Added aria support per 220905

(Portage version: 2.2_rc62/cvs/Linux x86_64)

1 files changed, 475 insertions, 0 deletions

diff --git a/sci-chemistry/cns/files/1.2.1-aria.patch b/sci-chemistry/cns/files/1.2.1-aria.patch
new file mode 100644
index 000000000000..35c962b882c9
--- /dev/null
+++ b/sci-chemistry/cns/files/1.2.1-aria.patch
@@ -0,0 +1,475 @@
+diff -arNu aria2.2/cns/src/cns.f aria2.2.new/cns/src/cns.f
+--- aria2.2/cns/src/cns.f	2007-08-22 17:25:51.000000000 +0200
++++ aria2.2.new/cns/src/cns.f	2009-06-14 15:28:39.907685273 +0200
+@@ -12,7 +12,7 @@
+ C  +          J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read,          +
+ C  +          L.M.Rice, T.Simonson, G.L.Warren                     +
+ C  +===============================================================+
+-C  + Copyright 1997-2007 Yale University                           +
++C  + Copyright 1997-2008 Yale University                           +
+ C  +===============================================================+
+ C  +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ C
+@@ -470,6 +470,7 @@
+       INTEGER      HNLEN, TMP, PTRSZ, STLEN
+       CHARACTER*(1) CNSPTMP
+       CHARACTER*(4) ST
++!$    integer omp_get_max_threads
+ C
+ C write header
+       WRITE(6,'(10X,A)')
+@@ -511,7 +512,7 @@
+      &'             J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read,',
+      &'             L.M.Rice, T.Simonson, G.L.Warren.'
+       WRITE(6,'(10X,A)')
+-     &' Copyright (c) 1997-2007 Yale University'
++     &' Copyright (c) 1997-2008 Yale University'
+       WRITE(6,'(10X,A)')
+      &'============================================================'
+ C
+@@ -526,6 +527,9 @@
+       WRITE(6,'(10X,7A)')
+      & ' Running on machine: ',HOSTNM(1:HNLEN),
+      & ' (',SYSNM(1:TMP),',',ST(1:STLEN),'-bit)'
++!$    write(6,'(31x,a,i3,a)') 'with',omp_get_max_threads(),
++!$   &  ' threads'
++!$C (to change use setenv OMP_NUM_THREADS x)
+ C
+       CALL GETNAM(USERNM,12,TMP)
+       WRITE(6,'(10X,2A)')
+diff -arNu aria2.2/cns/src/energy.f aria2.2.new/cns/src/energy.f
+--- aria2.2/cns/src/energy.f	2006-12-18 16:26:49.000000000 +0100
++++ aria2.2.new/cns/src/energy.f	2009-06-14 14:47:57.421262637 +0200
+@@ -23,7 +23,8 @@
+       INTEGER I, NDIM, N
+       DOUBLE PRECISION TOTAL
+       DOUBLE COMPLEX DCVAL
+-      DOUBLE COMPLEX EDUMMY
++CCC modifcation ATB 4/27/08
++      DOUBLE PRECISION EDUMMY
+ C parameters
+       DOUBLE PRECISION ZERO, ONE
+       PARAMETER (ZERO=0.0D0, ONE=1.0D0)
+diff -arNu aria2.2/cns/src/noe.f aria2.2.new/cns/src/noe.f
+--- aria2.2/cns/src/noe.f	2007-08-22 17:25:51.000000000 +0200
++++ aria2.2.new/cns/src/noe.f	2009-06-14 15:03:30.001587922 +0200
+@@ -36,8 +36,8 @@
+       INTEGER ISLCT(*), JSLCT(*)
+ C local
+       INTEGER I, II, NISLCT, NJSLCT, ICL1, ICL2, NN, ITEMP, IEMODE
+-      CHARACTER*4 CLASS, CLASS2, STEMP, SRESET
