Changeset 3fbbfbb

Timestamp:

06/16/10 08:25:47 (14 years ago)

Author:

Jan Meinke <j.meinke@…>

Branches:

master

Children:

5fef0d7

Parents:

9f146fa

Message:

Move to doxygen comments and smmp_p.

Doxygen comments in Fortran are !> ... !! ... !<. I'm planning move the API documentation from the
lyx file into the code. This should make it easier to get documentation for all the common block
variables as well.

Use import smmp_p to indicate the parallel version of the Python bindings.

Files:

• EXAMPLES/1bdd.seq (modified) (1 diff)
• INCL.H (modified) (2 diffs)
• algorithms.py (modified) (1 diff)
• enyshe.f (modified) (1 diff)
• enyshe_p.f (modified) (1 diff)
• main.f (modified) (3 diffs)
• partem_p.f (modified) (1 diff)
• protein.py (modified) (1 diff)
• rgyr.f (modified) (1 diff)
• timer.F90 (modified) (1 diff)
• universe.py (modified) (1 diff)
• utilities.f (modified) (3 diffs)

EXAMPLES/1bdd.seq

@@ -5 +5 @@
   SER GLN SER ALA ASN LEU LEU ALA GLU ALA 
   LYS LYS LEU ASN ASP ALA
+

INCL.H

@@ -8 +8 @@
       integer mxhbac, mxtybl, mxtyba, mxtyto, mxrt, mxvrrt, mxrtsu
       integer nrsty
-!      integer MAXLOGLEVEL, LOGFILEUNIT
+      integer MAXLOGLEVEL, LOGFILEUNIT
       double precision pi, pi2, pi4, crd, cdr, zero, one
       integer izero, ione
@@ -52 +52 @@
       integer enysolct
       double precision boxsize
+      common /log/MAXLOGLEVEL,LOGFILEUNIT
       common /counter/enysolct
       common /commonrandom/ seed

algorithms.py

@@ -11 +11 @@
 from protein import *
 
-class CanonicalMonteCarlo:
+class CanonicalMonteCarlo(object):
     """An implementation of a canonical Monte Carlo run using Metropolis weights.
     After a Monte-Carlo sweep over all internal variables, this implementation 

enyshe.f

@@ -10 +10 @@
 ! **************************************************************
 
+!> PURPOSE: Calculate internal energy of molecule 'nml' with ECEPP parameters
+!!
+!! CALLS: none
+!!
+!! The function loops over all moving sets within the molecule. Within
+!! this loop it loops over the van-der-Waals domains of each atom in the
+!! moving set and finally over the atoms that belong to the 1-4 interaction
+!! set.
+!< ............................................................................
 
       real*8 function enyshe(nml)
 
-! ............................................................................
-!
-! PURPOSE: Calculate internal energy of molecule 'nml' with ECEPP parameters
-!
-! CALLS: none
-!
-! The function loops over all moving sets within the molecule. Within
-! this loop it loops over the van-der-Waals domains of each atom in the
-! moving set and finally over the atoms that belong to the 1-4 interaction
-! set.
-! ............................................................................
 
       include 'INCL.H'

enyshe_p.f

@@ -13 +13 @@
       real*8 function enyshe(nml)
 
-!     ............................................................................
-!
-!     PURPOSE: Calculate internal energy of molecule 'nml' with ECEPP parameters
-!
-!     CALLS: none
-!
-!     The function loops over all moving sets within the molecule. Within
-!     this loop it loops over the van-der-Waals domains of each atom in the
-!     moving set and finally over the atoms that belong to the 1-4 interaction
-!     set.
-!     ............................................................................
+!>     PURPOSE: Calculate internal energy of molecule 'nml' with ECEPP parameters
+!!
+!!     CALLS: none
+!!
+!!     The function loops over all moving sets within the molecule. Within
+!!     this loop it loops over the van-der-Waals domains of each atom in the
+!!     moving set and finally over the atoms that belong to the 1-4 interaction
+!!     set.
+!<     ............................................................................
 
       include 'INCL.H'

main.f

@@ -19 +19 @@
       program main
 
+      use timer
       include 'INCL.H'
       include 'INCP.H'
-      double precision eps, temp, e, energy
+      double precision eps, temp, e, energy, enyshe_simple
 
