| 1 | #
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| 2 | eval 'exec perl $0 $*'
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| 3 | if 0;
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| 4 |
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| 5 | require QCParse;
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| 6 |
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| 7 | $prefix = "";
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| 8 | @files = ();
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| 9 | %files = ();
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| 10 | $writefiles = 1;
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| 11 | $echonames = 0;
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| 12 | $dir = "";
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| 13 | %basissets = (
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| 14 | "STO-2G" => [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20],
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| 15 | "STO-3G" => [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36],
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| 16 | "STO-3G*" => [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18],
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| 17 | "STO-6G" => [1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36],
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| 18 | "MINI (Huzinaga)" => [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20],
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| 19 | "MINI (Scaled)" => [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20],
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| 20 | "MIDI (Huzinaga)" => [1,2,3,4,5,6,7,8,9,10,11],
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| 21 | "DZ (Dunning)" => [1,3,5,6,7,8,9,10,13,14,15,16,17],
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| 22 | "DZP (Dunning)" => [1,3,5,6,7,8,9,10,13,14,15,16,17],
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| 23 | "DZP + Diffuse (Dunning)" => [1,5,6,7,8,9,10],
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| 24 | "3-21G" => [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36],
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| 25 | "3-21G*" => [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18],
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| 26 | "3-21++G" => [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18],
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| 27 | "3-21++G*" => [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18],
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| 28 | "4-31G" => [1,2,3,4,5,6,7,8,9,10,15,16,17],
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| 29 | "6-31G" => [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18],
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| 30 | "6-31G*" => [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18],
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| 31 | "6-31G**" => [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18],
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| 32 | "6-31+G*" => [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18],
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| 33 | "6-31++G" => [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18],
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| 34 | "6-31++G*" => [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18],
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| 35 | "6-31++G**" => [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18],
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| 36 | "6-311G" => [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,31,32,33,34,35,36],
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| 37 | "6-311G*" => [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,31,32,33,34,35,36],
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| 38 | "6-311G**" => [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,31,32,33,34,35,36],
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| 39 | "6-311G(2df,2pd)" => [1,2,3,4,5,6,7,8,9,10],
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| 40 | "6-311++G**" => [1,2,3,4,5,6,7,8,9,10],
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| 41 | "6-311++G(2d,2p)" => [1,2,3,4,5,6,7,8,9,10],
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| 42 | "6-311++G(3df,3pd)" => [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18],
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| 43 | "cc-pVDZ" => [1,2,5,6,7,8,9,10,13,14,15,16,17,18],
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| 44 | "cc-pVTZ" => [1,2,5,6,7,8,9,10,13,14,15,16,17,18],
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| 45 | "cc-pVQZ" => [1,2,5,6,7,8,9,10,13,14,15,16,17,18],
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| 46 | "cc-pV5Z" => [1,2,3,4,5,6,7,8,9,10,13,14,15,16,17,18],
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| 47 | "aug-cc-pVDZ" => [1,2,5,6,7,8,9,10,13,14,15,16,17,18],
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| 48 | "aug-cc-pVTZ" => [1,2,5,6,7,8,9,10,13,14,15,16,17,18],
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| 49 | "aug-cc-pVQZ" => [1,2,5,6,7,8,9,10,13,14,15,16,17,18],
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| 50 | "aug-cc-pV5Z" => [1,2,5,6,7,8,9,10,13,14,15,16,17,18],
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| 51 | "cc-pCVDZ" => [5,6,7,8,9,10],
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| 52 | "cc-pCVTZ" => [5,6,7,8,9,10],
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| 53 | "cc-pCVQZ" => [5,6,7,8,9,10],
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| 54 | "cc-pCV5Z" => [5,6,7,8,9,10],
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| 55 | "aug-cc-pCVDZ" => [5,6,7,8,9],