+-      DOUBLE PRECISION SCALE, RTEMP, NOEDST, THRESH
++      CHARACTER*4 CLASS, CLASS2, STEMP, SRESET, DENMODE
++      DOUBLE PRECISION SCALE, RTEMP, NOEDST, THRESH, GAMMA, KAPPA
+       LOGICAL MATCH
+ C parameter
+       DOUBLE PRECISION ZERO, ONE, SIX
+@@ -140,7 +140,7 @@
+      &     NPEAKI,HEAP(HPNPID),HEAP(HPNSPC),
+      &     HEAP(HPNPP1),HEAP(HPNPP2),HEAP(HPNHP1),HEAP(HPNHP2),
+      &     HEAP(HPNVOL),HEAP(HPCDIS),HEAP(HPCVOL),NATOM,ISLCT,NISLCT,
+-     &     JSLCT,NJSLCT,X,Y,Z)
++     &     JSLCT,NJSLCT,X,Y,Z,HEAP(HPDENINIT))
+ C===================================================================
+       ELSE IF (WD(1:4).EQ.'?   ') THEN
+       WRITE(6,'(A,I6,A,I6,A,/,A,F8.3,A,I6)')
+@@ -167,7 +167,8 @@
+ C
+ C get the class name:
+       CALL NEXTA4('class-name=',CLASS)
+-      CALL NEXTF('AVERaging=',RTEMP)
++CCC modification ATB 4/27/08
++      CALL NEXTF('AVEXponent=',RTEMP)
+       DO I=1,NOECCN
+       CALL EQSTWC(NOECNM(I),4,CLASS,4,1,1,MATCH)
+       IF (MATCH) THEN
+@@ -179,7 +180,8 @@
+ C
+ C get the class name:
+       CALL NEXTA4('class-name=',CLASS)
+-      CALL NEXTF('AVERaging=',RTEMP)
++CCC modification ATB 4/27/08
++      CALL NEXTF('OREXponent=',RTEMP)
+       DO I=1,NOECCN
+       CALL EQSTWC(NOECNM(I),4,CLASS,4,1,1,MATCH)
+       IF (MATCH) THEN
+@@ -585,6 +587,38 @@
+       IF (NOEICV.GT.0) CALL NOEPRI(THRESH,1)
+       END IF
+ C====================================================================
++CCC modification ATB 5/02/08
++      ELSE IF (WD(1:4).EQ.'OUTD') THEN
++      CALL NOEOUT(0)
++      IF (NOEICV.GT.0) CALL NOEOUT(1)
++C====================================================================
++CCC modification ATB 4/25/08
++      ELSE IF (WD(1:3).EQ.'DEN') THEN
++      CALL NEXTWD('DEN>')
++      IF (WD(1:4).NE.'INIT'.AND.WD(1:4).NE.'UPDA') THEN
++      WRITE(6,'(A)') ' %NOE-ERR: DEN expects INIT or UPDAte'
++      ELSE
++      DENMODE=WD(1:4)
++      GAMMA=0.0D0
++      KAPPA=0.0D0
++      IF (DENMODE.EQ.'UPDA') THEN
++      CALL NEXTWD('DEN>')
++      IF (WD(1:4).NE.'GAMM') THEN
++      WRITE(6,'(A)') ' %NOE-ERR: DEN UPDAte expects GAMMa parameter'
++      ELSE
++      CALL NEXTF('GAMMa=',GAMMA)
++      CALL NEXTWD('DEN>')
++      IF (WD(1:4).NE.'KAPP') THEN
++      WRITE(6,'(A)') ' %NOE-ERR: DEN UPDAte expects KAPPa parameter'
++      ELSE
++      CALL NEXTF('KAPPa=',KAPPA)
++      END IF
++      END IF
++      END IF 
++      CALL NOEDEN(DENMODE,GAMMA,KAPPA,0)
++      IF (NOEICV.GT.0) CALL NOEDEN(DENMODE,GAMMA,KAPPA,1)
++      END IF
++C====================================================================
+       ELSE IF (WD(1:4).EQ.'ANAL') THEN
+       CALL NEXTA4('ANALyse=',RANA)
+ C====================================================================
+@@ -683,7 +717,7 @@
+      &           NOEXCL,NPEAKI,NOEPID,NOESPC,NOEPP1,NOEPP2,NOEHP1,
