Changeset 4e219a3


Ignore:
Timestamp:
09/05/08 11:49:43 (16 years ago)
Author:
baerbaer <baerbaer@…>
Branches:
master
Children:
a52fb83
Parents:
229cc35
Message:

Update Lund init and BG/P compatibility.

  • Moved call of init_lundff after initialization of the molecule. The Lund

force field needs the molecule to calculate the hydrophobicity matrix.

  • Added bgp target to Makefile to compile SMMP on a BlueGene/P
  • Split if statement in setmvs to avoid out-of-range warning for array

access.

  • Changed setup of boundaries in Protein.zimmer() to match new version of

numpy.

git-svn-id: ​svn+ssh://svn.berlios.de/svnroot/repos/smmp/trunk@15 26dc1dd8-5c4e-0410-9ffe-d298b4865968

Files:
7 edited

Legend:

Unmodified
Added
Removed

  • EXAMPLES/parallel_tempering_p.f

    r229cc35 r4e219a3  
    125125      upchswitch=1
    126126      rndord=.true.
    127      
    128       if (ientyp.eq.2) call init_lundff
    129127!     =================================================================
    130128!     Distribute nodes to parallel tempering tasks
    … …  
    198196     &        fileNameMP(filebase, 6, 9, rep_id + 1))
    199197      endif
     198      call init_lund
     199      if (ientyp.eq.2) call init_lundff
    200200      if (ientyp.eq.3) call init_abgn
     201
    201202
    202203!     ========================================  start of parallel tempering run

  • Makefile

    r229cc35 r4e219a3  
    44
    55%_p.o : %_p.f
     6        $(MPIF90) $(F_FLAGS) $<
     7       
     8%_p.o : %_p.F
    69        $(MPIF90) $(F_FLAGS) $<
    710       
    … …  
    3639F_FLAGS=-c -O2 -g
    3740# Flags for Intel's ifort
    38 # F_FLAGS=-c -O3 -axW -g
     41# F_FLAGS=-c -O3 -axW -g -DONECALL -DBRANCHLESS
    3942# Flags for debugging build
    4043# F_FLAGS=-c -O0 -g
    … …  
    4851
    4952# Select your compiler
    50 F90=gfortran
    5153#F90=ifort
    5254#F90=pgf90
    5355#F90=xlf
     56F90=gfortran
    5457MPIF90=mpif90
    5558
    … …  
    9497        $(MPIF90) -o $(PROG) $(L_FLAGS) main_p.o $(OBJ) $(POBJ)
    9598
    96 # Cross compile for BlueGene/P
     99# Cross compile for BlueGene/L
    97100bgl: BGL_L_FLAGS = -L$(BGLSYS)/lib -lmpich.rts -lfmpich.rts -lmsglayer.rts -lrts.rts -ldevices.rts -qextname=flush
    98101bgl: F_FLAGS = -c -O5 -qhot -g -I$(BGLSYS)/include -L$(BGLSYS)/lib -qarch=440 -qtune=440 -qextname=flush
    … …  
    105108bgl: $(OBJ) $(POBJ) main_bgl_p.o
    106109        $(BGL_F90) -o $(PROG).rts $(BGL_L_FLAGS) main_bgl_p.o $(OBJ) $(POBJ) $(LIBSF_MPI)
     110
     111# Cross compile for BlueGene/P
     112bgp: BGP_SYS = /bgsys/drivers/ppcfloor/comm
     113bgp: DIRCOMP = /opt/ibmcmp/xlf/bg/11.1/bin
     114bgp: BGP_L_FLAGS = -O3 -qhot -g -I$(BGP_SYS)/include -qarch=440 -qtune=440 -qextname=flush
     115bgp: F_FLAGS = -c -O3 -qhot -g -I$(BGP_SYS)/include -qarch=440 -qtune=440 -qextname=flush
     116bgp: BGP_F90 = bgxlf
     117bgp: F90 = $(BGP_F90)
     118bgp: MPIF90 = $(BGP_F90)
     119bgp: LIBS=-Wl,-allow-multiple-definition $(MASS) $(ESSL) -L$(BGP_SYS)/lib -lmpich.cnk -ldcmfcoll.cnk -ldcmf.cnk -L/bgsys/drivers/ppcfloor/runtime/SPI -lSPI.cna -lrt -lpthread
     120
     121bgp: $(OBJ) $(POBJ) main_p.o
     122        $(BGP_F90) -o $(PROG).rts $(BGP_L_FLAGS) main_p.o $(OBJ) $(POBJ) $(LIBS)
    107123
    108124# Build the python bindings

