## apbs-users

 [apbs-users] question about charge coordinates in a .dx files From: Francois Berenger - 2011-12-22 07:50:20 ```Hello, I am a little worried about going to the Cartesian space from the i,j,k coordinates in a dx file. u(i,i,k) means charge at (i,j,k). I refer to the file format described here: http://www.poissonboltzmann.org/file-formats/mesh-and-data-formats/opendx-scalar-data should I do this: 1) x,y,z = xmin + i*hx, ymin + j*hy, zmin + k*hz or this: 2) xmax = nx * hx ymax = ny * hy zmax = nz * hz x,y,z = xmin + (xmax*i)/nx, ymin + (ymax*j)/ny, zmin + (zmax*k)/nz I am worried that 1) accumulates floating point errors. Is it OK with 2) or is it the same at the end. Thanks a lot, Francois. ```
 Re: [apbs-users] question about charge coordinates in a .dx files From: Baker, Nathan - 2011-12-22 18:48:15 ```Hello -- Both approaches should work equally well; #1 is how I usually implement this type of calculation. Thanks, __________________________________________________ Nathan Baker Pacific Northwest National Laboratory Tel: 509-375-3997 http://nabaker.me -----Original Message----- From: Francois Berenger [mailto:berenger@...] Sent: Wednesday, December 21, 2011 11:50 PM To: apbs-users@... Subject: [apbs-users] question about charge coordinates in a .dx files Hello, I am a little worried about going to the Cartesian space from the i,j,k coordinates in a dx file. u(i,i,k) means charge at (i,j,k). I refer to the file format described here: http://www.poissonboltzmann.org/file-formats/mesh-and-data-formats/opendx-scalar-data should I do this: 1) x,y,z = xmin + i*hx, ymin + j*hy, zmin + k*hz or this: 2) xmax = nx * hx ymax = ny * hy zmax = nz * hz x,y,z = xmin + (xmax*i)/nx, ymin + (ymax*j)/ny, zmin + (zmax*k)/nz I am worried that 1) accumulates floating point errors. Is it OK with 2) or is it the same at the end. Thanks a lot, Francois. ------------------------------------------------------------------------------ Write once. Port to many. Get the SDK and tools to simplify cross-platform app development. Create new or port existing apps to sell to consumers worldwide. Explore the Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join http://p.sf.net/sfu/intel-appdev _______________________________________________ apbs-users mailing list apbs-users@... https://lists.sourceforge.net/lists/listinfo/apbs-users ```
 Re: [apbs-users] question about charge coordinates in a .dx files From: Francois Berenger - 2012-04-23 07:59:02 ```I just observed this in OCaml: 1) accumulates floating point errors, as my intuition told me. If 1) is used throughout apbs, then it should be fine. However, if it is not, apbs electrostatic values at large grid coordinates (i,j,k) may not be the value that is at Cartesian position xmin + i*hx, ymin + j*hy, zmin + k*hz, but the value of a nearby position. Regards, F. On 12/23/2011 03:48 AM, Baker, Nathan wrote: > Hello -- > > Both approaches should work equally well; #1 is how I usually implement this type of calculation. > > Thanks, > > __________________________________________________ > Nathan Baker > Pacific Northwest National Laboratory > Tel: 509-375-3997 > http://nabaker.me > > > -----Original Message----- > From: Francois Berenger [mailto:berenger@...] > Sent: Wednesday, December 21, 2011 11:50 PM > To: apbs-users@... > Subject: [apbs-users] question about charge coordinates in a .dx files > > Hello, > > I am a little worried about going to the Cartesian space from the i,j,k coordinates in a dx file. u(i,i,k) means charge at (i,j,k). > > I refer to the file format described here: > http://www.poissonboltzmann.org/file-formats/mesh-and-data-formats/opendx-scalar-data > > should I do this: > > 1) x,y,z = xmin + i*hx, ymin + j*hy, zmin + k*hz > > or this: > > 2) > xmax = nx * hx > ymax = ny * hy > zmax = nz * hz > x,y,z = xmin + (xmax*i)/nx, ymin + (ymax*j)/ny, zmin + (zmax*k)/nz > > I am worried that 1) accumulates floating point errors. > > Is it OK with 2) or is it the same at the end. > > Thanks a lot, > Francois. > > ------------------------------------------------------------------------------ > Write once. Port to many. > Get the SDK and tools to simplify cross-platform app development. Create new or port existing apps to sell to consumers worldwide. Explore the Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join