+      $           NOEHP2,NOEVOL,NOECDI,
+      &           NOECVO,NATOM,ISLCT,NISLCT,
+-     &           JSLCT,NJSLCT,X,Y,Z)
++     &           JSLCT,NJSLCT,X,Y,Z,NOEDENINIT)
+ C
+ C Subroutine parses an NOE ASSIgn statement and
+ C puts the information into the NOE restraints list
+@@ -706,7 +740,7 @@
+       DOUBLE PRECISION NOEPP1(*),NOEPP2(*),NOEHP1(*),NOEHP2(*)
+       DOUBLE PRECISION NOEVOL(*), NOECDI(*),NOECVO(*)
+       INTEGER NATOM, ISLCT(*), NISLCT, JSLCT(*), NJSLCT
+-      DOUBLE PRECISION X(*), Y(*), Z(*)
++      DOUBLE PRECISION X(*), Y(*), Z(*), NOEDENINIT(*)
+ C local
+       INTEGER I, II, JJ, J, TISLCT, TJSLCT, PEAKID
+       LOGICAL SUCCES,OK
+@@ -737,6 +771,10 @@
+       CALL NEXTF('lower-average-distance=',NOELOW(NOENUM))
+       CALL NEXTF('higher-average-distance=',NOEHIG(NOENUM))
+ C
++C initialize initial DEN distance
++      NOEDENINIT(NOENUM)=ZERO
++
++C
+ C initialize time-average and running average stuff
+ C
+ C set the time-averaged distance and
+@@ -1732,6 +1770,232 @@
+       RETURN
+       END
+ C====================================================================
++      SUBROUTINE NOEOUT(ITEST)
++C
++C print a list of current NOE restraints
++C as assign statements
++C Front-end for NOEPR3
++      IMPLICIT NONE
++C I/O
++      INCLUDE 'cns.inc'
++      INCLUDE 'heap.inc'
++      INCLUDE 'noe.inc'
++      INTEGER ITEST
++C begin
++      CALL NOEPR3(ITEST,
++     &           HEAP(HPNORR),HEAP(HPNIPR),HEAP(HPNILS),HEAP(HPNJPR),
++     &           HEAP(HPNJLS),HEAP(HPNCND),HEAP(HPNRAV),HEAP(HPNRRV),
++     &           HEAP(HPNDIS),HEAP(HPNLOW),HEAP(HPNHIG),
++     &           HEAP(HPNVIO),HEAP(HPNCV), HEAP(HPNPID))
++
++      RETURN
++      END
++C====================================================================
++      SUBROUTINE NOEPR3(ITEST,
++     &           NOEORR,NOEIPR,NOEILS,NOEJPR,
++     &           NOEJLS,NOECND,NOERAV,NOERRV,
++     &           NOEDIS,NOELOW,NOEHIG,
++     &           NOEVIO,NOECV,NOEPID)
++      IMPLICIT NONE
++C I/O
++      INCLUDE 'cns.inc'
++      INCLUDE 'noe.inc'
++      INCLUDE 'mtf.inc'
++      INCLUDE 'pick.inc'
++      INCLUDE 'comand.inc'
++      INCLUDE 'numbers.inc'
++      INTEGER ITEST
++C
++C global NOE arrays on HEAP
++C restraint and atom pointers
++      INTEGER NOEORR(*),NOEIPR(*),NOEILS(*),NOEJPR(*),NOEJLS(*)
++C classes
++      INTEGER NOECND(*)
++C averages
++      DOUBLE PRECISION NOERAV(*),NOERRV(*)
++C target distance and errors
++      DOUBLE PRECISION NOEDIS(*),NOELOW(*),NOEHIG(*)
++C number of violations
++      INTEGER NOEVIO(*)
++C time average pointer, test set, restraint number
++      INTEGER NOECV(*), NOEPID(*)
++C
++C local
++      INTEGER N, K, I, J, CLASS, NORR
++      INTEGER I1, I2
++C begin
++      IF (NOENUM.GT.0) THEN
++C
++C loop over all classes
++      DO CLASS=1,NOECCN
++      IF (NOEPOT(CLASS).EQ.NOESYM.OR.
