From markwick at NMR.EMBL-Heidelberg.DE Fri Nov 1 18:59:42 2002 From: markwick at NMR.EMBL-Heidelberg.DE (Phineus Markwick) Date: Fri, 01 Nov 2002 18:59:42 +0100 Subject: [CPMD-list] constraints Message-ID: <3DC2C10E.2010303@NMR.EMBL-Heidelberg.DE> Hallo cpmd-list, I am trying to program a new type of constraint in cpmd. As it is a quasi-distance constraint (based on several multiple distances), I have followed in principle the distance constraint program that already exists. I introduce the new constraint in CONINP.F, defining the name of the new constraint and the atomic numbers that occur in the input line, the constraint "distance" and the LSHOVE value. In CNSTFC.F, I call the program FILLC(...) to read in the appropriate atomic coordinates, and then call the two constraint subroutines that are in CONSTR.F (funcconstraint.F and diffconstraint.F). In CONSTR.F I have already introduced the two new subroutines funcconstraint and diffconstraint. When I run cpmd with the new constraint, the program happliy runs through CONINP.F, CNSTFC.F and CONSTR.F. The program reads in all the atomic coordinates and runs through the two subroutines funccontraint and diffconstraint. Using the same terminology as in the existing constraint subroutines funcd and diffd, my new constraint subroutines generate both fd (fd =d-RO, the difference between the actual distance and the constraint distance) and the vector dR. At this point the program immediately stops with the error output: forrtl: error (75): floating point exception 0: __FINI_00_remove_gp_range [0x3ff81a6de38] 1: __FINI_00_remove_gp_range [0x3ff81a76e60] 2: __FINI_00_remove_gp_range [0x3ff800d5120] 3: cnstfc_ [./cnstfc.f: 118, 0x1201cb028] 4: detdof_ [./detdof.f: 191, 0x1201c9b10] 5: mdmain_ [./mdmain.f: 119, 0x1201daa00] 6: mdpt_ [./mdpt.f: 124, 0x1201d9ff0] 7: cpmd_ [./cpmd.f: 120, 0x12003dac4] 8: cpmd_stuttgart_ [./cpmd.f: 3, 0x12003d590] 9: main [for_main.c: 203, 0x1203fc66c] 10: __start [0x12003d3b8] time: command terminated abnormally. real 15.8 user 3.0 sys 2.6 The last line in the output file is the number of degrees of freedom.(which is correct). This error message suggests to me that at some point the program is being asked to do something stupid like divide some number by zero. This is not occuring in the two subroutines funcconstraint and diffconstraint, but at some later point in the program. The only two new variables generated by these two programs are fd and the vector dR, and these seem to be O.K. So, are there any other programs that I need to edit or introduce? In particular, I am concerned by the fact that for this new constraint, I have at no point defined either fd or dR other than to state that they exist as variables in the programs funcconstraint and diffconstraint. I would appreciate any help or comments, best regards, Phineus Markwick. From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Fri Nov 1 19:23:01 2002 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Fri, 01 Nov 2002 19:23:01 +0100 Subject: [CPMD-list] constraints In-Reply-To: <3DC2C10E.2010303@NMR.EMBL-Heidelberg.DE> Message-ID: <200211011823.gA1IN1t21579@yello.theochem.ruhr-uni-bochum.de> On Fri, 01 Nov 2002 18:59:42 +0100 Phineus Markwick wrote: > Hallo cpmd-list, hi phineus, > > I am trying to program a new type of constraint in cpmd. As it is a > quasi-distance constraint (based on several multiple distances), I have > followed in principle the distance constraint program that already exists. > > I introduce the new constraint in CONINP.F, defining the name of the new > constraint and the atomic numbers that occur in the input line, the > constraint "distance" and the LSHOVE value. > > In CNSTFC.F, I call the program FILLC(...) to read in the appropriate > atomic coordinates, and then call the two constraint subroutines that > are in CONSTR.F (funcconstraint.F and diffconstraint.F). > > In CONSTR.F I have already introduced the two new subroutines > funcconstraint and diffconstraint. > > When I run cpmd with the new constraint, the program happliy runs > through CONINP.F, CNSTFC.F and CONSTR.F. The program reads in all the > atomic coordinates and runs through the two subroutines funccontraint > and diffconstraint. are you sure? the following stack(?) trace suggests, that the error occurs somewhere at line 118 of the file cnstfc.f. pehaps on calling or returning from a subroutine/function call. cheers, axel. > > Using the same terminology as in the existing constraint subroutines > funcd and diffd, my new constraint subroutines generate both fd (fd > =d-RO, the difference between the actual distance and the constraint > distance) and the vector dR. > At this point the program immediately stops with the error output: > > > forrtl: error (75): floating point exception > 0: __FINI_00_remove_gp_range [0x3ff81a6de38] > 1: __FINI_00_remove_gp_range [0x3ff81a76e60] > 2: __FINI_00_remove_gp_range [0x3ff800d5120] > 3: cnstfc_ [./cnstfc.f: 118, 0x1201cb028] > 4: detdof_ [./detdof.f: 191, 0x1201c9b10] > 5: mdmain_ [./mdmain.f: 119, 0x1201daa00] > 6: mdpt_ [./mdpt.f: 124, 0x1201d9ff0] > 7: cpmd_ [./cpmd.f: 120, 0x12003dac4] > 8: cpmd_stuttgart_ [./cpmd.f: 3, 0x12003d590] > 9: main [for_main.c: 203, 0x1203fc66c] > 10: __start [0x12003d3b8] > time: command terminated abnormally. > > real 15.8 > user 3.0 > sys 2.6 > > The last line in the output file is the number of degrees of > freedom.(which is correct). > > This error message suggests to me that at some point the program is > being asked to do something stupid like divide some number by zero. > This is not occuring in the two subroutines funcconstraint and > diffconstraint, but at some later point in the program. The only two new > variables generated by these two programs are fd and the vector dR, and > these seem to be O.K. > > So, are there any other programs that I need to edit or introduce? > > In particular, I am concerned by the fact that for this new constraint, > I have at no point defined either fd or dR other than to state that they > exist as variables in the programs funcconstraint and diffconstraint. > > I would appreciate any help or comments, > best regards, > Phineus Markwick. > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > -- ======================================================================= Axel Kohlmeyer e-mail: axel.kohlmeyer at theochem.ruhr-uni-bochum.de Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673 Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045 D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From markwick at NMR.EMBL-Heidelberg.DE Sat Nov 2 18:18:05 2002 From: markwick at NMR.EMBL-Heidelberg.DE (Phineus Markwick) Date: Sat, 02 Nov 2002 18:18:05 +0100 Subject: [CPMD-list] constraints revisited Message-ID: <3DC408CD.5000205@NMR.EMBL-Heidelberg.DE> Dear cpmd-list, In trying to incorporate a new constraint into cpmd, I have a problem in the program CNSTFC.F at the point: DO K=1,KMAX DO N=1,NODIM ANORM(N,I)=ANORM(N,I)+DX(K)*ASKEL(N,I,K) ENDDO ENDDO ENDDO can anybody tell me exactly what the matrix ASKEL(N,I,K) is and where its components are defined? As I am now sure that the problem is in the program CNSTFC.F (thanks Axel!), I have included my edited version of this program as an attachment. In my test system, the distance constraint is formulated using the coordinates of 10 atoms, so dX (or dR) is a vector with 30 components, and KMAX=30. I think that the problem comes from the fact that all N*I*30 components of the matrix ASKEL are not defined. Once again, I would appreciate any help or comments, best regards, Phineus Markwick. -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: cnstfc.F Url: http://cpmd.org/pipermail/cpmd-list/attachments/20021102/2e484f55/attachment.cc From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Sat Nov 2 18:54:19 2002 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Sat, 02 Nov 2002 18:54:19 +0100 Subject: [CPMD-list] constraints revisited In-Reply-To: <3DC408CD.5000205@NMR.EMBL-Heidelberg.DE> Message-ID: <200211021754.gA2HsKK31119@yello.theochem.ruhr-uni-bochum.de> On Sat, 02 Nov 2002 18:18:05 +0100 Phineus Markwick wrote: > This is a multi-part message in MIME format. > --------------010009080001030009090302 > Content-Type: text/plain; charset=us-ascii; format=flowed > Content-Transfer-Encoding: 7bit > > Dear cpmd-list, hi phineus! > > In trying to incorporate a new constraint into cpmd, I have a problem in > the program CNSTFC.F at the point: > > DO K=1,KMAX > DO N=1,NODIM > ANORM(N,I)=ANORM(N,I)+DX(K)*ASKEL(N,I,K) > ENDDO > ENDDO > ENDDO > > can anybody tell me exactly what the matrix ASKEL(N,I,K) is and where > its components are defined? hmm, i really don't know a lot about cpmd internals, but this question can hopefully be answered anyway: [25|18:45]~/compile/cpmd/SOURCE> grep -n -i askel *.F *.inc cnstfc.F:92: ANORM(N,I)=ANORM(N,I)+DX(K)*ASKEL(N,I,K) detdof.F:114: CALL MEMORY(IP_ASKEL,12*NODIM*MCNSTR,'ASKEL') detdof.F:121: CALL AZZERO(ASKEL,12*NODIM*MCNSTR) detdof.F:228: IF(JX.NE.0) ASKEL(JX,I,NN+1)=1.0D0 detdof.F:229: IF(JY.NE.0) ASKEL(JY,I,NN+2)=1.0D0 detdof.F:230: IF(JZ.NE.0) ASKEL(JZ,I,NN+3)=1.0D0 detdof.F:245: IF(JX.NE.0) ASKEL(JX,I,NN+1)=FF detdof.F:246: IF(JY.NE.0) ASKEL(JY,I,NN+2)=FF detdof.F:247: IF(JZ.NE.0) ASKEL(JZ,I,NN+3)=FF cotr.inc:44:C == ASKEL(NODIM,MCNSTR,12) == cotr.inc:56: & CNSVAL(*),ANORM(NODIM,*),ASKEL(NODIM,MCNSTR,*), cotr.inc:62: * (IP_ANORM,ANORM),(IP_ASKEL,ASKEL),(IP_FCSTR,FCSTR ), cotr.inc:68: * IP_NTCNST,IP_CNSVAL,IP_ANORM,IP_ASKEL,IP_FCSTR, > > As I am now sure that the problem is in the program CNSTFC.F (thanks > Axel!), I have included my edited version of this program as an attachment. > In my test system, the distance constraint is formulated using the > coordinates of 10 atoms, so dX (or dR) is a vector with 30 components, > and KMAX=30. I think that the problem comes from the fact that all > N*I*30 components of the matrix ASKEL are not defined. > > Once again, I would appreciate any help or comments, now let's see what you have changed: [26|18:46]~/compile/cpmd/SOURCE> diff -u cnstfc.F ~/work/cnstfc.F --- cnstfc.F Tue Nov 14 13:21:19 2000 +++ /home/akohlmey/work/cnstfc.F Sat Nov 2 18:42:22 2002 @@ -14,7 +14,9 @@ LOGICAL LAGRA C Variables INTEGER ISUB,IA,IB,IC,ID,ITYP,I,J,K,N,KMAX,IX,IDAMAX - REAL*8 X1(3),X2(3),X3(3),X4(3),DX(12),CVAL + INTEGER IE,IFF,IG,IH,II,IJ + REAL*8 X1(3),X2(3),X3(3),X4(3),DX(30),CVAL + REAL*8 X5(3),X6(3),X7(3),X8(3),X9(3),X10(3) hmm, the DX(12) seems to correspond with the definition of askel in detdof.F:114. but let's continue: @@ -60,6 +68,23 @@ CALL FUNCD(FC(I),FV(I),CVAL,X1,X2) CALL DIFFD(DX,X1,X2) KMAX=6 + ELSEIF(ITYP.EQ.9) THEN +C..NEW CONSTRAINT + CALL FILLC(IA,TSCR,X1) + CALL FILLC(IB,TSCR,X2) + CALL FILLC(IC,TSCR,X3) + CALL FILLC(ID,TSCR,X4) + CALL FILLC(IE,TSCR,X5) + CALL FILLC(IFF,TSCR,X6) + CALL FILLC(IG,TSCR,X7) + CALL FILLC(IH,TSCR,X8) + CALL FILLC(II,TSCR,X9) + CALL FILLC(IJ,TSCR,X10) + CALL FUNCCONS(FC(I),FV(I),CVAL,X1,X2,X3,X4,X5,X6,X7,X8,X9,X10) + CALL DIFFCONS(DX,X1,X2,X3,X4,X5,X6,X7,X8,X9,X10) +C PRINT*,'DX=',DX +C PRINT*,'XS=',X1,X2,X3,X4,X5,X6,X7,X8,X9,X10 + KMAX=30 ELSEIF(ITYP.EQ.5) THEN ok, here you change kmax from 6 to 30, but the comment in cotr.inc:44 seems to indicate a limit of 12. oops. i would say, try replacing the in 12 detdof.F:114 and detdof.F:121 with 30. but someone who _really_ knows cpmd should confirm that. cheers, axel. > > best regards, > Phineus Markwick. > > --------------010009080001030009090302 > Content-Type: text/plain; > name="cnstfc.F" > Content-Transfer-Encoding: 