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app_delphi.cpp File Reference

Main function to generate the executable delphicpp. More...

#include "../delphi/delphi_data.h"
#include "../space/space.h"
#include "../solver/solver_fastSOR.h"
#include "../energy/energy.h"
#include "../site/site.h"

Functions

int main (int argc, char *argv[])
 

Detailed Description

Main function to generate the executable delphicpp.

Author
Chuan Li, chuan.nosp@m.li@c.nosp@m.lemso.nosp@m.n.ed.nosp@m.u

delphicpp is the object-oriented C++ version of the program DelPhi, which takes as input a Brookhaven database coordinate file format of a molecule or equivalent data for geometrical objects and/or charge distributions and calculates the electrostatic potential in and around the system, using a finite difference solution to the Poisson-Boltzmann equation. This can be done for any given concentration of any two different salts. The system can be composed of different parts having different dielectrics.

[QUICK REFERENCE TO ACCESS SVN REPOSITORY ON SERVER consus.clemson.edu]

  • TO SHOW LOG HISTORY FOR THIS PROJECT: svn log svn+ssh://username@consus.clemson.edu/home/common/delphi_distr/delphicpp
  • TO CHECKOUT THE LATEST REVERSION: svn co svn+ssh://username@consus.clemson.edu/home/common/delphi_distr/delphicpp
  • TO REMOVE/ADD FILES FROM A CHECKED-OUT PROJECT: svn rm <file/directory name> svn add <file/directory name>
  • TO REVIEW LOCAL CHANGES: svn status
  • TO COMMIT CHANGES: export SVN_EDITOR=/usr/bin/vim svn commit

  • TO UPDATE YOUR LOCAL FILES: svn update

    (See "subversion user guide" created by S. Sarkar and C. Li for other svn options)

[SUBMITTED REVERSIONS]

