Welcome to PGV home page JAPANESE

What's PGV ?

PGV (Polygon viewer) can see 3D polygon data. It's written by OpenGL + GLUT libraries. Then it gives very high quarity graphics (PGV another mean is Pretty Good Visualizer). PGV can output many formats of image file, it's able to use for a final output, I suppose.

PGV is developing for ATMIC ORBITAL output, it has some functions to display a molecular. But it's able to use for another purpose.
Color sample of atoms


How to install

Download binary file from this page (pgv or pgv.exe), and save your bin directory.

If your machine is Windows, please download glut32.dll too. Save it to system directory.
If you don't know system directory for your system, please search "opengl32.dll", and save to same directory. If you can't find "opengl32.dll", PGV doesn't work on your machine.

Basic operations

PGV needs one input data file. You can see usage "PGV -?". If Windows, you can drag & drop. Now If you start PGV without data file, it terminates soon.

PGV displays one window to display 3D objects. You can operate it with left mouse button. First it rotate to X or Y axis.
When you want to use functions, push function key or operate menu it's called by right mouse button. All functions is written on "PGV Functions".

If you want to terminate, push End key or quit select from menu.

There are some function key like below...
End keyProgram teminate
1-9 keyMouse mode (cf. menu)
J keyOutput jpeg file
Down,UpRotate -90, 90 degree on X(from Ver.1.5.17)
Left,RightRotate -90, 90 degree on Y (from Ver.1.5.17)
PageDown,PageUpRotate -90, 90 degree on Z (from Ver.1.5.17)

How to make pgv data file

How to make the orbital pgv data file.

  1. You have one density or orbital ascii output data file (ex. test.cube) by Gaussian94.
  2. First, you use "isoconv" (on Homepage) for convert to binary file. It outputs "iso.dat". If your data is orbital, output file name with orbital number like "isoXX.dat". If your data has some orbital, it outputs some files. You want to information of these binary files, please use "isocheck" (on Homepage).
    ex. isoconv.exe test.cube
  3. Next, convert to polygon data by "d2p". It outputs "iso(XX).pgv". This program need isolate value for separate 2 areas in your data space. If you don't understand isolate value, please refer maximum value of data it was displayed by "isoconv". In my experience, it is 0.1 - 0.05. You want to information of pgv file, please use "pcheck" (on Homepage).
    ex. d2p.exe iso10.dat 0.05

Other tools, "p2vrml" is convert from pgv file to VRML wrl file. "d2vrml" is convert from binary file to VRML wrl file. It is similar to PGV output. PGV has many functions, then it's output is reflected them.

If you want to apply another data, please modify "isoconv". If binary data is made for "d2p", you can make pgv file. When you modify "isoconv", you have to set data type "density". It's mean is that this data file has one polygon group.

"freq.pl" is sample program to make xys data file with frequency from Gaussian94 output.


Binary distribute

PGV Ver.2.3.3 Update 2006,3,10 Introduction of ICON

Windows(x86)[212kB](Ver.2.3.3 Up 2006,3,10) (Ver.2.2.1) (Ver.1.5.21) need glut32.dll
Windows(x86)[212kB](Ver.2.3.3 Up 2006,3,10) with console window need glut32.dll
SGI-IRIX5.3-MIPS[459kB](Ver.1.5.19 Up 1997,11,28)
SGI-IRIX5.3-MIPS[1837kB](Ver.1.5.19 Up 1999,2,24) Using Mesa 2.6
IBM-AIX4.1-PPC[1049kB](Ver.1.5.19 Up 1999,2,24) Using Mesa 2.6
HP-HPUX9-HPPA[1216kB](Ver.1.5.19 Up 1999,2,24) Using Mesa 2.6
SUN-SunOS5.5-SPARC[1286kB](Ver.1.5.19 Up 1999,2,24) Using Mesa 2.6
SUN-Solaris2.6-x86[1099kB](Ver.1.5.19 Up 1999,2,24) Using Mesa 2.6
LINUX2.0(X11R6)-x86[1131kB](Ver.1.5.19 Up 1999,2,24) Using Mesa 2.6
Macintosh PPC System7[1293kB](Ver.Beta based 1.5.13 Up 1997,8,19) Using Mesa for Mac
DLL file (for Ver.1.5.17 later) glut32.dll GLUT 3.5 for Win32[509kB]
New functions


Binary programs (Tools for DOS-x86)

ISOCONV.EXE[60kB]
ISOCHECK.EXE[39kB]
D2H.EXE[51kB]
D2P.EXE[75kB]
PCHECK.EXE[37kB]
P2VRML.EXE[54kB]
D2VRML.EXE[79kB]


Source distribute (Tools only)

ISOCONV.CUpdate 1996,11,18
ISOCHECK.CUpdate 1996,10,18
D2H.CUpdate 1996,10,18
D2P.CUpdate 1997,6,11
PCHECK.CUpdate 1996,10,18
P2VRML.CUpdate 1996,10,18
D2VRML.CUpdate 1997,6,11

How to make

They need a math library.
UNIX: cc -O d2p.c -o d2p -lm

If you make on DOS, they need to define "DOS".
DOS: cl -DDOS d2p.c

If you make on LINUX on x86, they need to define "DOS".
LINUX: cc -O d2p.c -o d2p -lm -DDOS


