 +C +H,1,RCH +H,1,RCH,2,HCH + +RCH=1.08097342 +HCH=133.83742404 diff --git a/Ref/Inputs_G1/CH3.xyz b/Ref/Inputs_G1/CH3.xyz new file mode 100644 index 0000000..094bd8b --- /dev/null +++ b/Ref/Inputs_G1/CH3.xyz @@ -0,0 +1,6 @@ +0,2 +C +H,1,CH +H,1,CH,2,120. +H,1,CH,2,120.,3,180.,0 +CH=1.08130823 diff --git a/Ref/Inputs_G1/CH3Cl.xyz b/Ref/Inputs_G1/CH3Cl.xyz new file mode 100644 index 0000000..388aac6 --- /dev/null +++ b/Ref/Inputs_G1/CH3Cl.xyz @@ -0,0 +1,10 @@ +0,1 +C +Cl,1,CCl +H,1,CH,2,HCCl +H,1,CH,2,HCCl,3,120.,0 +H,1,CH,2,HCCl,3,240.,0 + +CCl=1.79885648 +CH=1.08881113 +HCCl=108.3077969 diff --git a/Ref/Inputs_G1/CH3SH.xyz b/Ref/Inputs_G1/CH3SH.xyz new file mode 100644 index 0000000..65caa4b --- /dev/null +++ b/Ref/Inputs_G1/CH3SH.xyz @@ -0,0 +1,17 @@ +0,1 +C +S,1,CS +H,2,SH,1,CSH +H,1,CHA,2,HACS,3,180.,0 +X,1,1.,2,XCS,3,0.,0 +H,1,CHB,5,HALF,2,90.,0 +H,1,CHB,5,HALF,2,-90.,0 + +CS=1.82939003 +SH=1.34584251 +CHA=1.09139903 +CHB=1.09069821 +CSH=97.1035912 +HACS=106.02325623 +XCS=129.48465195 +HALF=55.21415843 diff --git a/Ref/Inputs_G1/CH4.xyz b/Ref/Inputs_G1/CH4.xyz new file mode 100644 index 0000000..3895f06 --- /dev/null +++ b/Ref/Inputs_G1/CH4.xyz @@ -0,0 +1,8 @@ +0,1 +C +H,1,RCH +H,1,RCH,2,109.47122063 +H,1,RCH,2,109.47122063,3,109.47122063,1 +H,1,RCH,2,109.47122063,3,109.47122063,-1 + +RCH=1.09185419 diff --git a/Ref/Inputs_G1/CH4O.xyz b/Ref/Inputs_G1/CH4O.xyz new file mode 100644 index 0000000..f43b194 --- /dev/null +++ b/Ref/Inputs_G1/CH4O.xyz @@ -0,0 +1,17 @@ +0,1 +C +O,1,AB +H,1,AH3,2,H3AB +H,2,BH9,1,H9BA,3,180.,0 +X,1,1.,2,BAH12,3,180.,0 +H,1,AH1,5,H1AH2,2,90.,0 +H,1,AH1,5,H1AH2,2,-90.,0 + +AB=1.41526798 +AH1=1.10037418 +AH3=1.09348232 +BH9=0.96129158 +H1AH2=54.13726394 +BAH12=131.31510075 +H3AB=106.94071399 +H9BA=107.8511363 diff --git a/Ref/Inputs_G1/CN.xyz b/Ref/Inputs_G1/CN.xyz new file mode 100644 index 0000000..c968479 --- /dev/null +++ b/Ref/Inputs_G1/CN.xyz @@ -0,0 +1,5 @@ +0,2 +C +N,1,R + +R=1.16945125 diff --git a/Ref/Inputs_G1/CO.xyz b/Ref/Inputs_G1/CO.xyz new file mode 100644 index 0000000..9ad27e9 --- /dev/null +++ b/Ref/Inputs_G1/CO.xyz @@ -0,0 +1,5 @@ +0,1 +O +C,1,RCO + +RCO=1.1309114 diff --git a/Ref/Inputs_G1/CO2.xyz b/Ref/Inputs_G1/CO2.xyz new file mode 100644 index 0000000..d4fe15f --- /dev/null +++ b/Ref/Inputs_G1/CO2.xyz @@ -0,0 +1,7 @@ +0,1 +C +O,1,R +X,1,1.,2,90. +O,1,R,3,90.,2,180.,0 + +R=1.16287946 diff --git a/Ref/Inputs_G1/CS.xyz b/Ref/Inputs_G1/CS.xyz new file mode 100644 index 0000000..f7bc3f2 --- /dev/null +++ b/Ref/Inputs_G1/CS.xyz @@ -0,0 +1,5 @@ +0,1 +C +S,1,CS + +CS=1.54093216 diff --git a/Ref/Inputs_G1/Cl.xyz b/Ref/Inputs_G1/Cl.xyz new file mode 