  • SMMP.kdevelop.filelist

    r229cc35 r4e219a3  
    11# KDevelop Custom Project File List
     2EXAMPLES
     3EXAMPLES/Makefile
     4EXAMPLES/Python
     5EXAMPLES/Python/annealing.py
     6EXAMPLES/Python/gui_example.py
     7EXAMPLES/Python/minimization.py
     8EXAMPLES/Python/muca.py
     9EXAMPLES/Python/regularization.py
     10EXAMPLES/annealing.f
     11EXAMPLES/minimization.f
     12EXAMPLES/multicanonical.f
     13EXAMPLES/parallel_tempering_p.f
     14EXAMPLES/parallel_tempering_s.f
     15EXAMPLES/partem_p.f
     16EXAMPLES/regularization.f
     17INCL.H
     18INCP.H
     19Makefile
    220addend.f
    321algorithms.py
    … …  
    2341enysol_p.f
    2442esolan.f
    25 EXAMPLES
    26 EXAMPLES/annealing.f
    27 EXAMPLES/Makefile
    28 EXAMPLES/minimization.f
    29 EXAMPLES/multicanonical.f
    30 EXAMPLES/parallel_tempering_p.f
    31 EXAMPLES/parallel_tempering_s.f
    32 EXAMPLES/partem_p.f
    33 EXAMPLES/Python
    34 EXAMPLES/Python/annealing.py
    35 EXAMPLES/Python/gui_example.py
    36 EXAMPLES/Python/minimization.py
    37 EXAMPLES/Python/muca.py
    38 EXAMPLES/Python/regularization.py
    39 EXAMPLES/regularization.f
    4043eyabgn.f
    4144getmol.f
    … …  
    4346hbond.f
    4447helix.f
    45 INCL.H
    4648incl_lund.h
    47 INCP.H
    4849init_energy.f
    4950init_molecule.f
     51main.f
     52main.py
    5053main_bgl_p.f
    51 main.f
    5254main_p.f
    53 main.py
    54 Makefile
    5555metropolis.f
    5656mincjg.f

  • contacts.f

    r229cc35 r4e219a3  
    1414! ..............................................................
    1515!
    16 ! CALCULATES NUMBER OF CONTACTS IN GIVEN CONFORMATION, NUMBER OF
    17 ! CONTACTS WHICH ARE THE SAME IN GIVEN AND REFERENCE ONFORMATION,
    18 ! AND THE HAMMING DISTANCE BETWEEN GIVEN  CONFORMATION AND THE
    19 ! REFERENCE CONFORMATIONa
     16! Calculates number of contacts in given conformation, number of
     17! contacts which are the same in given and reference conformation,
     18! and the hamming distance between given conformation and the
     19! reference conformation.
    2020!
    2121! CALLS: c_cont

  • main_p.f

    r229cc35 r4e219a3  
    127127      upchswitch=1
    128128      rndord=.true.
    129       if (ientyp.eq.2) call init_lundff
    130129!     =================================================================
    131130!     Distribute nodes to parallel tempering tasks
    … …  
    190189     &        fileNameMP(filebase, 6, 9, rep_id + 1))
    191190      endif
     191      call init_lund
     192!     Must call init_lundff *after* molecule has been loaded.
     193      if (ientyp.eq.2) call init_lundff
    192194      if (ientyp.eq.3) call init_abgn
    193195
    194196      nml = 1
     197
    195198
    196199!     RRRRRRRRRRMMMMMMMMMMMMSSSSSSSSSSDDDDDDDDDDDDD

  • protein.py

    r229cc35 r4e219a3  
    264264       
    265265    def zimmer(self):
    266         first = smmp.mol_i.irsml1[self.__id][0] - 1
    267         last = smmp.mol_i.irsml2[self.__id][0] - 1
    268         nrs = smmp.mol_i.irsml2[smmp.mol_i.ntlml - 1][0] - 1
     266        first = smmp.mol_i.irsml1[self.__id] - 1
     267        last = smmp.mol_i.irsml2[self.__id]
     268        nrs = smmp.mol_i.irsml2[smmp.mol_i.ntlml - 1] - 1
    269269        smmp.zimmer(last)
    270270        return smmp.zimme.zimm[first:last]
    271271
    272272    def __len__(self):
    273         return smmp.mol_i.irsml2[self.__id]  - smmp.mol_i.irsml1[self.__id]
     273        return smmp.mol_i.irsml2[self.__id]  - smmp.mol_i.irsml1[self.__id] + 1
    274274
    275275

  • setmvs.f

    r229cc35 r4e219a3  
    132132      j=l+l-ii
    133133      do while (j.le.k)
    134         if (j.lt.k.and.iadvr1(iorvr(j)).lt.iadvr1(iorvr(j+1))) j=j+1
     134!         if (j.lt.k.and.iadvr1(iorvr(j)).lt.iadvr1(iorvr(j+1))) j=j+1
     135        if (j.lt.k) then
     136            if (iadvr1(iorvr(j)).lt.iadvr1(iorvr(j+1))) then
     137                j = j + 1
     138            end if
     139        end if
    135140        if (n.lt.iadvr1(iorvr(j))) then
    136141          iorvr(i)=iorvr(j)
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