  • r01 chuan 2013July01 The 1st reversion in SVN.
  • r02 chuan 2013Nov25 1. Updated reading size and charge files in IO class.
    1. Updated excel file.
  • r03 chuan 2013Dec04 1. Completed reading/writing PDB file in IO class.
    1. Completed assigning size and charge to atoms.
  • r04 chuan 2013Dec05 fixed bugs in IO class.
  • r05 chuan 2013Dec10 major changes in prototypes, delphi, main and misc.
  • r06 chuan 2013Dec13 overhauled the subsystems of prototypes, delphi, misc, io.
    1. Now the part of code before surface construction is completed.
    2. Now the code requires GCC 4.3+ with option std=c++0x to compile due to the additional feature of initializing values when creating large arrays. (see comments in makefile)
  • r07 chuan 2013Dec24 Another set of major changes includes:
    1. Converted map<string,void *> to map<string,boost::any>
    2. Converted all regular and dynamically allocated multi-dimensional arrays to 1D stl::vector<T> in the map.
      The reasons to do so are: 1) contiguous memory allocation. 2) faster 1-layer loop instead of multi-layer loop. 3) Easier allocate/deallocate arrays
    3. Started using smart pointers instead of raw pointers in order to avoid possible memory leak.
    4. Removed datadistr(:) and ndistr from the map
    5. Now the class of DataContainer provides 4 template functions to access the map: 1) read-only by value: getKey_constRef 2) read-only by pointer: getKey_constPtr 3) writable access by value: getKey_Val 4) writable access by pointer: getKey_Ptr
    6. Reorganized the code structure.
  • r08 chuan 2014Jan07 Re-config the code to have datacontainer and datamarshal loosely paired.
  • n/a chuan 2014Jan10 1. Added new piece of code to read ibnum, ibgrd, iepsmp and idebmap from forSolver.dat without Lin's surface construction class.
    1. Fixed various bugs.
  • r09 chuan 2014Jan18 1st reversion to use Eclipse and Doxygen.
  • r10 chuan 2014Jan18 cleaned two additional files
  • r11 chuan 2014Feb17 completed solver class with other updates.
  • r12 chuan 2014Feb26 Added new class of writing site and phimap.
  • r13 chuan 2014Mar26 Added new directory of examples with 3 super-large proteins.
  • r14 LinWang 2014Apr03 Energy Class added
  • r15 LinLi 2014Apr03 space class and examples added
  • r16 LinLi 2014Apr03 app_delphi.cpp for space added
  • r17 lwang3 2014Apr07 Energy class modified: 1.Renamed variables. 2.Warning message added for some testing functions.
  • r18 lwang3 2014Apr08 Example files cleanup.
  • r19 chuan 2014Apr08 1. new function reset is added in datacontainer class for testing purpose.
    1. modified delphi95.r16 is added to svn.
  • r20 lwang3 2014Apr08 Fix bugs in delphi_datamarshal_getFunction.cpp. Now it can control energy output by parameter file instead of setting flags.
  • r21 chuan 2014Apr08 updated app_delphi.cpp to include all individual classes. F95 code have been updated accordingly.
  • r22 LinLi 2014Apr10 Space module has been tested using showmap, now the aftersurf.dat are identical in fortran and C++
  • r23 Chuan 2014Apr14 Modified app_delphi.cpp to show map after realizing every object.
  • r24 LinLi 2014Apr15 changed size of ibgrd from ibmx to ibnum
  • r25 Chuan 2014Apr21 1. Added new features for MCCE calling DelPhi
    1. Added calculated energies into data container.
    2. Various bug fixes. This version is the 1st version for integrated tests.
  • r26 chuan 2014Apr21 Fixed the bug of deblen.
  • r27 chuan 2014Apr23 Another update to clean debug info in the code.
  • r28 chuan 2014Apr23 Cleaned debug info in F95 code.
  • r29 chuan 2014May02 Fixed most format and form bugs in statements reported in DelphiCPP_testscript_2A26_r28_20140424.xlsx
  • r30 chuan 2014May10 1. Recoded reading functions using tokens.
    1. Fixed most bugs in functions reported in DelphiCPP_testscript_2A26_r28_20140424.xlsx
  • r31 chuan 2014May12 1. A few more bug fixes.
    1. 2 new proteins, 1AB1.pdb and 1SF4.pdb are added.
    2. Debug/ and Release/ are added.
  • r34 chuan 2014May16 1. Removed "\r" in statements.
    1. Introduced namespace "delphi" to fix ambiguous reference to "delphi_real" when compiling the program on Mac.
  • r35 LinWang 2014May18 1. Fixed the bug of printing multiple identical messages on screen when atom radius less than ZERO.
    1. Added energy_exceptions.h file and start using CWarning class for showing warning messages.
  • r36 chuan 2014May19 1. variables named prg* were changed to vct*.
    1. bug fixed for reading charge and size from pqr file
    2. flag MCCE and DEBUG_MCCE are added for calling delphicpp in mcce.
    3. Doxygen comments are added to files in and .
  • r37 LinWang 2014May20 Added more warning messages to energy_exceptions.h
  • r38 chuan 2014May21 A few bug fixes in CSite and CDelphiFastSOR::isFocusBndy.
  • r39 LinWang 2014May24 The test environment setup files are added to SVN.
  • r42 chuan 2014Jun02 1. defined the destructor of IAbstractModule to be virtual. (Atten: pSpace.release() needs to be replaced by pSpace.reset() after fixing the problem of memory leak.)
  • r43 chuan 2014Jun02 Added new debug flag DEBUG_OBJECT and message in constructors and destructors of all classes for debugging objects realization.
  • r44 chuan 2014Jun03 Merged the projects of delphicpp and mcce_delphicpp into one. (Atten: the problem of memory leak makes mcce_delphi too expensive to run on PC)
  • r45 chuan 2014Jun03 The following statements
    • CLCSRF
    • GRDCON
    • LOGGRP
    • MEMBRANEDATA
    • PHICON
    • RADPOL
    • NORMC
      and functions
    • out(srf,file="filename") or out(srf,file="filename",format=BEM)
    • out(frc,file="filename",format=r) or out(frc,file="filename",format=un)
    • out(unpdb,file="filename") or out(unpdb,file="filename",format="whatever")
    • out(unfrc,file="filename") or out(unfrc,file="filename",format="whatever")
    • buffz(xxxyyyzzzxxxyyyzzz) have been removed as discussed after the 1st round of tests.
  • r50 chuan 2014Jun17 1. Removed shortcuts to read PQR and PQR4 files.
    1. Documented