++     &    NOEPOT(CLASS).EQ.NOEHDI.OR.
++     &    NOEPOT(CLASS).EQ.NOE3DP) THEN
++      CALL WRNDIE(-5,'NOEPRI',
++     & 'DENOut not possible with POTEntial set to SYMM, HIGH, or 3DPO')
++      ELSE
++C
++C loop over all NOE's belonging to this class
++      DO N=1,NOENUM
++      IF ((ITEST.EQ.0.AND.NOECV(N).NE.NOEICV).OR.
++     &    (ITEST.EQ.1.AND.NOECV(N).EQ.NOEICV)) THEN
++      IF (NOECND(N).EQ.CLASS) THEN
++C
++C     WE ONLY TAKE THE FIRST FROM EACH SET
++      NORR=NOEORR(N)+1
++C
++C     DO I=NOEIPR(NORR)+1,NOEIPR(NORR+1)
++C
++C     WE ONLY TAKE THE FIRST FROM EACH SET
++      I=NOEIPR(NORR)+1
++      K=NOEILS(I)
++      I1=K
++C
++C     WE ONLY TAKE THE FIRST FROM EACH SET
++      J=NOEJPR(NORR)+1
++      K=NOEJLS(J)
++      I2=K
++C
++      WRITE(PUNIT,'(A,I6,A,I6,A,F6.3,A,F6.3,A,F6.3)') 
++     & 'ASSIGn (id ',
++     & I1, ' ) (id ', I2, ' ) ', NOEDIS(N), 
++     & ' ', NOELOW(N), ' ', NOEHIG(N)
++C
++      END IF
++      END IF
++      END DO
++      END IF
++      END DO
++      END IF
++      RETURN
++      END
++C====================================================================
++      SUBROUTINE NOEDEN(DENMODE,GAMMA,KAPPA,ITEST)
++C
++C print a list of current NOE restraints
++C Front-end for NOEPR2
++      IMPLICIT NONE
++C I/O
++      INCLUDE 'cns.inc'
++      INCLUDE 'heap.inc'
++      INCLUDE 'noe.inc'
++      CHARACTER*4 DENMODE
++      DOUBLE PRECISION GAMMA, KAPPA
++      INTEGER ITEST
++C begin
++      CALL NOEDEN2(DENMODE,GAMMA,KAPPA,ITEST,
++     &           HEAP(HPNORR),HEAP(HPNIPR),HEAP(HPNILS),HEAP(HPNJPR),
++     &           HEAP(HPNJLS),HEAP(HPNCND),HEAP(HPNRAV),HEAP(HPNRRV),
++     &           HEAP(HPNDIS),HEAP(HPNLOW),HEAP(HPNHIG),
++     &           HEAP(HPNVIO),HEAP(HPNCV), HEAP(HPNPID),
++     &           HEAP(HPDENINIT))
++
++      RETURN
++      END
++C====================================================================
++      SUBROUTINE NOEDEN2(DENMODE,GAMMA,KAPPA,ITEST,
++     &           NOEORR,NOEIPR,NOEILS,NOEJPR,
++     &           NOEJLS,NOECND,NOERAV,NOERRV,
++     &           NOEDIS,NOELOW,NOEHIG,
++     &           NOEVIO,NOECV,NOEPID,NOEDENINIT)
++      IMPLICIT NONE
++C I/O
++      INCLUDE 'cns.inc'
++      INCLUDE 'noe.inc'
++      INCLUDE 'mtf.inc'
++      INCLUDE 'pick.inc'
++      INCLUDE 'comand.inc'
++      INCLUDE 'numbers.inc'
++      CHARACTER*4 DENMODE
++      DOUBLE PRECISION GAMMA,KAPPA
++      INTEGER ITEST