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| 56 | "aug-cc-pCVTZ" => [5,6,7,8,9,10],
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| 57 | "aug-cc-pCVQZ" => [5,6,7,8,9,10],
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| 58 | "aug-cc-pCV5Z" => [5,6,7,8,9],
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| 59 | "NASA Ames ANO" => [1,5,6,7,8,9,10,13,15,22,26,28],
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| 60 | "pc-0" => [1,6,7,8,9,14,15,16,17],
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| 61 | "pc-1" => [1,6,7,8,9,14,15,16,17],
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| 62 | "pc-2" => [1,6,7,8,9,14,15,16,17],
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| 63 | "pc-3" => [1,6,7,8,9,14,15,16,17],
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| 64 | "pc-4" => [1,6,7,8,9,14,15,16,17],
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| 65 | "pc-0-aug" => [1,6,7,8,9,14,15,16,17],
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| 66 | "pc-1-aug" => [1,6,7,8,9,14,15,16,17],
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| 67 | "pc-2-aug" => [1,6,7,8,9,14,15,16,17],
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| 68 | "pc-3-aug" => [1,6,7,8,9,14,15,16,17],
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| 69 | "pc-4-aug" => [1,6,7,8,9,14,15,16,17]
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| 70 | );
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| 71 |
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| 72 | while ($_ = shift) {
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| 73 | if (/^-I(.*)/) {
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| 74 | $prefix = $1;
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| 75 | }
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| 76 | elsif (/^-p(.+)$/) {
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| 77 | $package = $1;
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| 78 | }
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| 79 | elsif (/^-p$/) {
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| 80 | $package = shift;
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| 81 | }
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| 82 | elsif (/^-e$/) {
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| 83 | $writefiles = 0;
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| 84 | $echonames = 1;
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| 85 | }
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| 86 | elsif (/^-d$/) {
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| 87 | $dir = shift;
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| 88 | $dir = "$dir/";
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| 89 | }
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| 90 | else {
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| 91 | unshift @files, $_;
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| 92 | }
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| 93 | }
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| 94 |
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| 95 | foreach $i (@files) {
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| 96 | process_file($i, $package);
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| 97 | }
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| 98 |
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| 99 | if ($echonames) {
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| 100 | for $i (keys(%files)) {
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| 101 | print "$i\n";
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| 102 | }
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| 103 | }
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| 104 |
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| 105 | sub process_file {
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| 106 | my $file = shift;
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| 107 | my $package = shift;
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| 108 | my $parse = new QCParse;
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| 109 |
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| 110 | my $fullfile = "$prefix/$file";
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| 111 | $parse->parse_file($fullfile);
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| 112 | if (! $echonames) {
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| 113 | print "File: $fullfile\n";
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| 114 | }
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| 115 |
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| 116 | $file =~ s/^.*\/([^\/]*)$/\1/;
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| 117 | $file =~ s/\..*$//;
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| 118 |
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| 119 | my $test_vars = {};
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| 120 | init_var($test_vars, $parse, "basis", "STO-3G");
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| 121 | init_var($test_vars, $parse, "auxbasis", "");
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| 122 | init_var($test_vars, $parse, "grid", "default");
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| 123 | init_var($test_vars, $parse, "symmetry", "C1");
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| 124 | init_var($test_vars, $parse, "method", "SCF");
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| 125 | init_var($test_vars, $parse, "calc", "energy");
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| 126 | init_var($test_vars, $parse, "fzc", 0);
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| 127 | init_var($test_vars, $parse, "fzv", 0);
