diff --git a/Ref/Atoms/Al.xyz b/Ref/Atoms/Al.xyz deleted file mode 100644 index 58f470f..0000000 --- a/Ref/Atoms/Al.xyz +++ /dev/null @@ -1,2 +0,0 @@ -0,2 -Al diff --git a/Ref/Atoms/B.xyz b/Ref/Atoms/B.xyz deleted file mode 100644 index 25c2c68..0000000 --- a/Ref/Atoms/B.xyz +++ /dev/null @@ -1,2 +0,0 @@ -0,2 -B diff --git a/Ref/Atoms/list_atoms b/Ref/Atoms/list_atoms index 98c2e8b..2c01c8f 100644 --- a/Ref/Atoms/list_atoms +++ b/Ref/Atoms/list_atoms @@ -1,7 +1,5 @@ list_atom=" -Al Be -B Cl C F diff --git a/Ref/Inputs_G1/C2H2.g09_zmat b/Ref/Inputs_G1/C2H2.g09_not_sure_zmat similarity index 100% rename from Ref/Inputs_G1/C2H2.g09_zmat rename to Ref/Inputs_G1/C2H2.g09_not_sure_zmat diff --git a/Ref/Inputs_G1/C2H2.xyz b/Ref/Inputs_G1/C2H2.xyz new file mode 100644 index 0000000..b629b6a --- /dev/null +++ b/Ref/Inputs_G1/C2H2.xyz @@ -0,0 +1,6 @@ +4 +0,1 +C 0.000000 0.000000 0.000000 +C 0.000000 0.000000 1.198909 +H 0.000000 0.000000 2.261078 +H 0.000000 0.000000 -1.062169 diff --git a/Ref/Inputs_G1/CH3SH.xyz b/Ref/Inputs_G1/CH3SH.xyz new file mode 100644 index 0000000..e1dd0d1 --- /dev/null +++ b/Ref/Inputs_G1/CH3SH.xyz @@ -0,0 +1,8 @@ +6 +0,1 +C 0.000000 0.000000 0.000000 +S 0.000000 0.000000 1.829390 +H 1.335512 0.000000 1.995822 +H -1.048998 0.000000 -0.301256 +H 0.480253 0.895780 -0.395674 +H 0.480253 -0.895780 -0.395674 diff --git a/Ref/Inputs_G1/CH4.g09_zmat b/Ref/Inputs_G1/CH4.g09_not_sure_zmat similarity index 100% rename from Ref/Inputs_G1/CH4.g09_zmat rename to Ref/Inputs_G1/CH4.g09_not_sure_zmat diff --git a/Ref/Inputs_G1/CH4.xyz b/Ref/Inputs_G1/CH4.xyz index fd07d70..7aef167 100644 --- a/Ref/Inputs_G1/CH4.xyz +++ b/Ref/Inputs_G1/CH4.xyz @@ -1,7 +1,8 @@ 4 0,1 -C 0.00000000000000 0.00000000000000 0.00000000000000 -H 1.19124933910072 1.19124933910072 1.19124933910072 -H -1.19124933910072 -1.19124933910072 1.19124933910072 -H 1.19124933910072 -1.19124933910072 -1.19124933910072 -H -1.19124933910072 1.19124933910072 -1.19124933910072 +C 0.000000 0.000000 0.000000 +H 0.000000 0.000000 1.091854 +H 1.029410 0.000000 -0.363951 +H -0.514705 0.891495 -0.363951 +H -0.514705 -0.891495 -0.363951 + diff --git a/Ref/Inputs_G1/CO2.g09_zmat b/Ref/Inputs_G1/CO2.g09_not_sure_zmat similarity index 100% rename from Ref/Inputs_G1/CO2.g09_zmat rename to Ref/Inputs_G1/CO2.g09_not_sure_zmat diff --git a/Ref/Inputs_G1/CO2.xyz b/Ref/Inputs_G1/CO2.xyz new file mode 100644 index 0000000..a3ef0d9 --- /dev/null +++ b/Ref/Inputs_G1/CO2.xyz @@ -0,0 +1,6 @@ +3 +0,1 +C 0.000000 0.000000 0.000000 +O 0.000000 0.000000 1.162879 +O 0.000000 0.000000 -1.162879 + diff --git a/Ref/Inputs_G1/H2S.g09_zmat b/Ref/Inputs_G1/H2S.g09_not_sure_zmat similarity index 100% rename from Ref/Inputs_G1/H2S.g09_zmat rename to Ref/Inputs_G1/H2S.g09_not_sure_zmat diff --git a/Ref/Inputs_G1/H2S.xyz b/Ref/Inputs_G1/H2S.xyz new file mode 100644 index 0000000..ca42a80 --- /dev/null +++ b/Ref/Inputs_G1/H2S.xyz @@ -0,0 +1,5 @@ +3 +0,1 +S 0.000000 0.000000 