100644 index 0000000..7d2160b --- /dev/null +++ b/Ref/Inputs_G1/Cl.xyz @@ -0,0 +1,2 @@ +0,2 +Cl diff --git a/Ref/Inputs_G1/Cl2.xyz b/Ref/Inputs_G1/Cl2.xyz new file mode 100644 index 0000000..85261f1 --- /dev/null +++ b/Ref/Inputs_G1/Cl2.xyz @@ -0,0 +1,5 @@ +0,1 +Cl +Cl,1,R + +R=2.01648224 diff --git a/Ref/Inputs_G1/ClF.xyz b/Ref/Inputs_G1/ClF.xyz new file mode 100644 index 0000000..c6102ea --- /dev/null +++ b/Ref/Inputs_G1/ClF.xyz @@ -0,0 +1,5 @@ +0,1 +F +Cl,1,R1 + +R1=1.64275079 diff --git a/Ref/Inputs_G1/ClO.xyz b/Ref/Inputs_G1/ClO.xyz new file mode 100644 index 0000000..880a367 --- /dev/null +++ b/Ref/Inputs_G1/ClO.xyz @@ -0,0 +1,5 @@ +0,2 +Cl +O,1,R + +R=1.59262773 diff --git a/Ref/Inputs_G1/F.xyz b/Ref/Inputs_G1/F.xyz new file mode 100644 index 0000000..d50f310 --- /dev/null +++ b/Ref/Inputs_G1/F.xyz @@ -0,0 +1,2 @@ +0,2 +F diff --git a/Ref/Inputs_G1/F2.xyz b/Ref/Inputs_G1/F2.xyz new file mode 100644 index 0000000..987043f --- /dev/null +++ b/Ref/Inputs_G1/F2.xyz @@ -0,0 +1,5 @@ +0,1 +F +F,1,FF + +FF=1.38792514 diff --git a/Ref/Inputs_G1/H.xyz b/Ref/Inputs_G1/H.xyz new file mode 100644 index 0000000..a89c19f --- /dev/null +++ b/Ref/Inputs_G1/H.xyz @@ -0,0 +1,2 @@ +0,2 +H diff --git a/Ref/Inputs_G1/H2CO.xyz b/Ref/Inputs_G1/H2CO.xyz new file mode 100644 index 0000000..4317c1b --- /dev/null +++ b/Ref/Inputs_G1/H2CO.xyz @@ -0,0 +1,9 @@ +0,1 +O +C,1,RCO +H,2,RH,1,THETA +H,2,RH,1,THETA,3,180.,0 + +RCO=1.19995954 +THETA=122.47953272 +RH=1.1108676 diff --git a/Ref/Inputs_G1/H2O.xyz b/Ref/Inputs_G1/H2O.xyz new file mode 100644 index 0000000..acb9d7a --- /dev/null +++ b/Ref/Inputs_G1/H2O.xyz @@ -0,0 +1,7 @@ +0,1 +O +H,1,OH +H,1,OH,2,HOH + +OH=0.96210248 +HOH=103.71685008 diff --git a/Ref/Inputs_G1/H2O2.xyz b/Ref/Inputs_G1/H2O2.xyz new file mode 100644 index 0000000..a8cdcc4 --- /dev/null +++ b/Ref/Inputs_G1/H2O2.xyz @@ -0,0 +1,10 @@ +0,1 +O +O,1,AA +H,1,AH4,2,H4AA +H,2,AH4,1,H4AA,3,H4AAH8,0 + +AA=1.44582784 +AH4=0.9672488 +H4AA=100.44937014 +H4AAH8=112.33679746 diff --git a/Ref/Inputs_G1/H2S.xyz b/Ref/Inputs_G1/H2S.xyz new file mode 100644 index 0000000..efbb13f --- /dev/null +++ b/Ref/Inputs_G1/H2S.xyz @@ -0,0 +1,8 @@ +0,1 +S +X,1,1. +H,1,R,2,A +H,1,R,2,A,3,180.,0 + +R=1.34531822 +A=46.20925632 diff --git a/Ref/Inputs_G1/H3COH.xyz b/Ref/Inputs_G1/H3COH.xyz new file mode 100644 index 0000000..f43b194 --- /dev/null +++ b/Ref/Inputs_G1/H3COH.xyz @@ -0,0 +1,17 @@ +0,1 +C +O,1,AB +H,1,AH3,2,H3AB +H,2,BH9,1,H9BA,3,180.,0 +X,1,1.,2,BAH12,3,180.,0 +H,1,AH1,5,H1AH2,2,90.,0 +H,1,AH1,5,H1AH2,2,-90.,0 + +AB=1.41526798 +AH1=1.10037418 +AH3=1.09348232 +BH9=0.96129158 +H1AH2=54.13726394 +BAH12=131.31510075 +H3AB=106.94071399 +H9BA=107.8511363 diff --git a/Ref/Inputs_G1/H3CSH.xyz b/Ref/Inputs_G1/H3CSH.xyz new file mode 100644 index 0000000..65caa4b --- /dev/null +++ b/Ref/Inputs_G1/H3CSH.xyz @@ -0,0 +1,17 @@ +0,1 +C +S,1,CS +H,2,SH,1,CSH +H,1,CHA,2,HACS,3,180.,0 +X,1,1.,2,XCS,3,0.,0 +H,1,CHB,5,HALF,2,90.,0 +H,1,CHB,5,HALF,2,-90.,0 + +CS=1.82939003 +SH=1.34584251 +CHA=1.09139903 +CHB=1.09069821 +CSH=97.1035912 +HACS=106.02325623 +XCS=129.48465195 +HALF=55.21415843 diff --git a/Ref/Inputs_G1/H3CSH.zmt b/Ref/Inputs_G1/H3CSH.zmt new file mode 100644 index 0000000..e4b39cf --- /dev/null +++ b/Ref/Inputs_G1/H3CSH.zmt @@ -0,0 +1,16 @@ +C +S 1 CS +H 2 SH 1 CSH +H 1 CHA 2 HACS 3 180. +X 1 1. 2 XCS 3 0. +H 1 CHB 5 HALF 2 90. +H 1 CHB 5 HALF 2 -90. + +CS 1.82939003 +SH 1.34584251 +CHA 1.09139903 +CHB 1.09069821 +CSH 97.1035912 +HACS 106.02325623 +XCS 129.48465195 +HALF 55.21415843 diff --git a/Ref/Inputs_G1/HCN.xyz b/Ref/Inputs_G1/HCN.xyz new file mode 100644 index 0000000..8517cd0 --- /dev/null +++ b/Ref/Inputs_G1/HCN.xyz @@ -0,0 +1,8 @@ +0,1 +C +N,1,AB +X,1,1.,2,90. +H,1,AH,3,90.,2,180.,0 + +AB=1.15174191 +AH=1.06658792 diff --git a/Ref/Inputs_G1/HCO.xyz b/Ref/Inputs_G1/HCO.xyz new file mode 100644 index 0000000..d2b7124 --- /dev/null +++ b/Ref/Inputs_G1/HCO.xyz @@ -0,0 +1,8 @@ +0,2 +C +O,1,CO +H,1,CH,2,HCO + +CO=1.17621067 +CH=1.12859543 +HCO=124.03532275 diff --git a/Ref/Inputs_G1/HCl.xyz b/Ref/Inputs_G1/HCl.xyz new file mode 100644 index 0000000..3fd1528 --- /dev/null +++ b/Ref/Inputs_G1/HCl.xyz @@ -0,0 +1,5 @@ +0,1 +Cl +H,1,R + +R=1.28367324 diff --git a/Ref/Inputs_G1/HF.xyz b/Ref/Inputs_G1/HF.xyz new file mode 100644 index 0000000..9881cf2 --- /dev/null +++ b/Ref/Inputs_G1/HF.xyz @@ -0,0 +1,5 @@ +0,1 +F +H,1,R + +R=0.91945793 diff --git a/Ref/Inputs_G1/HOCl.xyz b/Ref/Inputs_G1/HOCl.xyz new file mode 100644 index 0000000..f5571d8 --- /dev/null +++ b/Ref/Inputs_G1/HOCl.xyz @@ -0,0 +1,8 @@ +0,1 +O +H,1,OH +Cl,1,OCl,2,HOCl + +OH=0.96804646 +OCl=1.7074574 +HOCl=102.46612245 diff --git a/Ref/Inputs_G1/Li.xyz b/Ref/Inputs_G1/Li.xyz new file mode 100644 index 0000000..e965a72 --- /dev/null +++ b/Ref/Inputs_G1/Li.xyz @@ -0,0 +1,2 @@ +0,2 +Li diff --git a/Ref/Inputs_G1/Li2.xyz b/Ref/Inputs_G1/Li2.xyz new file mode 100644 index 0000000..b5c5ead --- /dev/null +++ b/Ref/Inputs_G1/Li2.xyz @@ -0,0 +1,5 @@ +0,1 +Li +Li,1,R + +R=2.72127987 diff --git a/Ref/Inputs_G1/LiF.xyz b/Ref/Inputs_G1/LiF.xyz new file mode 100644 index 0000000..e63c816 --- /dev/null +++ b/Ref/Inputs_G1/LiF.xyz @@ -0,0 +1,5 @@ +0,1 +Li +F,1,LiF + +LiF=1.56359565 diff --git a/Ref/Inputs_G1/LiH.xyz b/Ref/Inputs_G1/LiH.xyz new file mode 100644 