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| 128 | init_var($test_vars, $parse, "docc", "auto");
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| 129 | init_var($test_vars, $parse, "socc", "auto");
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| 130 | init_var($test_vars, $parse, "multiplicity", 1);
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| 131 | init_var($test_vars, $parse, "gradient", "default");
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| 132 | init_var($test_vars, $parse, "molecule", "molecule");
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| 133 | init_var($test_vars, $parse, "orthog_method", "default");
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| 134 | init_var($test_vars, $parse, "lindep_tol", "default");
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| 135 | init_var($test_vars, $parse, "integral_buffer", "opaque");
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| 136 | init_var($test_vars, $parse, "integral_package", "intv3");
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| 137 | my @molecule_symmetry = $parse->value_as_array("test_molecule_symmetry");
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| 138 | my @molecule_fzc = $parse->value_as_array("test_molecule_fzc");
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| 139 | my @molecule_fzv = $parse->value_as_array("test_molecule_fzv");
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| 140 | my @molecule_docc = $parse->value_as_array("test_molecule_docc");
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| 141 | my @molecule_socc = $parse->value_as_array("test_molecule_socc");
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| 142 | my @molecule_mult = $parse->value_as_array("test_molecule_multiplicity");
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| 143 | my @molecule_gradient = $parse->value_as_array("test_molecule_gradient");
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| 144 | my @molecule_followed = $parse->value_as_array("test_molecule_followed");
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| 145 | my @molecule_fixed = $parse->value_as_array("test_molecule_fixed");
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| 146 | my $do_cca = "";
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| 147 | my $tmp_do_cca = $parse->value("do_cca");
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| 148 | if ($tmp_do_cca eq "yes") {
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| 149 | $do_cca = "yes";
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| 150 | }
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| 151 |
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| 152 | my @keys = keys(%{$test_vars});
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| 153 | my $index = {};
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| 154 | my $size = {};
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| 155 | my $i;
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| 156 | foreach $i (@keys) {
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| 157 | $index->{$i} = 0;
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| 158 | $size->{$i} = scalar(@{$test_vars->{$i}});
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| 159 | }
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| 160 | for ($i=0; $i < $nkeys; $i++) { $vals->{$i} = 0; }
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| 161 | # this is equivalent to a nested loop for each test var,
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| 162 | # but is much easier to maintain
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| 163 | do {
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| 164 | my $basis = $test_vars->{"basis"}->[$index->{"basis"}];
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| 165 | my $auxbasis = $test_vars->{"auxbasis"}->[$index->{"auxbasis"}];
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| 166 | my $grid = $test_vars->{"grid"}->[$index->{"grid"}];
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| 167 | my $fzc = $test_vars->{"fzc"}->[$index->{"fzc"}];
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| 168 | my $fzv = $test_vars->{"fzv"}->[$index->{"fzv"}];
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| 169 | my $docc = $test_vars->{"docc"}->[$index->{"docc"}];
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| 170 | my $socc = $test_vars->{"socc"}->[$index->{"socc"}];
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| 171 | my $mult = $test_vars->{"multiplicity"}->[$index->{"multiplicity"}];
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| 172 | my $gradient = $test_vars->{"gradient"}->[$index->{"gradient"}];
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| 173 | my $method = $test_vars->{"method"}->[$index->{"method"}];
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| 174 | my $calc = $test_vars->{"calc"}->[$index->{"calc"}];
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| 175 | my $symmetry = $test_vars->{"symmetry"}->[$index->{"symmetry"}];
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| 176 | my $molecule = $test_vars->{"molecule"}->[$index->{"molecule"}];
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| 177 | my $fixed = $molecule_fixed[$index->{"fixed"}];
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| 178 | my $followed = $molecule_fixed[$index->{"followed"}];
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| 179 | my $orthog_method = $test_vars->{"orthog_method"}->[$index->{"orthog_method"}];
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| 180 | my $lindep_tol = $test_vars->{"lindep_tol"}->[$index->{"lindep_tol"}];
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| 181 | my $integral_buffer = $test_vars->{"integral_buffer"}->[$index->{"integral_buffer"}];