++C
++C global NOE arrays on HEAP
++C restraint and atom pointers
++      INTEGER NOEORR(*),NOEIPR(*),NOEILS(*),NOEJPR(*),NOEJLS(*)
++C classes
++      INTEGER NOECND(*)
++C averages
++      DOUBLE PRECISION NOERAV(*),NOERRV(*)
++C target distance and errors
++      DOUBLE PRECISION NOEDIS(*),NOELOW(*),NOEHIG(*)
++C number of violations
++      INTEGER NOEVIO(*)
++C time average pointer, test set, restraint number
++      INTEGER NOECV(*), NOEPID(*)
++C initial den distance
++      DOUBLE PRECISION NOEDENINIT(*)
++C
++C local
++      DOUBLE PRECISION EN, NOERMS, NOERM2(NOECMX), THRESH
++      DOUBLE COMPLEX DBCOMP
++      DOUBLE PRECISION DBPREC
++      INTEGER NOENU2(NOECMX)
++      INTEGER NOEVIT
++      INTEGER N, K, I, J, CLASS, NOENUML, NORR
++      CHARACTER*6 SSAVE
++      CHARACTER*11 SSPOT
++      LOGICAL QHEAD
++C begin
++      THRESH=-0.1
++      NOERMS=ZERO
++      NOEVIT=0
++      NOENUML=0
++      IF (NOENUM.GT.0) THEN
++C
++C
++C loop over all classes
++      DO CLASS=1,NOECCN
++      NOENU2(CLASS)=0
++      NOERM2(CLASS)=ZERO
++      NOEVIO(CLASS)=0
++      IF (NOEPOT(CLASS).EQ.NOESYM.OR.
++     &    NOEPOT(CLASS).EQ.NOEHDI.OR.
++     &    NOEPOT(CLASS).EQ.NOE3DP) THEN
++      CALL WRNDIE(-5,'NOEPRI',
++     & 'DEN not possible with POTEntial set to SYMM, HIGH, or 3DPO')
++      ELSE
++C
++C loop over all NOE's belonging to this class
++      QHEAD=.TRUE.
++      DO N=1,NOENUM
++      IF ((ITEST.EQ.0.AND.NOECV(N).NE.NOEICV).OR.
++     &    (ITEST.EQ.1.AND.NOECV(N).EQ.NOEICV)) THEN
++      IF (NOECND(N).EQ.CLASS) THEN
++      NOENUML=NOENUML+1
++C
++C get NOE energy, current distance (in PCDATA(PCGEOM), and other results
++      CALL ENOE(EN,'ANAL',N)
++      NOERMS=NOERMS+PCDATA(PCDEVI)**2
++      NOERM2(CLASS)=NOERM2(CLASS)+PCDATA(PCDEVI)**2
++      NOENU2(CLASS)=NOENU2(CLASS)+1
++      IF (ABS(PCDATA(PCDEVI)).GT.THRESH) THEN
++      NOEVIO(CLASS)=NOEVIO(CLASS)+1
++      NOEVIT=NOEVIT+1
++      END IF
++C
++      IF (DENMODE.EQ.'INIT') THEN
++C
++C initialization
++      NOEDENINIT(N)=PCDATA(PCGEOM)
++CCCCxxx      NOEDIS(N)=PCDATA(PCGEOM)
++      ELSE
++C
++C update step
++      NOEDIS(N)=NOEDIS(N)+KAPPA*(GAMMA*(PCDATA(PCGEOM)-NOEDIS(N))+ 
++     &          (ONE-GAMMA)*(NOEDENINIT(N)-NOEDIS(N)) )       
++      END IF
++C
++      END IF      
++      END IF
++      END DO
++      END IF
++      END DO
++C
++      END IF
++      RETURN
++      END