index 0000000..34243f8 --- /dev/null +++ b/Ref/Inputs_G1/LiH.xyz @@ -0,0 +1,5 @@ +0,1 +Li +H,1,R + +R=1.61452972 diff --git a/Ref/Inputs_G1/Mg.xyz b/Ref/Inputs_G1/Mg.xyz new file mode 100644 index 0000000..2d715bb --- /dev/null +++ b/Ref/Inputs_G1/Mg.xyz @@ -0,0 +1,2 @@ +0,1 +Mg diff --git a/Ref/Inputs_G1/N.xyz b/Ref/Inputs_G1/N.xyz new file mode 100644 index 0000000..738dbeb --- /dev/null +++ b/Ref/Inputs_G1/N.xyz @@ -0,0 +1,2 @@ +0,4 +N diff --git a/Ref/Inputs_G1/N2.xyz b/Ref/Inputs_G1/N2.xyz new file mode 100644 index 0000000..f51758e --- /dev/null +++ b/Ref/Inputs_G1/N2.xyz @@ -0,0 +1,5 @@ +0,1 +N +N,1,NN + +NN=1.0987918 diff --git a/Ref/Inputs_G1/N2H4 b/Ref/Inputs_G1/N2H4 new file mode 100644 index 0000000..598292d --- /dev/null +++ b/Ref/Inputs_G1/N2H4 @@ -0,0 +1,15 @@ +0,1 +N +N,1,AA +H,1,AH4,2,H4AA +H,1,AH5,2,H5AA,3,H4AH5,1 +H,2,AH4,1,H4AA,3,H4AAH7,0 +H,2,AH5,1,H5AA,5,H4AH5,1 + +AA=1.43687706 +AH4=1.01893091 +AH5=1.01495037 +H4AA=111.61361711 +H5AA=106.79854321 +H4AH5=106.64730213 +H4AAH7=27.6651151 diff --git a/Ref/Inputs_G1/N2H4.xyz b/Ref/Inputs_G1/N2H4.xyz new file mode 100644 index 0000000..598292d --- /dev/null +++ b/Ref/Inputs_G1/N2H4.xyz @@ -0,0 +1,15 @@ +0,1 +N +N,1,AA +H,1,AH4,2,H4AA +H,1,AH5,2,H5AA,3,H4AH5,1 +H,2,AH4,1,H4AA,3,H4AAH7,0 +H,2,AH5,1,H5AA,5,H4AH5,1 + +AA=1.43687706 +AH4=1.01893091 +AH5=1.01495037 +H4AA=111.61361711 +H5AA=106.79854321 +H4AH5=106.64730213 +H4AAH7=27.6651151 diff --git a/Ref/Inputs_G1/NH.xyz b/Ref/Inputs_G1/NH.xyz new file mode 100644 index 0000000..d2f8a7c --- /dev/null +++ b/Ref/Inputs_G1/NH.xyz @@ -0,0 +1,5 @@ +0,3 +N +H,1,RNH + +RNH=1.0447328 diff --git a/Ref/Inputs_G1/NH2.xyz b/Ref/Inputs_G1/NH2.xyz new file mode 100644 index 0000000..58da34c --- /dev/null +++ b/Ref/Inputs_G1/NH2.xyz @@ -0,0 +1,7 @@ +0,2 +N +H,1,RBH +H,1,RBH,2,HBH + +RBH=1.03128471 +HBH=101.91770685 diff --git a/Ref/Inputs_G1/NH3.xyz b/Ref/Inputs_G1/NH3.xyz new file mode 100644 index 0000000..783f042 --- /dev/null +++ b/Ref/Inputs_G1/NH3.xyz @@ -0,0 +1,9 @@ +0,1 +N +X,1,1. +H,1,RNH,2,XNH +H,1,RNH,2,XNH,3,120.,0 +H,1,RNH,2,XNH,3,240.,0 + +RNH=1.01719433 +XNH=113.26166981 diff --git a/Ref/Inputs_G1/NO.xyz b/Ref/Inputs_G1/NO.xyz new file mode 100644 index 0000000..1f86f39 --- /dev/null +++ b/Ref/Inputs_G1/NO.xyz @@ -0,0 +1,5 @@ +0,2 +N +O,1,r + +r=1.15122729 diff --git a/Ref/Inputs_G1/Na.xyz b/Ref/Inputs_G1/Na.xyz new file mode 100644 index 0000000..5da4012 --- /dev/null +++ b/Ref/Inputs_G1/Na.xyz @@ -0,0 +1,2 @@ +0,2 +Na diff --git a/Ref/Inputs_G1/Na2.xyz b/Ref/Inputs_G1/Na2.xyz new file mode 100644 index 0000000..ff75052 --- /dev/null +++ b/Ref/Inputs_G1/Na2.xyz @@ -0,0 +1,5 @@ +0,1 +Na +Na,1,R + +R=3.0149584 diff --git a/Ref/Inputs_G1/NaCl.xyz b/Ref/Inputs_G1/NaCl.xyz new file mode 100644 index 0000000..e2798f9 --- /dev/null +++ b/Ref/Inputs_G1/NaCl.xyz @@ -0,0 +1,5 @@ +0,1 +Na +Cl,1,NaCl + +NaCl=2.3607642 diff --git a/Ref/Inputs_G1/O.xyz b/Ref/Inputs_G1/O.xyz new file mode 100644 index 0000000..3386c80 --- /dev/null +++ b/Ref/Inputs_G1/O.xyz @@ -0,0 +1,2 @@ +0,3 +O diff --git a/Ref/Inputs_G1/O2.xyz b/Ref/Inputs_G1/O2.xyz new file mode 100644 index 0000000..bb98a4e --- /dev/null +++ b/Ref/Inputs_G1/O2.xyz @@ -0,0 +1,5 @@ +0,3 +O +O,1,r + +r=1.20639068 diff --git a/Ref/Inputs_G1/OH.xyz b/Ref/Inputs_G1/OH.xyz new file mode 100644 index 0000000..76ec52a --- /dev/null +++ b/Ref/Inputs_G1/OH.xyz @@ -0,0 +1,5 @@ +0,2 +O +H,1,ROH + +ROH=0.97613331 diff --git a/Ref/Inputs_G1/P.xyz b/Ref/Inputs_G1/P.xyz new file mode 100644 index 0000000..cf585a3 --- /dev/null +++ b/Ref/Inputs_G1/P.xyz @@ -0,0 +1,2 @@ +0,4 +P diff --git a/Ref/Inputs_G1/P2.xyz b/Ref/Inputs_G1/P2.xyz new file mode 100644 index 0000000..c26204e --- /dev/null +++ b/Ref/Inputs_G1/P2.xyz @@ -0,0 +1,5 @@ +0,1 +P +P,1,PP + +PP=1.8953162 diff --git a/Ref/Inputs_G1/PH2.xyz b/Ref/Inputs_G1/PH2.xyz new file mode 100644 index 0000000..0275b1f --- /dev/null +++ b/Ref/Inputs_G1/PH2.xyz @@ -0,0 +1,8 @@ +0,2 +P +X,1,1. +H,1,R,2,A +H,1,R,2,A,3,180.,0 + +R=1.42692167 +A=45.79311753 diff --git a/Ref/Inputs_G1/PH3.xyz b/Ref/Inputs_G1/PH3.xyz new file mode 100644 index 0000000..20b547a --- /dev/null +++ b/Ref/Inputs_G1/PH3.xyz @@ -0,0 +1,9 @@ +0,1 +P +X,1,1. +H,1,R,2,BETA +H,1,R,2,BETA,3,120.,0 +H,1,R,2,BETA,3,-120.,0 + +R=1.42205572 +BETA=122.9486097 diff --git a/Ref/Inputs_G1/S.xyz b/Ref/Inputs_G1/S.xyz new file mode 100644 index 0000000..e217193 --- /dev/null +++ b/Ref/Inputs_G1/S.xyz @@ -0,0 +1,2 @@ +0,3 +S diff --git a/Ref/Inputs_G1/S2.xyz b/Ref/Inputs_G1/S2.xyz new file mode 100644 index 0000000..308489a --- /dev/null +++ b/Ref/Inputs_G1/S2.xyz @@ -0,0 +1,5 @@ +0,3 +S +S,1,R + +R=1.91215538 diff --git a/Ref/Inputs_G1/SO.xyz b/Ref/Inputs_G1/SO.xyz new file mode 100644 index 0000000..a33a9f8 --- /dev/null +++ b/Ref/Inputs_G1/SO.xyz @@ -0,0 +1,5 @@ +0,3 +O +S,1,OS + +OS=1.49681906 diff --git a/Ref/Inputs_G1/SO2.xyz b/Ref/Inputs_G1/SO2.xyz new file mode 100644 index 0000000..871d47f --- /dev/null +++ b/Ref/Inputs_G1/SO2.xyz @@ -0,0 +1,7 @@ +0,1 +S +O,1,SO +O,1,SO,2,OSO + +SO=1.44255426 +OSO=119.22404594 diff --git a/Ref/Inputs_G1/Si.xyz b/Ref/Inputs_G1/Si.xyz new file mode 100644 index 0000000..b3efce4 --- /dev/null +++ b/Ref/Inputs_G1/Si.xyz @@ -0,0 +1,2 @@ +0,3 +Si diff --git a/Ref/Inputs_G1/Si2.xyz b/Ref/Inputs_G1/Si2.xyz