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| 182 | my $integral_package = $test_vars->{"integral_package"}->[$index->{"integral_package"}];
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| 183 | # if i got an array of molecule names then i expect
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| 184 | # an array of point groups, one for each molecule
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| 185 | if ($molecule ne "molecule") {
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| 186 | my $molindex = $index->{"molecule"};
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| 187 | $symmetry = $molecule_symmetry[$molindex];
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| 188 | if ($symmetry eq "") {
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| 189 | printf "\n";
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| 190 | printf "index = %d\n", $molindex;
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| 191 | printf "symmetry not set for a molecule array\n";
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| 192 | exit 1;
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| 193 | }
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| 194 | # check for frozen orbitals
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| 195 | if ($#molecule_fzc >= $molindex) {
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| 196 | $fzc = $molecule_fzc[$molindex];
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| 197 | }
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| 198 | if ($#molecule_fzv >= $molindex) {
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| 199 | $fzv = $molecule_fzv[$molindex];
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| 200 | }
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| 201 | # check for occupations
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| 202 | if ($#molecule_docc >= $molindex) {
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| 203 | $docc = $molecule_docc[$molindex];
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| 204 | }
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| 205 | if ($#molecule_socc >= $molindex) {
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| 206 | $socc = $molecule_socc[$molindex];
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| 207 | }
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| 208 | if ($#molecule_mult >= $molindex) {
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| 209 | $mult = $molecule_mult[$molindex];
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| 210 | }
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| 211 | if ($#molecule_gradient >= $molindex) {
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| 212 | $gradient = $molecule_gradient[$molindex];
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| 213 | }
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| 214 | # check for fixed coordinates
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| 215 | $fixed = $molecule_fixed[$molindex];
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| 216 | if ($fixed eq "-") {
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| 217 | $fixed = "";
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| 218 | }
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| 219 | # check for followed coordinates
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| 220 | $followed = $molecule_followed[$molindex];
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| 221 | if ($followed eq "-") {
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| 222 | $followed = "";
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| 223 | }
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| 224 | }
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| 225 |
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| 226 | # the filename to use for the calc
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| 227 | my $fcalc;
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| 228 |
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| 229 | # only need fzc and fzv for correlated calculations
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| 230 | if (!($method =~ /MP2/i)
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| 231 | && !($method =~ /OPT1/i)
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| 232 | && !($method =~ /OPT2[2]/i)
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| 233 | && !($method =~ /ZAPT2/i)) {
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| 234 | $fzc = "";
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| 235 | $fzv = "";
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| 236 | }
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| 237 | if ($calc eq "energy") {
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| 238 | $parse->set_value("optimize", "no");
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| 239 | $parse->set_value("frequencies", "no");
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| 240 | $fcalc = "";
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| 241 | }
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| 242 | elsif ($calc eq "opt") {
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| 243 | $parse->set_value("optimize", "yes");
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| 244 | $parse->set_value("frequencies", "no");
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| 245 | $fcalc = "opt";
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| 246 | }
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| 247 | elsif ($calc eq "freq") {
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| 248 | $parse->set_value("optimize", "no");
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| 249 | $parse->set_value("frequencies", "yes");