7bit > Content-Disposition: inline; > filename="cnstfc.F" > > C ================================================================== > SUBROUTINE CNSTFC(TAU0,TSCR,DXPAR,CNMAX,LAGRA) > C ==--------------------------------------------------------------== > IMPLICIT NONE > INCLUDE 'system.h' > INCLUDE 'ions.inc' > INCLUDE 'cotr.inc' > INCLUDE 'rmas.inc' > INCLUDE 'tpar.inc' > INCLUDE 'adat.inc' > INCLUDE 'ener.inc' > C Arguments > REAL*8 TAU0(3,NAX,NSX),TSCR(3,NAX*NSX),DXPAR(*),CNMAX > LOGICAL LAGRA > C Variables > INTEGER ISUB,IA,IB,IC,ID,ITYP,I,J,K,N,KMAX,IX,IDAMAX > INTEGER IE,IFF,IG,IH,II,IJ > REAL*8 X1(3),X2(3),X3(3),X4(3),DX(30),CVAL > REAL*8 X5(3),X6(3),X7(3),X8(3),X9(3),X10(3) > C ==--------------------------------------------------------------== > CALL TISET(' CNSTFC',ISUB) > CNMAX=0.0D0 > C No constraints -> return. > IF(MCNSTR.EQ.0) RETURN > CALL DUM2(TAU0,TSCR) > CALL AZZERO(ANORM,MCNSTR*NODIM) > DO I=1,MCNSTR > CVAL=CNSVAL(I) > ITYP=NTCNST(1,I) > IA=NTCNST(2,I) > IB=NTCNST(3,I) > IC=NTCNST(4,I) > ID=NTCNST(5,I) > IE=NTCNST(6,I) > IFF=NTCNST(7,I) > IG=NTCNST(8,I) > IH=NTCNST(9,I) > II=NTCNST(10,I) > IJ=NTCNST(11,I) > IF(ITYP.EQ.1) THEN > C..stretch > CALL FILLC(IA,TSCR,X1) > CALL FILLC(IB,TSCR,X2) > CALL FUNCR(FC(I),FV(I),CVAL,X1,X2) > CALL DIFFR(DX,X1,X2) > KMAX=6 > C..angle > ELSEIF(ITYP.EQ.2) THEN > CALL FILLC(IA,TSCR,X1) > CALL FILLC(IB,TSCR,X2) > CALL FILLC(IC,TSCR,X3) > CALL FUNCT(FC(I),FV(I),CVAL,X1,X2,X3) > CALL DIFFT(DX,X1,X2,X3) > KMAX=9 > ELSEIF(ITYP.EQ.3) THEN > C..dihedral angle > CALL FILLC(IA,TSCR,X1) > CALL FILLC(IB,TSCR,X2) > CALL FILLC(IC,TSCR,X3) > CALL FILLC(ID,TSCR,X4) > CALL FUNCO(FC(I),FV(I),CVAL,X1,X2,X3,X4) > CALL DIFFO(DX,X1,X2,X3,X4) > KMAX=12 > ELSEIF(ITYP.EQ.4) THEN > C..distance > CALL FILLC(IA,TSCR,X1) > CALL FILLC(IB,TSCR,X2) > CALL FUNCD(FC(I),FV(I),CVAL,X1,X2) > CALL DIFFD(DX,X1,X2) > KMAX=6 > ELSEIF(ITYP.EQ.9) THEN > C..NEW CONSTRAINT > CALL FILLC(IA,TSCR,X1) > CALL FILLC(IB,TSCR,X2) > CALL FILLC(IC,TSCR,X3) > CALL FILLC(ID,TSCR,X4) > CALL FILLC(IE,TSCR,X5) > CALL FILLC(IFF,TSCR,X6) > CALL FILLC(IG,TSCR,X7) > CALL FILLC(IH,TSCR,X8) > CALL FILLC(II,TSCR,X9) > CALL FILLC(IJ,TSCR,X10) > CALL FUNCCONS(FC(I),FV(I),CVAL,X1,X2,X3,X4,X5,X6,X7,X8,X9,X10) > CALL DIFFCONS(DX,X1,X2,X3,X4,X5,X6,X7,X8,X9,X10) > C PRINT*,'DX=',DX > C PRINT*,'XS=',X1,X2,X3,X4,X5,X6,X7,X8,X9,X10 > KMAX=30 > ELSEIF(ITYP.EQ.5) THEN > C..out of plane > CALL FILLC(IA,TSCR,X1) > CALL FILLC(IB,TSCR,X2) > CALL FILLC(IC,TSCR,X3) > CALL FILLC(ID,TSCR,X4) > CALL FUNCP(FC(I),FV(I),CVAL,X1,X2,X3,X4) > CALL DIFFP(DX,X1,X2,X3,X4) > KMAX=12 > ELSEIF(ITYP.EQ.6) THEN > C..coordination number > CALL COORNUM(IA,TSCR,NAT,ANORM(1,I),LSKPTR, > * FC(I),FV(I),CVAL) > KMAX=0 > ELSEIF(ITYP.EQ.7) THEN > C..difference between distances- 3 atoms > CALL FILLC(IA,TSCR,X1) > CALL FILLC(IB,TSCR,X2) > CALL FILLC(IC,TSCR,X3) > CALL FUNCDD(FC(I),FV(I),CVAL,X1,X2,X3) > CALL DIFFDD(DX,X1,X2,X3) > KMAX=9 > ELSE > WRITE(*,*) ' CNSTFC! I=',I,' TYPE=',ITYP > CALL STOPGM('CNSTFC','UNKNOWN TYPE OF CONSTRAINT') > END IF > > PRINT*,'hallo world 1' > > DO K=1,KMAX > DO N=1,NODIM > ANORM(N,I)=ANORM(N,I)+DX(K)*ASKEL(N,I,K) > ENDDO > ENDDO > ENDDO > > PRINT*,'hallo world 2' > > ECNSTR=0.0D0 > CALL AZZERO(FCSTR,NODIM) > DO I=1,MCNSTR > DO J=1,NODIM > IF(LAGRA) THEN > FCSTR(J)=FCSTR(J)+XLAGR(I)*ANORM(J,I) > ELSE > FCSTR(J)=FCSTR(J)+CSIGM(I)*ANORM(J,I)*FC(I) > ECNSTR=ECNSTR+0.5D0*CSIGM(I)*FC(I)*FC(I) > ENDIF > ENDDO > ENDDO > IX=IDAMAX(NODIM,FCSTR(1),1) > CNMAX=ABS(FCSTR(IX)) > CALL DAXPY(NODIM,1.0D0,FCSTR(1),1,DXPAR(1),1) > CALL TIHALT(' CNSTFC',ISUB) > C ==--------------------------------------------------------------== > RETURN > END > C ================================================================== > SUBROUTINE FILLC(IAT,TAU,X) > C ==--------------------------------------------------------------== > C == Extract the coordinates X(1:3) of IAT index in TAU (TSCR) == > C == Works also if dummy atoms == > C ==--------------------------------------------------------------== > IMPLICIT NONE > INCLUDE 'system.h' > INCLUDE 'ions.inc' > INCLUDE 'cotr.inc' > C Arguments > INTEGER IAT > REAL*8 TAU(3,NAX*NSX),X(3) > C Local > INTEGER ID,NAA,ITYP > C ==--------------------------------------------------------------== > IF(IAT.LE.0) THEN > C Do nothing > RETURN > ELSEIF(IAT.LE.NAT) THEN > C Real atoms > X(1)=TAU(1,IAT) > X(2)=TAU(2,IAT) > X(3)=TAU(3,IAT) > ELSEIF(IAT.LE.NAT+NDAT) THEN > C Dummy atoms (type 2). > NAA=IAT-NAT > ITYP=LISTDA(NAA,1) > ID=LISTDA(NAA,2) > IF(ITYP.EQ.2) THEN > X(1)=DUMMY2(1,ID) > X(2)=DUMMY2(2,ID) > X(3)=DUMMY2(3,ID) > ENDIF > ENDIF > C ==--------------------------------------------------------------== > RETURN > END > C ================================================================== > SUBROUTINE COORNUM(IA,TSCR,NAT,AN,LSK,FCI,FVI,CVAL) > C ==--------------------------------------------------------------== > IMPLICIT NONE > INCLUDE 'system.h' > INCLUDE 'cotr.inc' > C Arguments > INTEGER IA,NAT,LSK(3,NAT) > REAL*8 TSCR(3,*),AN(*),FCI,FVI,CVAL > C Variables > REAL*8 X0,Y0,Z0,DX,DY,DZ,DD,FF,DF > INTEGER IAT,K,L1,L2,L3 > C ==--------------------------------------------------------------== > L1 = LSK(1,IA) > L2 = LSK(2,IA) > L3 = LSK(3,IA) > X0 = TSCR(1,IA) > Y0 = TSCR(2,IA) > Z0 = TSCR(3,IA) > FVI = 0.D0 > DO IAT=1,NAT > DX=TSCR(1,IAT)-X0 > DY=TSCR(2,IAT)-Y0 > DZ=TSCR(3,IAT)-Z0 > CALL PBC(DX,DY,DZ,DX,DY,DZ,1,APBC,IBRAV) > DD=SQRT(DX*DX+DY*DY+DZ*DZ) > C..exclude self interaction > IF(DD.GT.1.D-2) THEN > DF=C_KAPPA*(DD-C_RC) > FVI=FVI+1.D0/(EXP(DF)+1.D0) > FF=-0.5*C_KAPPA/(COSH(DF)+1.D0)/DD > IF(LSK(1,IAT).NE.0) THEN > K=LSK(1,IAT) > AN(K)=AN(K)+FF*DX > ENDIF > IF(LSK(2,IAT).NE.0) THEN > K=LSK(2,IAT) > AN(K)=AN(K)+FF*DY > ENDIF > IF(LSK(3,IAT).NE.0) THEN > K=LSK(3,IAT) > AN(K)=AN(K)+FF*DZ > ENDIF > IF(L1.NE.0) AN(L1)=AN(L1)-FF*DX > IF(L2.NE.0) AN(L2)=AN(L2)-FF*DY > IF(L3.NE.0) AN(L3)=AN(L3)-FF*DZ > ENDIF > ENDDO > FCI=FVI-CVAL > C ==--------------------------------------------------------------== > RETURN > END > C ================================================================== > > --------------010009080001030009090302-- > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > -- ======================================================================= Axel Kohlmeyer e-mail: axel.kohlmeyer at theochem.ruhr-uni-bochum.de Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673 Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045 D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From dft_cpmd at yahoo.com Mon Nov 4 22:22:49 2002 From: dft_cpmd at yahoo.com (R Jkhurdakar) Date: Mon, 4 Nov 2002 13:22:49 -0800 (PST) Subject: [CPMD-list] MD at fixed tempeature Message-ID: <20021104212249.26490.qmail@web13208.mail.yahoo.com> Hi! I'm interested in a molecular dynamics simulation of a molecule at 300K. I'm somewhat consfused with the choice of appropriate KEWYWORD to achieve this. I want to calculate averages at 300K. So I'm using the following input for the CPMD section. &CPMD MOLECULAR DYNAMICS CP QUENCH BO EMASS 800 TIMESTEP 25 TEMPERATURE 300 TRAJECTORY SAMPLE 10 MOVIE 5 &END My question is if the about input is correct or should I use the keyword TEMPCONTROL IONS followed by 300 50 on the next line? Any help or comments would be appreciated. Many Thanks, RJ __________________________________________________ Do you Yahoo!? HotJobs - Search new jobs daily now http://hotjobs.yahoo.com/ From v.gogonea at csuohio.edu Tue Nov 5 00:59:09 2002 From: v.gogonea at csuohio.edu (Valentin Gogonea) Date: Mon, 04 Nov 2002 18:59:09 -0500 Subject: [CPMD-list] getting the CPMD code Message-ID: <69149BF6-F051-11D6-AA84-003065CDB448@csuohio.edu> Hi, I am trying for a week to get the CPMD