From: Miguel <mi...@jm...> - 2005-07-15 14:47:34
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Given a .cube file with volumetric scalar data samples, one could construct several surfaces using 'cutoff' values. I believe that Richard said that the standard 'cutoffs' are 0.02 and -0.0= 2 I need to better understand what types of control is desired to construct= these surfaces. Q: Does anyone ever want to construct a surface based upon a range of values? As in, between 0.02 and 0.04 ? Assume that you are going to construct positive and negative surfaces independently. I am thinking of something like volumetric someName 0.03 dots =22path/to/file.cube=22 color volumetric blue volumetric otherName -0.03 mesh =22path/to/file.cube=22 color volumetric red volumetric whatever 0.02 filled =22path/to/file.cube=22 volumetric someName off volumetric otherName color volumetric translucent volumetric someName dots on mesh on filled off volumetric whatever mesh on filled on Q: Can I assume that a negative cutoff value means that the person is interested in values less than the negative cutoff value? Put another way= ... it will never be the case that someone would have an upper bound of positive infinity but a lower bound less than zero. Miguel |
From: Park Won-K. <wk...@gm...> - 2005-07-16 03:09:45
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2005/7/15, Miguel <mi...@jm...>: > Given a .cube file with volumetric scalar data samples, one could > construct several surfaces using 'cutoff' values. >=20 > I believe that Richard said that the standard 'cutoffs' are 0.02 and -0.0= 2 >=20 the following link show about "cutoffs" vs orbitals. smaller value results larger surfaces. 0.05~0.08 is more reliable value I t= hink http://www.cup.uni-muenchen.de/oc/zipse/lv18099/orb_MOLDEN.html > I need to better understand what types of control is desired to construct > these surfaces. >=20 > Q: Does anyone ever want to construct a surface based upon a range of > values? As in, between 0.02 and 0.04 ? >=20 > Assume that you are going to construct positive and negative surfaces > independently. >=20 > I am thinking of something like >=20 > volumetric someName 0.03 dots "path/to/file.cube" > color volumetric blue > volumetric otherName -0.03 mesh "path/to/file.cube" > color volumetric red > volumetric whatever 0.02 filled "path/to/file.cube" >=20 > volumetric someName off > volumetric otherName > color volumetric translucent >=20 > volumetric someName dots on mesh on filled off > volumetric whatever mesh on filled on > the following link explain about generic density cube. http://astronomy.swin.edu.au/~pbourke/geomformats/cube/ and it is differnt with the Molecular density cube by "MO related infomatio= n" and one can simply distinguish this two type of cubes as described in following link. ----- from the gcube2plt.c source in the gopenmol ----- (http://ftp.ccl.net/cca/software/SOURCES/C/scarecrow/gcube2plt.c) For molecular orbital output, NAtoms will be less than zero, and an additio= nal record follows the data for the final atom (in format lOI5 if the file is formatted): NMO, ( MO ( I ), I =3D 1, NMO ) Number of MOs and their numbers ------ > volumetric someName 0.03 dots "path/to/file.cube" > color volumetric blue > volumetric otherName -0.03 mesh "path/to/file.cube" > color volumetric red then, how about to use "mo" option like as volumetric someName 0.03 mo dots,mesh "path/to/file.cube" or volumetric someName -0.03,0.03 dots,mesh "path/to/file.cube" then someName.1someName.2 surfaces are generated automatically >=20 > Q: Can I assume that a negative cutoff value means that the person is > interested in values less than the negative cutoff value? Put another way > ... it will never be the case that someone would have an upper bound of > positive infinity but a lower bound less than zero. >=20 >=20 > Miguel > |
From: Miguel <mi...@jm...> - 2005-07-16 11:48:09
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The following links have conflicting information about whether Bohrs or Angstroms are used in .cube files: > the following link explain about generic density cube. > http://astronomy.swin.edu.au/=7Epbourke/geomformats/cube/ Regarding the cube vectors, this link says: If the sign of the number of voxels in a dimension is positive then the units are Angstroms, if negative then Bohr. > ----- from the gcube2plt.c source in the gopenmol ----- > (http://ftp.ccl.net/cca/software/SOURCES/C/scarecrow/gcube2plt.c) But this code does not check for a negative voxel count and always always= converts from Bohrs to Angstroms: fscanf(Input_p,=22%d %f %f %f=22,&N1,&N1X1,&N1Y1,&N1Z1); N1X1 *=3D BOHR_RADIUS; N1Y1 *=3D BOHR_RADIUS; N1Z1 *=3D BOHR_RADIUS; printf(=22Number of points: %d, in direction (x,y,z) %f %f %f=5Cn=22,= N1,N1X1,N1Y1,N1Z1); Similarly, this code always scales the origin by Angstroms/Bohr /* now starts the data ... */ sscanf(Text,=22%d %f %f %f=22,&Natoms,&Xorig,&Yorig,&Zorig); Xorig *=3D BOHR_RADIUS; Yorig *=3D BOHR_RADIUS; Zorig *=3D BOHR_RADIUS; printf(=22Number of atoms: %d, x-, y-, z-origin (in Anstrom): %f,%f,%= f=5Cn=22, abs(Natoms),Xorig,Yorig,Zorig); MolecularOrbitals =3D 0; if(Natoms < 0) MolecularOrbitals =3D 1; Natoms =3D abs(Natoms); *** I am going to assume that the CODE is correct, that everything in a .cube file is stored in Bohrs *** > For molecular orbital output, NAtoms will be less than zero, and an > additional > record follows the data for the final atom (in format lOI5 if the file > is formatted): > > NMO, ( MO ( I ), I =3D 1, NMO ) Number of MOs and= > their numbers > ------ Thank you for making this more clear. >> volumetric someName 0.03 dots =22path/to/file.cube=22 >> color volumetric blue >> volumetric otherName -0.03 mesh =22path/to/file.cube=22 >> color volumetric red > > then, how about to use =22mo=22 option like as > > volumetric someName 0.03 mo dots,mesh =22path/to/file.cube=22 > or > volumetric someName -0.03,0.03 dots,mesh =22path/to/file.cube=22 > > then someName.1someName.2 surfaces are generated automatically I will do something like this. Miguel |