http://p.sf.net/sfu/intel-appdev _______________________________________________ > apbs-users mailing list > apbs-users@... > https://lists.sourceforge.net/lists/listinfo/apbs-users > > ------------------------------------------------------------------------------ > Write once. Port to many. > Get the SDK and tools to simplify cross-platform app development. Create > new or port existing apps to sell to consumers worldwide. Explore the > Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join > http://p.sf.net/sfu/intel-appdev > _______________________________________________ > apbs-users mailing list > apbs-users@... > https://lists.sourceforge.net/lists/listinfo/apbs-users ```
 Re: [apbs-users] question about charge coordinates in a .dx files From: Baker, Nathan - 2012-04-23 13:33:56 ```Interesting; thank you for looking into this! Tucker, can you please see if/how this impacts any of our APBS validation test cases? Thanks, __________________________________________________ Nathan Baker Pacific Northwest National Laboratory Tel:  +1-509-375-3997 http://nabaker.me -----Original Message----- From: Francois Berenger [mailto:berenger@...] Sent: Monday, April 23, 2012 12:59 AM To: apbs-users@... Subject: Re: [apbs-users] question about charge coordinates in a .dx files I just observed this in OCaml: 1) accumulates floating point errors, as my intuition told me. If 1) is used throughout apbs, then it should be fine. However, if it is not, apbs electrostatic values at large grid coordinates (i,j,k) may not be the value that is at Cartesian position xmin + i*hx, ymin + j*hy, zmin + k*hz, but the value of a nearby position. Regards, F. On 12/23/2011 03:48 AM, Baker, Nathan wrote: > Hello -- > > Both approaches should work equally well; #1 is how I usually implement this type of calculation. > > Thanks, > > __________________________________________________ > Nathan Baker > Pacific Northwest National Laboratory > Tel: 509-375-3997 > http://nabaker.me > > > -----Original Message----- > From: Francois Berenger [mailto:berenger@...] > Sent: Wednesday, December 21, 2011 11:50 PM > To: apbs-users@... > Subject: [apbs-users] question about charge coordinates in a .dx files > > Hello, > > I am a little worried about going to the Cartesian space from the i,j,k coordinates in a dx file. u(i,i,k) means charge at (i,j,k). > > I refer to the file format described here: > http://www.poissonboltzmann.org/file-formats/mesh-and-data-formats/ope > ndx-scalar-data > > should I do this: > > 1) x,y,z = xmin + i*hx, ymin + j*hy, zmin + k*hz > > or this: > > 2) > xmax = nx * hx > ymax = ny * hy > zmax = nz * hz > x,y,z = xmin + (xmax*i)/nx, ymin + (ymax*j)/ny, zmin + (zmax*k)/nz > > I am worried that 1) accumulates floating point errors. > > Is it OK with 2) or is it the same at the end. > > Thanks a lot, > Francois. > > ---------------------------------------------------------------------- > -------- > Write once. Port to many. > Get the SDK and tools to simplify cross-platform app development. > Create new or port existing apps to sell to consumers worldwide. > Explore the Intel AppUpSM program developer opportunity. > appdeveloper.intel.com/join http://p.sf.net/sfu/intel-appdev > _______________________________________________ > apbs-users mailing list > apbs-users@... > https://lists.sourceforge.net/lists/listinfo/apbs-users > > ---------------------------------------------------------------------- > -------- > Write once. Port to many. > Get the SDK and tools to simplify cross-platform app development. > Create new or port existing apps to sell to consumers worldwide. > Explore the Intel AppUpSM program developer opportunity. > appdeveloper.intel.com/join http://p.sf.net/sfu/intel-appdev > _______________________________________________ > apbs-users mailing list > apbs-users@... > https://lists.sourceforge.net/lists/listinfo/apbs-users ------------------------------------------------------------------------------ For Developers, A Lot Can Happen In A Second. Boundary is the first to Know...and Tell You. Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! http://p.sf.net/sfu/Boundary-d2dvs2 _______________________________________________ apbs-users mailing list apbs-users@... https://lists.sourceforge.net/lists/listinfo/apbs-users ```