code from the cpmd website. I accepted the license terms, I filled in the information and sent it two times, but I got no answer. Can anybody give me any suggestion what should I do or contact to get the CPDM source code (for academia). Thank you, Valentin Cleveland State University From MENONM at engr.sc.edu Tue Nov 5 01:13:42 2002 From: MENONM at engr.sc.edu (MENON, MAHESH ) Date: Mon, 4 Nov 2002 19:13:42 -0500 Subject: [CPMD-list] qery on KS energy calculation and eigenvalues Message-ID: Hello Fellow Colleagues, I have a few queries on CPMD related calculations. Hope some of you can clear my queries. 1) In Kohn-Sham Energy calculation, how to calculate "number of empty states and number of occupied states" for a molecule?. In CPMD manual, in the example for one water molecule, in one case this value is 'zero' and other case is 'four'. Could anyone explain this? KOHN-SHAM ENERGIES N N = ?? 2) Is it possible to do geometry optimization in Kohn-Sham energy calculations? I mean, is it possible to do calculations with OPTIMIZE GEOMETRY KOHN-SHAM ENERGIES The reason why I asked this is because it says both are mutually exclusive. But in the example section (pg 53) it is given that both optimization step and Kohn-Sham Energies can be used. OPTIMIZE WAVEFUNCTION KOHN-SHAM ENERGIES When I tried to do that particular example, the output says "both are mutually exclusive" and stops. So, Is it is possible to do geometry optimization in Kohn-Sham energy calculation, then what modification I have to do? 3) I also tried to calculate the Eigenvalues by printing the keyword "PRINT ON INFO EIGENVALUES". My input file looks like this: &CPMD OPTIMIZE WAVEFUNCTION INITIALIZE WAVEFUNCTION RANDOM STRUCTURE BONDS ANGLES PRINT ON INFO EIGENVALUES STORE 2 ISOLATED MOLECULE &END But with this input, eigenvalues are neither printed in the output file nor in any other files. If I want the eigen values in the output file, what I have to do? Wish some of you can help me out. Thanks in advance, Regards, M. Menon -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20021104/984ab749/attachment.html From cur at zurich.ibm.com Tue Nov 5 08:47:34 2002 From: cur at zurich.ibm.com (Alessandro Curioni) Date: Tue, 5 Nov 2002 08:47:34 +0100 Subject: [CPMD-list] getting the CPMD code Message-ID: You should have received your password one week ago. Please re-check your e-mail . Regards Alessandro CURIONI, PhD Research Staff Member Computational Biochemistry and Material Science group IBM Research Division - Zurich Research Laboratory Saumerstrasse 4 8003 Rueschlikon - Switzerland e-mail: cur at zurich.ibm.com www: www.zurich.ibm.com Tel: +41-1-7248633 Fax: +41-1-7248958 Valentin Gogonea cc: Sent by: Subject: [CPMD-list] getting the CPMD code cpmd-list-admin at c pmd.org 11/05/2002 12:59 AM Hi, I am trying for a week to get the CPMD code from the cpmd website. I accepted the license terms, I filled in the information and sent it two times, but I got no answer. Can anybody give me any suggestion what should I do or contact to get the CPDM source code (for academia). Thank you, Valentin Cleveland State University _______________________________________________ CPMD-list mailing list CPMD-list at cpmd.org http://www.cpmd.org/mailman/listinfo/cpmd-list From Ari.P.Seitsonen at iki.fi Tue Nov 5 13:29:07 2002 From: Ari.P.Seitsonen at iki.fi (Ari.P.Seitsonen at iki.fi) Date: Tue, 5 Nov 2002 13:29:07 +0100 Subject: [CPMD-list] MD at fixed tempeature In-Reply-To: <20021104212249.26490.qmail@web13208.mail.yahoo.com> (message from R Jkhurdakar on Mon, 4 Nov 2002 13:22:49 -0800 (PST)) References: <20021104212249.26490.qmail@web13208.mail.yahoo.com> Message-ID: <200211051229.gA5CT6R09962@magadino.cscs.ch> Dear Dr Jkhurdakar, > I'm interested in a molecular dynamics simulation > of a molecule at 300K. I'm somewhat consfused with > the