new file mode 100644 index 0000000..dda436d --- /dev/null +++ b/Ref/Inputs_G1/Si2.xyz @@ -0,0 +1,5 @@ +0,3 +Si +Si,1,R + +R=2.27042797 diff --git a/Ref/Inputs_G1/Si2H6.xyz b/Ref/Inputs_G1/Si2H6.xyz new file mode 100644 index 0000000..274aac7 --- /dev/null +++ b/Ref/Inputs_G1/Si2H6.xyz @@ -0,0 +1,13 @@ +0,1 +Si +Si,1,R +H,1,SIH,2,SICC +H,1,SIH,2,SICC,3,120.,0 +H,1,SIH,2,SICC,3,-120.,0 +H,2,SIH,1,SICC,3,180.,0 +H,2,SIH,1,SICC,6,120.,0 +H,2,SIH,1,SICC,6,-120.,0 + +SICC=110.49912192 +SIH=1.48548901 +R=2.35421744 diff --git a/Ref/Inputs_G1/SiH2_1A1.xyz b/Ref/Inputs_G1/SiH2_1A1.xyz new file mode 100644 index 0000000..28709e2 --- /dev/null +++ b/Ref/Inputs_G1/SiH2_1A1.xyz @@ -0,0 +1,8 @@ +0,1 +Si +X,1,1. +H,1,R,2,A +H,1,R,2,A,3,180.,0 + +R=1.52561661 +A=45.67372696 diff --git a/Ref/Inputs_G1/SiH2_3B1.xyz b/Ref/Inputs_G1/SiH2_3B1.xyz new file mode 100644 index 0000000..f168c72 --- /dev/null +++ b/Ref/Inputs_G1/SiH2_3B1.xyz @@ -0,0 +1,8 @@ +0,3 +Si +X,1,1. +H,1,R,2,A +H,1,R,2,A,3,180.,0 + +R=1.48656291 +A=59.20730743 diff --git a/Ref/Inputs_G1/SiH3.xyz b/Ref/Inputs_G1/SiH3.xyz new file mode 100644 index 0000000..a723889 --- /dev/null +++ b/Ref/Inputs_G1/SiH3.xyz @@ -0,0 +1,9 @@ +0,2 +Si +X,1,1. +H,1,R,2,BETA +H,1,R,2,BETA,3,120.,0 +H,1,R,2,BETA,3,-120.,0 + +R=1.48480778 +BETA=107.89090342 diff --git a/Ref/Inputs_G1/SiH4.xyz b/Ref/Inputs_G1/SiH4.xyz new file mode 100644 index 0000000..709b96c --- /dev/null +++ b/Ref/Inputs_G1/SiH4.xyz @@ -0,0 +1,8 @@ +0,1 +Si +H,1,R +H,1,R,2,109.47122063 +H,1,R,2,109.47122063,3,120.,0 +H,1,R,2,109.47122063,3,-120.,0 + +R=1.48241986 diff --git a/Ref/Inputs_G1/SiO.xyz b/Ref/Inputs_G1/SiO.xyz new file mode 100644 index 0000000..a8d5aab --- /dev/null +++ b/Ref/Inputs_G1/SiO.xyz @@ -0,0 +1,5 @@ +0,1 +Si +O,1,sio + +sio=1.51282579 diff --git a/Ref/Inputs_G1/atomization_energies b/Ref/Inputs_G1/atomization_energies new file mode 100644 index 0000000..d16d086 --- /dev/null +++ b/Ref/Inputs_G1/atomization_energies @@ -0,0 +1,56 @@ + val full +BeH 212.50 212.50 +C2H2 1685.16 1695.79 +C2H4 2348.65 2358.75 +C2H6 2971.49 2981.64 +CH 350.91 351.60 +CH2_1A1 755.71 757.45 +CH2_3B1 793.88 797.23 +CH3 1282.77 1287.21 +CH3Cl 1650.66 1656.17 +CH4 1752.56 1757.82 +CN 753.39 758.56 +CO 1083.14 1087.57 +CO2 1625.87 1633.95 +CS 715.40 719.47 +Cl2 247.16 248.22 +ClF 261.80 262.43 +ClO 270.00 271.20 +F2 162.15 162.31 +H2CO 1561.51 1567.43 +H2O 973.05 974.94 +H2O2 1124.05 1126.34 +H2S 766.92 768.72 +H3COH 2141.49 2147.84 +H3CSH 4016.15 4038.49 +HCN 1303.41 1310.97 +HCO 1164.33 1169.59 +HCl 448.52 449.58 +HF 592.09 593.02 +HOCl 693.67 695.38 +Li2 101.24 101.24 +LiF 583.12 583.99 +LiH 