0.000000 +H 0.971148 0.000000 0.930996 +H -0.971148 0.000000 0.930996 diff --git a/Ref/Inputs_G1/H3COH.g09_zmat b/Ref/Inputs_G1/H3COH.g09_not_sure_zmat similarity index 100% rename from Ref/Inputs_G1/H3COH.g09_zmat rename to Ref/Inputs_G1/H3COH.g09_not_sure_zmat diff --git a/Ref/Inputs_G1/H3COH.xyz b/Ref/Inputs_G1/H3COH.xyz new file mode 100644 index 0000000..7a6a787 --- /dev/null +++ b/Ref/Inputs_G1/H3COH.xyz @@ -0,0 +1,8 @@ +6 +0,1 +C 0.000000 0.000000 0.000000 +O 0.000000 0.000000 1.415268 +H 1.046033 0.000000 -0.318621 +H -0.915011 0.000000 1.709947 +H -0.484190 -0.891768 -0.425597 +H -0.484190 0.891768 -0.425597 diff --git a/Ref/Inputs_G1/H3CSH.zmt b/Ref/Inputs_G1/H3CSH.zmt deleted file mode 100644 index e4b39cf..0000000 --- a/Ref/Inputs_G1/H3CSH.zmt +++ /dev/null @@ -1,16 +0,0 @@ -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.g09_zmat b/Ref/Inputs_G1/HCN.g09_not_sure_zmat similarity index 100% rename from Ref/Inputs_G1/HCN.g09_zmat rename to Ref/Inputs_G1/HCN.g09_not_sure_zmat diff --git a/Ref/Inputs_G1/HCN.xyz b/Ref/Inputs_G1/HCN.xyz new file mode 100644 index 0000000..7cd4140 --- /dev/null +++ b/Ref/Inputs_G1/HCN.xyz @@ -0,0 +1,5 @@ +3 +0,1 +C 0.000000 0.000000 0.000000 +N 0.000000 0.000000 1.151742 +H 0.000000 0.000000 -1.066588 diff --git a/Ref/Inputs_G1/N2H4.g09_zmat b/Ref/Inputs_G1/N2H4.g09_not_sure_zmat similarity index 100% rename from Ref/Inputs_G1/N2H4.g09_zmat rename to Ref/Inputs_G1/N2H4.g09_not_sure_zmat diff --git a/Ref/Inputs_G1/N2H4.xyz b/Ref/Inputs_G1/N2H4.xyz new file mode 100644 index 0000000..1c87553 --- /dev/null +++ b/Ref/Inputs_G1/N2H4.xyz @@ -0,0 +1,8 @@ +6 +0,1 +N 0.000000 0.000000 0.000000 +N 0.000000 0.000000 1.436877 +H 0.947289 0.000000 -0.375319 +H -0.428970 0.871819 -0.293328 +H 0.838991 0.439829 1.812196 +H 0.024859 -0.971321 1.730205 diff --git a/Ref/Inputs_G1/NH3.g09_zmat b/Ref/Inputs_G1/NH3.g09_not_sure_zmat similarity index 100% rename from Ref/Inputs_G1/NH3.g09_zmat rename to Ref/Inputs_G1/NH3.g09_not_sure_zmat diff --git a/Ref/Inputs_G1/NH3.xyz b/Ref/Inputs_G1/NH3.xyz new file mode 100644 index 0000000..15d8065 --- /dev/null +++ b/Ref/Inputs_G1/NH3.xyz @@ -0,0 +1,6 @@ +4 +0,1 +N 0.000000 0.000000 0.000000 +H 0.934507 0.000000 -0.401722 +H -0.467254 -0.809307 -0.401722 +H -0.467254 0.809307 -0.401722 diff --git a/Ref/Inputs_G1/PH2.g09_zmat b/Ref/Inputs_G1/PH2.g09_not_sure_zmat similarity index 100% rename from Ref/Inputs_G1/PH2.g09_zmat rename to Ref/Inputs_G1/PH2.g09_not_sure_zmat diff --git a/Ref/Inputs_G1/PH2.xyz b/Ref/Inputs_G1/PH2.xyz new file mode 100644 index 0000000..6eace75 --- /dev/null +++ b/Ref/Inputs_G1/PH2.xyz @@ -0,0 +1,5 @@ +3 +0,2 +P 0.000000 0.000000 0.000000 +H 1.022856 0.000000 0.994923 +H -1.022856 0.000000 0.994923 diff --git a/Ref/Inputs_G1/PH2.zmt b/Ref/Inputs_G1/PH2.zmt deleted file mode 100644 index d86a3b8..0000000 --- a/Ref/Inputs_G1/PH2.zmt +++ /dev/null @@ -1,7 +0,0 @@ -P -X 1 1. -H 1 R 2 A -H 1 R 2 A 3 180. - -R 1.42692167 -A 45.79311753 diff --git a/Ref/Inputs_G1/PH3.g09_zmat b/Ref/Inputs_G1/PH3.g09_not_sure_zmat similarity index 100% rename from Ref/Inputs_G1/PH3.g09_zmat rename to Ref/Inputs_G1/PH3.g09_not_sure_zmat diff --git a/Ref/Inputs_G1/PH3.xyz b/Ref/Inputs_G1/PH3.xyz new file mode 100644 index 0000000..1a82847 --- /dev/null +++ b/Ref/Inputs_G1/PH3.xyz @@ -0,0 +1,7 @@ +4 +0,1 +P 0.000000 0.000000 0.000000 +H 1.193330 0.000000 -0.773437 +H -0.596665 -1.033455 -0.773437 +H -0.596665 1.033455 -0.773437 + diff --git a/Ref/Inputs_G1/README b/Ref/Inputs_G1/README deleted file mode 100644 index efe7408..0000000 --- a/Ref/Inputs_G1/README +++ /dev/null @@ -1,4 +0,0 @@ -First create the ezfio for all set of molecule: -./create_ezfio_from_g09_xyz.sh cc-pvdz # here in the cc-pvdz basis for instance -then shoot the ROHF and DFT correction -sbatch script_G2_VD.sh diff --git a/Ref/Inputs_G1/SiH3.g09_zmat b/Ref/Inputs_G1/SiH3.g09_not_sure_zmat similarity index 100% rename from Ref/Inputs_G1/SiH3.g09_zmat rename to Ref/Inputs_G1/SiH3.g09_not_sure_zmat diff --git a/Ref/Inputs_G1/SiH3.xyz b/Ref/Inputs_G1/SiH3.xyz new file mode 100644 index 0000000..914d4cf --- /dev/null +++ b/Ref/Inputs_G1/SiH3.xyz @@ -0,0 +1,6 @@ +4 +0,2 +Si 0.000000 0.000000 0.000000 +H 1.413007 0.000000 -0.456141 +H -0.706504 -1.223700 -0.456141 +H -0.706504 1.223700 -0.456141 diff --git a/Ref/Inputs_G1/atomization_energies b/Ref/Inputs_G1/atomization_energies deleted file mode 100644 index fe8d540..0000000 --- a/Ref/Inputs_G1/atomization_energies +++ /dev/null @@ -1,57 +0,0 @@ -# atomization energies (in kJ/mol) for valence only or including core-valence effects - 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/produce_HF.sh b/Ref/Inputs_G1/produce_HF.sh new file mode 100755 index 0000000..d347745 --- /dev/null +++ b/Ref/Inputs_G1/produce_HF.sh @@ -0,0 +1,19 @@ +source list_molecules +source list_atoms + +basis=$1 + +rm data_HF_$basis +#for i in $list_atom +# do +# file="${basis}/${i}.ezfio.scf_2.out" +# EHF=`grep "SCF energy" $file | cut -d "y" -f 2` +# echo $i $EHF >> data_HF_$basis +#done + +for i in $list_mol + do + file="${basis}/${i}.ezfio.scf_2.out" + EHF=`grep "SCF energy" $file | cut -d "y" -f 2` + echo $i $EHF >> data_HF_$basis +done diff --git a/Ref/Inputs_G1/produce_tables_g09.sh b/Ref/Inputs_G1/produce_tables_g09.sh new file mode 100755 index 0000000..24d1a35 --- /dev/null +++ b/Ref/Inputs_G1/produce_tables_g09.sh @@ -0,0 +1,10 @@ + + +for i in *.out + do + system=${i%.out} + echo $system + file=$i + EHF=`grep "E(ROHF) = -76.0265262687" $file | cut -d "=" -f 2 | cut -d "A" -f 1` + ECCSDT=`grep "CCSD(T)=" $file | tail -1 | cut -d ")" -f 2 | cut -d "=" -f 2 | cut -d "\\" -f 1` +done diff --git a/Ref/Inputs_G1/script_G2_VD.sh b/Ref/Inputs_G1/script_G2_VD.sh index 7e90b51..260f55a 100755 --- a/Ref/Inputs_G1/script_G2_VD.sh +++ b/Ref/Inputs_G1/script_G2_VD.sh @@ -48,7 +48,6 @@ for i in *ezfio 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