choice of appropriate KEWYWORD to achieve this. > I want to calculate averages at 300K. So I'm using > the > following input for the CPMD section. > &CPMD > MOLECULAR DYNAMICS CP > QUENCH BO > EMASS > 800 > TIMESTEP > 25 > TEMPERATURE > 300 > TRAJECTORY SAMPLE > 10 > MOVIE > 5 > &END > > My question is if the about input is correct or > should I use the keyword TEMPCONTROL IONS followed > by 300 50 on the next line? > Any help or comments would be appreciated. First of all, if your cluster is not very large, the temperature will fluctuate quite much during the simulation; you can decrease the fluctuations somewhat by using a Nose thermostat, but this might lead to somewhat unphysical trajectories as well. Secondly, if you specify only "TEMPERATURE" (same as "TEMPERATURE IONS") this only specifies the initial temperature, if the initial structure was relaxed to the global minimum you'll end up at around half of the initial temperature specified due to equilibration between kinetic and potential energy. So you can use "TEMPCONTROL IONS", but please notice that the temperature will fluctuate around the average, and you shouldn't take physical averages of trajectories with the rescaling switched on, i.e. the "TEMPCONTROL IONS" should only be used in the beginning to equilibrate the system. Hopefully this helps somewhat. Greetings, apsi -- -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ Tel +41 1 635 44 97 / Fax +41 1 635 68 38 / GSM +41 79 719 09 35 Anschrift: Physikalisch Chemisches Institut (PCI), Universit?t Z?rich (UniZh) Indirizzo: Winterthurerstra?e 190, CH-8057 Z?rich Address: Schweiz / Svizzera / Suisse / Svizra / Switzerland From Ari.P.Seitsonen at iki.fi Tue Nov 5 14:10:58 2002 From: Ari.P.Seitsonen at iki.fi (Ari.P.Seitsonen at iki.fi) Date: Tue, 5 Nov 2002 14:10:58 +0100 Subject: [CPMD-list] qery on KS energy calculation and eigenvalues In-Reply-To: (MENONM@engr.sc.edu) References: Message-ID: <200211051310.gA5DAwx11365@magadino.cscs.ch> Dear Dr Menon, > 1) > In Kohn-Sham Energy calculation, how to calculate "number of empty states > and number of occupied states" for a molecule?. In CPMD manual, in the > example for one water molecule, in one case this value is 'zero' and other > case is 'four'. Could anyone explain this? > > KOHN-SHAM ENERGIES > N > > N = ?? This depends on how many unoccupied/virtual states you want to obtain. N=0 means that the true Kohn-Sham states (i.e. those which diagonalise the Lambda matrix on the right hand side of the KS equations) are wanted, without any unoccupied states; this corresponds to a diagonalisation of the matrix <\phi_j|H|\phi_i>. > 2) > Is it possible to do geometry optimization in Kohn-Sham energy calculations? > I mean, is it possible to do calculations with > OPTIMIZE GEOMETRY > KOHN-SHAM ENERGIES > > The reason why I asked this is because it says both are mutually exclusive. > But in the example section (pg 53) it is given that both optimization step > and Kohn-Sham Energies can be used. > OPTIMIZE WAVEFUNCTION > KOHN-SHAM ENERGIES > > When I tried to do that particular example, the output says "both are > mutually exclusive" and stops. > So, Is it is possible to do geometry optimization in Kohn-Sham energy > calculation, then what modification I have to do? It is not possible to do them in the same run, this wouldn't bring much advantage: the Kohn-Sham states (neither KS wavefunctions nor eigenvalues) are not needed during the geometry optimisation. You can calculate the Kohn-Sham states in another job with a RESTART. > 3) > I also tried to calculate the Eigenvalues by printing the keyword "PRINT ON > INFO EIGENVALUES". My input file looks like this: > &CPMD > OPTIMIZE WAVEFUNCTION > INITIALIZE WAVEFUNCTION RANDOM > STRUCTURE BONDS ANGLES > PRINT ON INFO EIGENVALUES > STORE > 2 > ISOLATED MOLECULE > &END > > But with this