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| 250 | $fcalc = "frq";
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| 251 | }
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| 252 | elsif ($calc eq "optfreq") {
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| 253 | $parse->set_value("optimize", "yes");
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| 254 | $parse->set_value("frequencies", "yes");
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| 255 | $fcalc = "optfrq";
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| 256 | }
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| 257 | else {
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| 258 | print "Bad value for calc: $calc\n";
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| 259 | exit 1;
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| 260 | }
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| 261 |
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| 262 | my $fextra = ""; # extra filename modifiers
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| 263 | $parse->set_value("basis", $basis);
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| 264 | $parse->set_value("auxbasis", $auxbasis);
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| 265 | $parse->set_value("grid", $grid);
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| 266 | $parse->set_value("method", $method);
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| 267 | $parse->set_value("symmetry", $symmetry);
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| 268 | $parse->set_value("integral_buffer", $integral_buffer);
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| 269 | $parse->set_value("integral_package", $integral_package);
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| 270 | $parse->set_value("fzc", $fzc);
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| 271 | $parse->set_value("fzv", $fzv);
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| 272 | $parse->set_value("docc", $docc);
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| 273 | $parse->set_value("socc", $socc);
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| 274 | $parse->set_value("state", $mult);
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| 275 | if ($gradient ne "default") {
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| 276 | if ($method =~ /v[12](lb)?$/) {
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| 277 | # these methods don't support gradients
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| 278 | $parse->set_value("gradient", "no");
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| 279 | }
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| 280 | else {
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| 281 | $parse->set_value("gradient", $gradient);
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| 282 | }
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| 283 | }
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| 284 | if ($orthog_method ne "default") {
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| 285 | $parse->set_value("orthog_method", $orthog_method);
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| 286 | if ($orthog_method eq "gramschmidt") {
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| 287 | $fextra = "gs$fextra";
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| 288 | }
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| 289 | elsif ($orthog_method eq "canonical") {
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| 290 | $fextra = "can$fextra";
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| 291 | }
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| 292 | elsif ($orthog_method eq "symmetric") {
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| 293 | $fextra = "sym$fextra";
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| 294 | }
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| 295 | else {
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| 296 | $fextra = "$orthog_method$fextra";
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| 297 | }
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| 298 | }
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| 299 | if ($lindep_tol ne "default") {
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| 300 | $parse->set_value("lindep_tol", $lindep_tol);
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| 301 | my $ldtolindex = $index->{"lindep_tol"};
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| 302 | $fextra = "t$ldtolindex$fextra";
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| 303 | }
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| 304 | $parse->set_value("molecule", $parse->value($molecule));
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| 305 | $parse->set_value("fixed", $parse->value($fixed));
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| 306 | $parse->set_value("followed", $parse->value($followed));
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| 307 | my $qcinput = new QCInput($parse);
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| 308 | my $fmol = $molecule;
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| 309 | $fmol = "" if ($molecule eq "molecule");
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| 310 | $fmol = tofilename($fmol);
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| 311 |
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| 312 | # make sure that the basis set exists for all of the
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| 313 | # atoms in the molecule
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| 314 | my $molobject = $qcinput->molecule();
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| 315 | my $allowedatoms = $basissets{$basis};
