Control of a PAMoC run is realized through keywords and options which are entered in the form of single-line data-input sections:
Keywords and options can be entered also as environment variables or on the command line. In the latter case the keyword must be prepended by the minus sign (-).
The following notations will be used to represent keywords and options. The “Lucida Sans Typewriter” monospaced font family denotes keywords recognized by PAMoC. These have to be typed as shown, but may be in upper or lower case. Keywords which have the same meaning and produce the same action are enclosed in parentheses "()" with a vertical bar "|" as the delimiter, i.e. ( keyword1 | keyword2 | … | keywordN ). A double vertical bar "||" is used to delimite two mutually exclusive options. Parentheses "( )" can be omitted if no ambiguity occurs. Keywords may require one or more parameters: italic text embedded in brackets "< >" is used for parameters and options which should be replaced with actual values. Brackets "< >" usually indicate a set of parameters and options and can be omitted if no ambiguity occurs. Square brackets "[ ]" denote optional keywords and options.
A complete list of keywords is given below, both alphabetically ordered, and grouped according to the topics or categories to which they refer.
| number | names | description |
|---|---|---|
| 1 | (stopidf | interface | stopafteridf) | Stop after reading the IDF |
| 2 | (stopmom | moments | stopaftermom) | Stop after moment calculation |
| 3 | (ecryst | stopecryst) | Stop after ECryst calculation |
| 4 | (noecryst | skipecryst) | Skip ECryst calculation |
| 5 | (stoptop | toponly | stopaftertop) | Stop after Topological Analysis |
| 6 | (topo2 | usetopo2 | t2) | g |
| 7 | (grid | usegrid | usegridtop) | g |
| 8 | (t2err | chkt2f | chktopo2f) | g |
| 9 | (sym | usesym | usesymmetry) | g |
| 10 | (crys | crystal) | g |
| 11 | (normchg | normalize | chargenorm) | g |
| 12 | lsqfit | Least-squares Multipole Analysis |
| 13 | (novar | noesd | novariance ) | g |
| 14 | (diagvar | diagvarcov) | g |
| 15 | (dbgmom | -dbgnumom) | g |
| 16 | dft | g |
| 17 | export_dma | g |
| 18 | nomolrec | g |
| 19 | (scapop | vr1994 | valray1994) | g |
| 20 | (nim | noelprop | skipinnermom) | g |
| 21 | (nct | nocrytop | skipcrystop ) | g |
| 22 | not used | |
| 23 | not used | |
| 24 | not used | |
| 25 | (lhb | ilhb | loosehb) | Include Loose Hydrogen Bonds |
| 26 | not used | |
| 27 | (readtop | rdtop | gettop) | READ TOPology from disk file |
| 28 | savetop | SAVE TOPology on disk file |
| 29 | (bader | qtaim) | QTAIM partitioning |
| 30 | epmm | EP/MM |
| 31 | (ecprt | ecrystprt) | E-Cryst extended Printing |
| 32 | (xderr | xderror) | g |
| number | names | description | default value |
|---|
$ ' ' , '-lmx ', '-maxmulord', ! 1)
$ '-igs' , '-intgrid', '-numacc' , ! 2)
$ '-or ' , '-origin ', '-momentor' , ! 3)
$ ' ' , ' ', '-usedma' , ! 4)
$ ' ' , '-clutyp ', '-cludim' , ! 5)
$ ' ' , '-maxerr ', '-maxlap' , ! 6)
$ ' ' , '-atm' , '-atoms' , ! 7)
$ ' ' , '-dim' , '-dimer' , ! 8)
$ '-iem' , '-ecm' , ' ' , ! 9)
$ '-arp' , '-apre' , '-AtmParRep', ! 10)
$ '-adp' , '-apde' , '-AtmParDsp', ! 11)
$ '-damp', '-dfde' , '-DampDisp' , ! 12)
$ '-iam' , '-pro' , '-promol' , ! 13)
$ '-pet' , '-pent' , '-penthresh', ! 14)
$ '-sm ' , '-shift' , '-shiftmom' , ! 15)
$ ' ' , '-prtmom ', '-printmom' , ! 16)
$ ' ' , '-rir' , '-radrule' , ! 17)
$ ' ' , '-stdrad' , '-stdquad' , ! 18)
$ ' ' , '-logk' , '-knowles' , ! 19)
$ ' ' , '-handy' , ' ' , ! 20)
$ ' ' , '-rcov' , '-covrad' , ! 21)
$ ' ' , '-prtdma' , '-printdma' , ! 22)
$ '-svc' , '-sclvcm' , '-scalevcm' , ! 23)