-      integer maxloglevel, logfileunit, iabin, imin, maxit, nequi
-      integer nsweep, nmes, ncalls, nacalls
+      integer iabin, imin, maxit, nequi
+      integer nsweep, nmes, ncalls, nacalls, i
 
       common/updstats/ncalls(5),nacalls(5)
@@ -42 +43 @@
 !     Set the maximum log level. The larger the number the more detailed
 !     the log.
-      MAXLOGLEVEL = 1
+      MAXLOGLEVEL = 100
 !     File unit to use for the log file.
       LOGFILEUNIT = 27
@@ -112 +113 @@
 !      call outvar(0, ' ')
 !     To do a canonical Monte Carlo simulation uncomment the lines below
-       nequi = 100
-       nsweep = 50000
-       nmes = 10
-       temp = 300.0
-       lrand = .true.
-       E = energy()
-       write (logString, *) E, eyel,eyvw,eyhb,eyvr
-       call outpdb(1, "polyA.pdb")
+      nequi = 100
+      nsweep = 500
+      nmes = 10
+      temp = 300.0
+      lrand = .true.
+      E = energy()
+      write (logString, *) E, eyel,eyvw,eyhb,eyvr
+      call outpdb(1, "polyrQ.pdb")
 !      Canonical Monte Carlo
-       call canon(nequi, nsweep, nmes, temp, lrand)
+      call init_timer()
+      call start_timer(1)
+      call canon(nequi, nsweep, nmes, temp, lrand)
+      call stop_timer(1)
 
+      E = 0
+!      call start_timer(1)
+!      do i =1, nsweep
+!         E = E + enyshe_simple()
+!      end do
+!      call stop_timer(1)
+      call evaluate(1)
+      print *,timingData(1)%average, "s.", E
 !      For simulated annealing uncomment the lines below
 !      tmin = 200.0

partem_p.f

@@ -11 +11 @@
 !     **************************************************************
 
+!>
+!!     PURPOSE: SIMULATION OF PROTEINS BY PARALLEL TEMPERING ALGORITHM
+!!     ON PARALLEL COMPUTERS USING MPI
+!!
+!!     switch: Choses the starting configuration:
+!!     -1 - stretched configuration
+!!     0 - don't change anything
+!!     1 - random start configuration
+!!
+!!     CALLS:  addang,contacts,energy,hbond,helix,iendst,metropolis,
+!!     outvar,(rand),rgyr
+!<
       subroutine  partem_p(num_rep, nequi, nswp, nmes, nsave, newsta,
      &                     switch, rep_id, partem_comm)
-!     
-!     PURPOSE: SIMULATION OF PROTEINS BY PARALLEL TEMPERING ALGORITHM 
-!     ON PARALLEL COMPUTERS USING MPI
-!     
-!     switch: Choses the starting configuration:
-!     -1 - stretched configuration
-!     0 - don't change anything
-!     1 - random start configuration
-!     
-!     CALLS:  addang,contacts,energy,hbond,helix,iendst,metropolis,
-!     outvar,(rand),rgyr
-!     
       include 'INCL.H'
       include 'INCP.H'

protein.py

@@ -6 +6 @@
 #
 import sys
-import smmp
+import smmp_p as smmp
 from math import *
 

rgyr.f

@@ -11 +11 @@
 
 
-      subroutine rgyr(nml, rgy, ee)
+!> CALCULATES THE RADIUS-OF-GYRATION AND THE END-TO-END DISTANCE
+!! FOR A GIVEN PROTEIN CONFORMATION
+!! If nml == 0, calculate the radius of gyration for all molecules
+!!
+!!     rgy  = radius-of-gyration
+!!     ee   = end-to-end distance
+!!
+!! REQUIREMENTS: c_alfa has to be called BEFORE call of this subroutine
+!!
+!! CALLS: NONE
+!<
+          subroutine rgyr(nml, rgy, ee)
 
-! CALCULATES THE RADIUS-OF-GYRATION AND THE END-TO-END DISTANCE
-! FOR A GIVEN PROTEIN CONFORMATION
-! If nml == 0, calculate the radius of gyration for all molecules
-!
-!     rgy  = radius-of-gyration
-!     ee   = end-to-end distance
-!
-! REQUIREMENTS: c_alfa has to be called BEFORE call of this subroutine
-!
-! CALLS: NONE
-!
       include 'INCL.H'
       

timer.F90

@@ -59 +59 @@
             ! Initialize timers
             allocate (timingData(initialTimerCount))
-            forall(i = 1:initialTimerCount)
+!            forall(i = 1:initialTimerCount)
+            do i = 1, initialTimerCount
                 timingData(i) = TimingStructure(0, -1.0, -1.0, -1.0, -1.0, 0.0, &
                         0.0, -1.0, -1.0)
-            end forall
+!            end forall
+            end do
         end subroutine init_timer
     

universe.py

@@ -4 +4 @@
 #                      Jan H. Meinke, Sandipan Mohanty
 #
-import smmp
+import smmp_p as smmp
 from math import *
 

utilities.f

@@ -7 +7 @@
 ! *********************************************************************
 