242.27 242.27 +N2 951.59 955.82 +N2H4 1827.15 1832.69 +NH 346.38 347.02 +NH2 761.30 762.95 +NH3 1242.94 1245.99 +NO 636.75 639.28 +Na2 71.55 71.78 +NaCl 411.98 412.96 +O2 504.36 505.88 +OH 447.50 448.30 +P2 485.14 489.29 +PH2 644.21 645.47 +PH3 1010.33 1012.24 +S2 431.42 433.94 +SO 526.33 528.72 +SO2 1086.86 1091.61 +Si2 431.42 433.94 +Si2H6 2626.11 2631.54 +SiH2_1A1 642.99 643.11 +SiH2_3B1 557.56 555.72 +SiH3 954.30 953.44 +SiH4 1358.08 1357.91 +SiO 804.83 809.19 diff --git a/Ref/Inputs_G1/create_ezfio_from_g09_xyz.sh b/Ref/Inputs_G1/create_ezfio_from_g09_xyz.sh new file mode 100755 index 0000000..a09198d --- /dev/null +++ b/Ref/Inputs_G1/create_ezfio_from_g09_xyz.sh @@ -0,0 +1,12 @@ +source ~/.bashrc + . ~/qp2/quantum_package.rc + +basis=$1 + +for i in *.xyz + do + comand=`qp_create_ezfio_from_g09_zmat $i $1` + echo $comand + eval $comand +done + diff --git a/Ref/Inputs_G1/list_atoms b/Ref/Inputs_G1/list_atoms new file mode 100644 index 0000000..98c2e8b --- /dev/null +++ b/Ref/Inputs_G1/list_atoms @@ -0,0 +1,17 @@ +list_atom=" +Al +Be +B +Cl +C +F +H +Li +Mg +Na +N +O +P +Si +S +" diff --git a/Ref/Inputs_G1/list_molecules b/Ref/Inputs_G1/list_molecules new file mode 100644 index 0000000..ddf74ae --- /dev/null +++ b/Ref/Inputs_G1/list_molecules @@ -0,0 +1,57 @@ +list_mol=" +BeH +C2H2 +C2H4 +C2H6 +CH +CH2_1A1 +CH2_3B1 +CH3 +CH3Cl +CH4 +CN +CO +CO2 +CS +Cl2 +ClF +ClO +F2 +H2CO +H2O +H2O2 +H2S +H3COH +H3CSH +HCN +HCO +HCl +HF +HOCl +Li2 +LiF +LiH +N2 +N2H4 +NH +NH2 +NH3 +NO +Na2 +NaCl +O2 +OH +P2 +PH2 +PH3 +S2 +SO +SO2 +Si2 +Si2H6 +SiH2_1A1 +SiH2_3B1 +SiH3 +SiH4 +SiO +" diff --git a/Ref/Inputs_G1/qp_create_ezfio_from_g09_zmat b/Ref/Inputs_G1/qp_create_ezfio_from_g09_zmat new file mode 100755 index 0000000..02c0579 --- /dev/null +++ b/Ref/Inputs_G1/qp_create_ezfio_from_g09_zmat @@ -0,0 +1,91 @@ +#!/usr/bin/env python2 +""" +convert zmatrix and input for spin multiplicity and charge from the SI of +J. Chem. Phys. 131, 154112 (2009); https://doi.org/10.1063/1.3247288 + +into a zmatrix usable by the QP, and spits the correct command to execute +Usage: + qp_create_ezfio_from_g09_zmat g09_zmat basis + +Produces the ezfio folder g09_zmat.ezfio + +""" + +import sys +import os +import subprocess + + +try: + import qp_path +except ImportError: + print "source .quantum_package.rc" + raise +try: + QP_ROOT = os.environ["QP_ROOT"] + QP_EZFIO = os.environ["QP_EZFIO"] +except KeyError: + print "Error: QP_ROOT environment variable not found." + sys.exit(1) +else: + sys.path = [QP_EZFIO + "/Python", + QP_ROOT + "/install/resultsFile", + QP_ROOT + "/install", + QP_ROOT + "/scripts"] + sys.path + + + +def