++C====================================================================
+       SUBROUTINE ENOE(EN,ANALYS,NA)
+ C
+ C Routine computes force field for NOE restraints
+@@ -3357,6 +3621,7 @@
+       HPNRRV=0
+       HPNNSP=0
+       HPNDIS=0
++      HPDENINIT=0
+       HPNLOW=0
+       HPNHIG=0
+       HPNWGH=0
+@@ -3373,7 +3638,6 @@
+       HPNVOL=0
+       HPCVOL=0
+       HPCDIS=0
+-      HPNPRD=0
+ C
+ C
+ C reset other variables
+@@ -3463,6 +3727,7 @@
+       IF (HPNRRV.NE.0) CALL FREHP(HPNRRV,IREAL8(NOEMAX))
+       IF (HPNNSP.NE.0) CALL FREHP(HPNNSP,INTEG4(NOEMAX))
+       IF (HPNDIS.NE.0) CALL FREHP(HPNDIS,IREAL8(NOEMAX))
++      IF (HPDENINIT.NE.0) CALL FREHP(HPDENINIT,IREAL8(NOEMAX))
+       IF (HPNLOW.NE.0) CALL FREHP(HPNLOW,IREAL8(NOEMAX))
+       IF (HPNHIG.NE.0) CALL FREHP(HPNHIG,IREAL8(NOEMAX))
+       IF (HPNWGH.NE.0) CALL FREHP(HPNWGH,IREAL8(NOEMAX))
+@@ -3495,6 +3760,7 @@
+       HPNRRV=0
+       HPNNSP=0
+       HPNDIS=0
++      HPDENINIT=0
+       HPNLOW=0
+       HPNHIG=0
+       HPNWGH=0
+@@ -3511,7 +3777,6 @@
+       HPNVOL=0
+       HPCVOL=0
+       HPCDIS=0
+-      HPNPRD=0
+ C
+ C now allocate new space
+       IF (NOENEW.GT.0) THEN
+@@ -3536,6 +3801,7 @@
+       HPNRRV=ALLHP(IREAL8(NOENEW))
+       HPNNSP=ALLHP(INTEG4(NOENEW))
+       HPNDIS=ALLHP(IREAL8(NOENEW))
++      HPDENINIT=ALLHP(IREAL8(NOENEW))
+       HPNCND=ALLHP(INTEG4(NOENEW))
+       HPNJLS=ALLHP(INTEG4(NOENEW))
+       HPNJPR=ALLHP(INTEG4(NOENEW))
+diff -arNu aria2.2/cns/src/noe.inc aria2.2.new/cns/src/noe.inc
+--- aria2.2/cns/src/noe.inc	2007-08-22 17:25:51.000000000 +0200
++++ aria2.2.new/cns/src/noe.inc	2009-06-14 15:24:50.995208687 +0200
+@@ -29,6 +29,9 @@
+ C list for distances and +/- error estimates (heap pointers)
+       INTEGER HPNDIS, HPNLOW, HPNHIG
+ C
++C list for initial DEN distances
++      INTEGER HPDENINIT
++C
+ C individual weights on restraints
+       INTEGER HPNWGH
+ C
+@@ -119,7 +122,7 @@
+       INTEGER HPNVIO, HPNEXC, HPNNUM
+ 
+ C peak identifier
+-      INTEGER NPEAKI, HPNPID, HPNPRD
++      INTEGER NPEAKI, HPNPID
+ C
+ C
+ C
+@@ -142,7 +145,7 @@
+      &              NMONO,  RAVEXP, NOECOR, NOEICV, 
+      &              HPNVIO, HPNEXC, HPNNUM,
+      &              NPEAKI, HPNPID, IDIMER, HPNPP1, HPNPP2, 
+-     &              HPNHP1, HPNHP2, HPNVOL, HPCVOL, HPCDIS, HPNPRD
++     &              HPNHP1, HPNHP2, HPNVOL, HPCVOL, HPCDIS, HPDENINIT
+ C
+ C     character string block
+ C