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generate input file man page from config.rs
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,48 @@ | ||
| .TP | ||
| .B geometry \fIString\fR | ||
| The initial geometry to use for the computation. Both XYZ and Z-matrix geometries are accepted. | ||
| .TP | ||
| .B optimize \fIbool\fR | ||
| Whether or not to perform a geometry optimization on the input | ||
| .TP | ||
| .B charge \fIisize\fR | ||
| The molecular charge. This value can be spliced into the template using the {{.charge}} directive. | ||
| .TP | ||
| .B step_size \fIf64\fR | ||
| The size of the displacement to take in the QFF coordinates. | ||
| .TP | ||
| .B sleep_int \fIusize\fR | ||
| The interval in seconds to wait between loops checking if any jobs have finished. | ||
| .TP | ||
| .B job_limit \fIusize\fR | ||
| The maximum number of jobs to submit at once, as determined by the number of individual input files. This distinction is important when chunk_size is greater than 1 because the maximum number of jobs submitted to the queue will be job_limit / chunk_size . | ||
| .TP | ||
| .B chunk_size \fIusize\fR | ||
| The number of individual calculations to bundle into a single queue submission. | ||
| .TP | ||
| .B coord_type \fICoordType\fR | ||
| The type of coordinate to use in the QFF. Currently-supported values are "sic", "cart", and "normal". Note that SIC QFFs require an additional input file called intder.in to define the internal coordinates. | ||
| .TP | ||
| .B template \fITemplateSrc\fR | ||
| The template input file for the quantum chemistry program. Supported formatting directives depend on the program in question. Molpro supports {{.geom}} for the geometry and {{.charge}} for the molecular charge, while Mopac expects a static template. | ||
| .TP | ||
| .B hybrid_template \fIOption<TemplateSrc>\fR | ||
| An optional template file for the cubic and quartic portion of the QFF. If this is provided, the regular template is used only for the harmonic portion of the QFF, and this is used for the rest of the points. | ||
| .TP | ||
| .B queue_template \fIOption<TemplateSrc>\fR | ||
| The template input file for the queuing system. Supported formatting directives include {{.basename}} for the base name of the submit script, which is useful for naming the job in the queue, and {{.filename}} for the name of the quantum chemistry program input file. Not all program and queue combinations expand these, however. | ||
| .TP | ||
| .B program \fIProgram\fR | ||
| The quantum chemistry program to use in running the QFF. Currently-supported values are "cfour", "dftb+", "molpro", "mopac". | ||
| .TP | ||
| .B queue \fIQueue\fR | ||
| The queuing system to use in running the QFF. Currently-supported values are "local", which uses bash to run computations directly, "pbs", and "slurm". | ||
| .TP | ||
| .B findiff \fIOption<bool>\fR | ||
| Whether to use finite differences or least-squares fitting for the potential energy surface. Currently normal coordinates are the only coord_type to use this option, so it has a default value of false, meaning use the fitted version of normal coordinates. Setting this option to true forces the use of finite differences for the normal coordinate QFF. | ||
| .TP | ||
| .B check_int \fIusize\fR | ||
| The interval at which to write checkpoint files. Every coordinate type will write an initial checkpoint (res.chk), but this interval determines whether or not checkpoints are written while the single-point energies are being run. A value of 0 will disable checkpoints entirely. This interval refers to the number of polling iterations that have occurred, not the number of jobs that have completed. The iteration count is shown in the log file when the number of jobs remaining is printed. | ||
| .TP | ||
| .B weights \fIOption<Vec<f64>>\fR | ||
| An optional vector of atomic masses to use for normal coordinate generation and Spectro. |
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| .SH EXAMPLE | ||
| The following is an example input file for c-C3H2 in SICs in Mopac on the Slurm | ||
| queuing system: | ||
| .nf | ||
| .rs | ||
|
|
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,16 @@ | ||
| #!/usr/bin/awk -f | ||
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| /struct RawConfig/,/^}$/ { | ||
| if ($1 ~ /\/\/\//) { | ||
| for (i = 2; i <= NF; i++) { | ||
| buf = buf " " $i | ||
| } | ||
| } else if (/^$/ || /struct/ || /^}$/) { | ||
| # pass | ||
| } else { # field name | ||
| field = substr($1, 1, length($1) - 1) # trim colon | ||
| type = substr($2, 1, length($2) - 1) # trim comma | ||
| printf ".TP\n.B %s \\fI%s\\fR\n%s\n", field, type, substr(buf, 2) | ||
| buf = "" | ||
| } | ||
| } |
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