findall(sub, string): + """ + >>> text = "Allowed Hello Hollow" + >>> tuple(findall('ll', text)) + (1, 10, 16) + """ + index = 0 - len(sub) + try: + while True: + index = string.index(sub, index + len(sub)) + yield index + except ValueError: + pass + +filepath = sys.argv[1] +basis = sys.argv[2] +icount = 0 +zmat = [] +with open(filepath, "r") as fp: + cipsi = [] + for line in fp: + if (icount == 0 ): + a=line.split(',') + charge = int(a[0]) + spin = int(a[1]) + else: + a=line.split() + if(len(a)>0): + n=a[0].count(',') + if(n > 6): + listfind=list(findall(',', a[0])) + char=a[0] + a[0]=char[0:listfind[n-1]] + + b=a[0].replace(',', ' ') + b=b.replace('=', ' ') + zmat.append(b) + else: + b=" " + zmat.append(b) + + icount += 1 + +c = filepath.split('.') +file_origin = c[0] +ezfio = file_origin+".ezfio" +zmat_file = file_origin+".zmt" +file_zmat = open(zmat_file,"w+") +for l in zmat: + file_zmat.write(l +'\n') + +command="qp_create_ezfio -m %s -c %s -b %s -o %s %s" % (spin,charge,basis,ezfio,zmat_file) +print command +#os.system(command) diff --git a/Ref/Inputs_G1/script_G2_VD.sh b/Ref/Inputs_G1/script_G2_VD.sh new file mode 100644 index 0000000..7e90b51 --- /dev/null +++ b/Ref/Inputs_G1/script_G2_VD.sh @@ -0,0 +1,56 @@ +#!/bin/bash + +# jobname: +#SBATCH -J D + +# initial working directory: +#SBATCH -D ./ + +# standard output and error: +#SBATCH -o ./test.out.%j +#SBATCH -e ./test.err.%j + +# queue or partition: +#SBATCH --partition=p.48h + +# Number of nodes and cores: +#SBATCH --nodes=1 +#SBATCH --ntasks=1 +#SBATCH --tasks-per-node=1 +#SBATCH --cpus-per-task=40 + +# mail: +#SBATCH --mail-type=end,fail +#SBATCH --mail-user=e.giner@fkf.mpg.de + +# wall clock limit: +#SBATCH --time=47:58:00 + +# run the program: + +module purge +source ~/.bashrc + . ~/qp2/quantum_package.rc + +#export OMP_NUM_THREADS=1 + +export OMP_NUM_THREADS=40 # 40 coeurs +export OMP_PROC_BIND=false + +############################################################################ + + +for i in *ezfio + do + ezfio=$i + + qp_run scf $ezfio | tee ${ezfio}.scf_1.out + qp_set_frozen_core ${ezfio} + qp_run cis $ezfio | tee ${ezfio}.cis.out + qp_run save_natorb $ezfio | tee ${ezfio}.natorb.out + qp_run scf $ezfio | tee ${ezfio}.scf_1.out + qp_run scf $ezfio | tee ${ezfio}.scf_2.out + qp_run all_mu_of_r_corrections ${ezfio} | tee ${ezfio}.DFT.out + +done + diff --git a/Ref/Inputs_G1/test b/Ref/Inputs_G1/test new file mode 100644 index 0000000..6dd6efd --- /dev/null +++ b/Ref/Inputs_G1/test @@ -0,0 +1,16 @@ + o + o 1 oo + h 1 ho 2 hoo + h 2 ho 1 hoo 3 dih + +oo 1.475 +ho 0.95 +hoo 94.8 +dih 119.8 + +0,1 +O +C,1,RCO + +RCO=1.1309114 +