Sample data

List sorted by atom

List sorted by molecular wight

List sorted by name

List separated by kind
alkanemethane, ethane,...
alkene, dieneethene(ethylene), propene(propylene)...
alkyneethyne(acetylene), propyne(methylacethylene),...
alcoholmethanol, ethanol,...
carboxylic acidmethanoic acid, ethanoic acid,...
aldehydemethanal(formaldehyde), ethanal(acetaldehyde),...
etherdimethyl ether, ethylmethyl ether,...
ketone, ketenepropanone(acetone), butanone,...
aminemethylamine, ethylamine,...
nitrilehydrocyanic acid, ethanenitrile, propanenitrile,...
amidemethanamide(formamie), ethanamide(acetamide),...
alkyl halidefluoromethane, chloromethane, bromomethane,...
cycloalkanecyclopropane, cyclobutane,...
bicycloalkanebicyclobutane, bicyclopentane,...
aromaticbenzene, naphthalene,...
fullereneC60, C84,...
otherh2o, nh3,...

Sample data (other molecular)

retinalC20H28O15649
vitamin AC20H28O216450
Chlorophyllide B HsC37H38O7N4Mg35687
DIOXIN
PCDD
MCDD2 kinds
DCDD10 kinds
TrCDD14 kinds
TCDD22 kinds
PeCDD14 kinds
HxCDD10 kinds
HpCDD2 kinds
OCDD1 kind
PCDF
MCDF4 kinds
DCDF16 kinds
TrCDF28 kinds
TCDF38 kinds
PeCDF28 kinds
HxCDF16 kinds
HpCDF4 kinds
OCDF1 kind

Sample data (compare base function)

ammonia HOMO
ammonia LUMO

Sample data (other)

Head bulided from MRI photos

Images...

Original image of poster for open house 1997 JPEG 900x1200pixel TrueColor 405kByte


High level operations !?

  1. Control file : later Ver.1.5.5

    When start PGV with "-c" option, PGV try to read "pgv.ctl" on same directory.
    When start PGV with "-cc" option, PGV try to read "pgv.ctl" on current directory. (later Ver.1.5.18)
    You want to read other control file, please use "-cFullPathName". You have to no space between -c and FullPathName. If you enter only file name, PGV refer to current directory.
    You can setup initial state to view or MACRO operation by control file.
    For example, you want to movie, you need some image file. MACRO operation is very easy to get them.
    Detail of control file, please refer "Control file commands"

    From Ver.1.5.18, PGV can output control file. If you use it, You can reappear same display.
    For example, you want to compare to some orbital, you can display same status.

    1. First, you decide angle and output control file.
    2. Output file is "pgv0000.ctl". It rename to "pgv.ctl", and modify some entry.
      • In [MACRO] block, erase comment out "#" mark to "output jpeg" and "quit" line.
    3. Last, you make batch file or shell script file for all orbitals.
      pgv -cc isoXX.dat
      rename pgv0000.jpg isoXX.jpg
    4. You modify to output html file together, you can compare by web browser. (sample.pl)

  2. Comment display : laser Ver.1.5.9

    When start PGV with "-m" option, you can display some comment in PGV window.
    For example, -mtest or -m"test 123". If your comment has space, you have to use "".
    "-f" option set font size. You can use like "-f1". Parameters is 1 - 4. Large font is 1.
    "-p" option set position. You can use like "-p1". Parameters is 1 or 2. 1 is left up, 2 is left bottom.
    But comment is not always displayed. I can't understand it...

  3. View angle change : later Ver.1.5.14

    OpenGL view angle set to Y axis (vartical).
    This mean, when you resize window X (holizontal) size, object size is same, but resize Y size, object size is modified.
    Then PGV can modify view angle. It like zoom. 3 mode, "Zoom", "Move Z" and "View angle" is very similar, please notice distotion and try them.

  4. Web help application

    If you use for Web help application, please set MIME type. It is "application / X-polygon-viewer", and extention is "pgv". If you want to set for "xyz", "pdb", please check Chemical MIME type.
    http://biotech.icmb.utexas.edu/mime/mimelist.html

  5. Windows95/98/NT file type

    Windows95/98/NT user can use drag & drop.
    If you set file type "pgv" and set execute application "PGV", only click to data file.
    Binary "with console" is always open DOS window together. PGV displays some information to console window. If you have some trouble, please use it on behalf of normal PGV.


Libraries

GLUT Lib for UNIX / GLUT Lib for WindowsNT/95
JPEG Lib
Mesa Lib

Papers (Fig. and Ref.)

Masaaki Tomura, Yoshiro Yamashita,
"An Unsymmetrical Tetrathiafulvalene with a Fused 1,2,5-Thiadiazole Ring and Methylthio Groups",
Molecules, 14(10), 4266-4274 (2009)

Papers (Fig.)

Shinkoh Nanbu, Toshimasa Ishida, Hiroki Nakamura,
"Atomic hydrogen transmission through five-membered carbon ring by the mechanism of non-adiabatic tunneling",
Chem. Phys. 324, 721-732 (2006)
[P4D Sample 4052kB]

PGV EG Page, last update 2009/10/24
Copyright(C) 1996-2009 F.Mizutani,RCCS / mizutani@ims.ac.jp