-!! Calculate the best way to distribute the work load across processors.
-!  It calculates the average number of interactions and then tries to
-!  assign a number of interactions to each processor that is as close
-!  as possible to the average. The routine should be called once for
-!  every molecule in the system.
-!
-!  @param num_ppr Number of processors per replica
-!  @param nml index of molecule or zero.
-!
-!  @author Jan H. Meinke
+!> Calculate the best way to distribute the work load across processors.
+!!  It calculates the average number of interactions and then tries to
+!!  assign a number of interactions to each processor that is as close
+!!  as possible to the average. The routine should be called once for
+!!  every molecule in the system.
+!!
+!!  @param num_ppr Number of processors per replica
+!!  @param nml index of molecule or zero.
+!!
+!!  @author Jan H. Meinke
+!<
       subroutine distributeWorkLoad(num_ppr,nml)
 
@@ -117 +118 @@
       end subroutine distributeWorkLoad
 
-!-----------------------------------------------------------------------
-!     The function fileNameMP takes a template of a file name in the
-!     variable base. The position of the first and last character that
-!     may be replaced by rank in the string are given in i1 (first) and
-!     i2 (last).
-!     The function returns an empty string if the rank would need more
-!     characters than is allowed by the template.
-!     For example,
-!     \code
-!     rank = 11
-!     fileName = fileNameMP('base_0000.dat', 6, 9, rank)
-!     write (logString, *), fileName
-!     \endcode
-!     will output base_0011.dat.
-!
-!     @param base the base file name, e.g., base_0000.dat.
-!     @param i1 index of the first character that may be replaced
-!     @param i2 index of the last character that may be replaced
-!     @param rank the number that should be inserted into the file name.
-!
-!     @return file name for rank
-!-----------------------------------------------------------------------
+!>
+!!     The function fileNameMP takes a template of a file name in the
+!!     variable base. The position of the first and last character that
+!!     may be replaced by rank in the string are given in i1 (first) and
+!!     i2 (last).
+!!     The function returns an empty string if the rank would need more
+!!     characters than is allowed by the template.
+!!     For example,
+!!     \code
+!!     rank = 11
+!!     fileName = fileNameMP('base_0000.dat', 6, 9, rank)
+!!     write (logString, *), fileName
+!!     \endcode
+!!     will output base_0011.dat.
+!!
+!!     @param base the base file name, e.g., base_0000.dat.
+!!     @param i1 index of the first character that may be replaced
+!!     @param i2 index of the last character that may be replaced
+!!     @param rank the number that should be inserted into the file name.
+!!
+!!     @return file name for rank
+!<
       character*80 function fileNameMP(base, i1, i2, rank)
 
@@ -172 +173 @@
 
 
-!----------------------------------------------------------------------
-!     Add messages to log. This routine takes the log (debugging) mes-
-!     sages and writes them to the log file if the log level is less or
-!     equal to the maximum log level given by the global variable
-!     MAXLOGLEVEL.
-!
-!     @author Jan H. Meinke
-!
-!     @param loglevel level at which this message should be added to
-!            the log.
-!     @param message message to be written to the log.
-!     @param rank global rank of this node if running an MPI job zero
-!            otherwise.
-!----------------------------------------------------------------------
+!>
+!!     Add messages to log. This routine takes the log (debugging) mes-
+!!     sages and writes them to the log file if the log level is less or
+!!     equal to the maximum log level given by the global variable
+!!     MAXLOGLEVEL.
+!!
+!!     @author Jan H. Meinke
+!!
+!!     @param loglevel level at which this message should be added to
+!!            the log.
+!!     @param message message to be written to the log.
+!!     @param rank global rank of this node if running an MPI job zero
+!!            otherwise.
+!<
       subroutine addLogMessage(loglevel, message, rank)
 
-      integer maxloglevel, logfileunit
+         integer MAXLOGLEVEL, LOGFILEUNIT
+         common /log/MAXLOGLEVEL, LOGFILEUNIT
 
          integer :: loglevel, rank