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| 316 | my $ok = 1;
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| 317 | for $symbol (0..($molobject->n_atom()-1)) {
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| 318 | my $z = $molobject->z($symbol);
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| 319 | my $gotit = 0;
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| 320 | for $ztmp (@{$allowedatoms}) {
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| 321 | if ($ztmp == $z) {
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| 322 | $gotit = 1;
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| 323 | last;
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| 324 | }
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| 325 | }
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| 326 | $ok = 0 if (! $gotit);
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| 327 | }
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| 328 |
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| 329 | my $spinok = 1;
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| 330 | if (($method =~ /MP2/i) && $mult > 1) {
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| 331 | $spinok = 0;
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| 332 | }
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| 333 |
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| 334 | my $inputfile;
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| 335 | $method = tofilename($method);
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| 336 | $basis = tofilename($basis);
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| 337 | $auxbasis = tofilename($auxbasis);
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| 338 | $symmetry = tofilename($symmetry);
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| 339 | if ($do_cca eq "yes"){
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| 340 | $intbuf = tofilename($integral_buffer);
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| 341 | $intpack = tofilename($integral_package);
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| 342 | }
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| 343 | else {
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| 344 | $intbuf = "";
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| 345 | $intpack = "";
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| 346 | }
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| 347 | if ($grid eq "default") {$grid = "";}
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| 348 | my $basename = "$dir$file\_$fmol$method$grid$fzc$fzv$basis$auxbasis$symmetry$fcalc$fextra$intbuf$intpack";
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| 349 | my $writer;
|
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| 350 |
|
|---|
| 351 | if ($package eq "g94") {
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| 352 | $writer = new G94InputWriter($qcinput);
|
|---|
| 353 | $inputfile = "$basename.com";
|
|---|
| 354 | }
|
|---|
| 355 | elsif ($package eq "mpqc") {
|
|---|
| 356 | $writer = new MPQCInputWriter($qcinput);
|
|---|
| 357 | $inputfile = "$basename.in";
|
|---|
| 358 | }
|
|---|
| 359 |
|
|---|
| 360 | if (! $ok) {
|
|---|
| 361 | if (! $echonames) {
|
|---|
| 362 | printf "skipping $inputfile since basis not available\n";
|
|---|
| 363 | }
|
|---|
| 364 | }
|
|---|
| 365 | elsif (! $spinok) {
|
|---|
| 366 | if (! $echonames) {
|
|---|
| 367 | printf "skipping $inputfile due to mult/method combo\n";
|
|---|
| 368 | }
|
|---|
| 369 | }
|
|---|
| 370 | else {
|
|---|
| 371 | if ($writefiles) {
|
|---|
| 372 | $writer->write_input("$inputfile.tmp");
|
|---|
| 373 | $writer->write_qcinput("$basename.qci");
|
|---|
| 374 | if ($files{"$inputfile"}) {
|
|---|
| 375 | unlink("$inputfile.tmp");
|
|---|
| 376 | }
|
|---|
| 377 | else {
|
|---|
| 378 | $files{"$inputfile"} = 1;
|
|---|
| 379 | my $ret = 1;
|
|---|
| 380 | $ret = system("cmp $inputfile $inputfile.tmp > /dev/null 2>&1")/256
|
|---|
| 381 | if (-f "$inputfile");
|
|---|
| 382 | if ($ret != 0) {
|
|---|
| 383 | print "writing $inputfile\n";
|
|---|
| 384 | rename("$inputfile.tmp", "$inputfile");
|
|---|
| 385 | }
|
|---|
| 386 | else {
|
|---|
| 387 | unlink("$inputfile.tmp");
|
|---|
| 388 | print "$inputfile is unchanged\n";
|
|---|
| 389 | }
|
|---|
| 390 | }
|
|---|
| 391 | }
|
|---|
| 392 | else {
|
|---|
| 393 | $files{"$inputfile"} = 1;
|
|---|
| 394 | }
|
|---|
| 395 | }
|
|---|
| 396 |
|
|---|
| 397 | } while (incr($index,$size));
|
|---|
| 398 | }
|
|---|
| 399 |
|
|---|
| 400 | sub incr {
|
|---|
| 401 | my $index = shift;
|
|---|
| 402 | my $size = shift;
|
|---|
| 403 | my @keys = keys(%{$index});
|
|---|
| 404 | my $i;
|
|---|
| 405 | my $dozero = 0;
|
|---|
| 406 | while ($i = shift(@keys)) {
|
|---|
| 407 | if ($index->{$i} < $size->{$i} - 1) {
|
|---|
| 408 | $index->{$i}++;
|
|---|
| 409 | return 1;
|
|---|
| 410 | }
|
|---|
| 411 | else {
|
|---|
| 412 | $index->{$i} = 0;
|
|---|
| 413 | }
|
|---|
| 414 | }
|
|---|
| 415 | return 0;
|
|---|
| 416 | }
|
|---|
| 417 |
|
|---|
| 418 | sub init_var {
|
|---|
| 419 | my $vars = shift;
|
|---|
| 420 | my $parse = shift;
|
|---|
| 421 | my $name = shift;
|
|---|
| 422 | my $default = shift;
|
|---|
| 423 | my $testname = "test_$name";
|
|---|
| 424 | my @ar = $parse->value_as_array($testname);
|
|---|
| 425 | if ($#ar < 0) { @ar = ( $default ); }
|
|---|
| 426 | $vars->{$name} = \@ar;
|
|---|
| 427 | }
|
|---|
| 428 |
|
|---|
| 429 | sub tofilename {
|
|---|
| 430 | my $raw = shift;
|
|---|
| 431 | $raw =~ tr/A-Z/a-z/;
|
|---|
| 432 | $raw =~ s/-//g;
|
|---|
| 433 | $raw =~ s/ //g;
|
|---|
| 434 | $raw =~ s/\*/s/g;
|
|---|
| 435 | $raw =~ s/\+/p/g;
|
|---|
| 436 | $raw =~ s/\'/prime/g;
|
|---|
| 437 | $raw =~ s./.slash.g;
|
|---|
| 438 | $raw;
|
|---|
| 439 | }
|
|---|