input, eigenvalues are neither printed in the output file nor > in any other files. If I want the eigen values in the output file, what I > have to do? I believe that the PRINT INFO ... is more meant for dynamical runs. In jobs including only the optimisation of the electronic structure one can use the Kohn-Sham energies. Greetings, apsi -- -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ Tel +41 1 635 44 97 / Fax +41 1 635 68 38 / GSM +41 79 719 09 35 Anschrift: Physikalisch Chemisches Institut (PCI), Universit?t Z?rich (UniZh) Indirizzo: Winterthurerstra?e 190, CH-8057 Z?rich Address: Schweiz / Svizzera / Suisse / Svizra / Switzerland From yjjiang at mail.shcnc.ac.cn Tue Nov 5 14:49:42 2002 From: yjjiang at mail.shcnc.ac.cn (Yongjun Jiang) Date: Tue, 5 Nov 2002 21:49:42 +0800 Subject: [CPMD-list] I couldn't receive the user name and password. Message-ID: <200211060437.gA64bpFe014846@mail.shcnc.ac.cn> Dear CPMD Developers, I am very interesting in CPMD. I have done the process indicating as your WWW submission, and information is shown: Your application has been sent succesfully! You will receive an e-mail with the password to download CPMD very soon! Check your e-mails! But there are no letters from you. How will I get the program? yjjiang at mail.shcnc.ac.cn From dft_cpmd at yahoo.com Wed Nov 6 21:48:02 2002 From: dft_cpmd at yahoo.com (R Jkhurdakar) Date: Wed, 6 Nov 2002 12:48:02 -0800 (PST) Subject: [CPMD-list] MD at fixed tempeature In-Reply-To: <200211051229.gA5CT6R09962@magadino.cscs.ch> Message-ID: <20021106204802.4395.qmail@web13204.mail.yahoo.com> Dear Apsi, Thanks for suggestions. How much fluctuation from the desired Temperature is generally accepted? For example, for simulation at 300K for a system containing about 8 atoms, are the fluctuation of +-70K around 300K acceptable? If I've correctly understood your mail, I use the following input for CPMD section to get the desired initial TEMP. & CPMD MOLECULAR DYNAMICS QUENCH BO TEMPERATURE 300 MAXSTEP 10 & Then I rerun the simulation with the following section. & CPMD MOLECULAR DYNAMICS RESTART WAVEFUNCTION COORDINATES VELOCITIES GEOFILE QUENCH BO MAXSTEP 1000 &END And perform the averages after discarding first few picoseconds for equilibration. Is this the correct way to siumlate an isolated system at 300K with CPMD. Thanks once again, Regards, RJ --- Ari.P.Seitsonen at iki.fi wrote: > > Dear Dr Jkhurdakar, > > > I'm interested in a molecular dynamics > simulation > > of a molecule at 300K. I'm somewhat consfused with > > > the choice of appropriate KEWYWORD to achieve > this. > > I want to calculate averages at 300K. So I'm > using > > the > > following input for the CPMD section. > > &CPMD > > MOLECULAR DYNAMICS CP > > QUENCH BO > > EMASS > > 800 > > TIMESTEP > > 25 > > TEMPERATURE > > 300 > > TRAJECTORY SAMPLE > > 10 > > MOVIE > > 5 > > &END > > > > My question is if the about input is correct or > > should I use the keyword TEMPCONTROL IONS > followed > > by 300 50 on the next line? > > Any help or comments would be appreciated. > > First of all, if your cluster is not very large, the > temperature will > fluctuate quite much during the simulation; you can > decrease the > fluctuations somewhat by using a Nose thermostat, > but this might lead > to somewhat unphysical trajectories as well. > > Secondly, if you specify only "TEMPERATURE" (same > as "TEMPERATURE > IONS") this only specifies the initial temperature, > if the initial > structure was relaxed to the global minimum you'll > end up at around > half of the initial temperature specified due to > equilibration between > kinetic and potential energy. So you can use > "TEMPCONTROL IONS", but > please notice that the temperature will fluctuate > around the average, > and you shouldn't take physical averages of > trajectories with the > rescaling switched on, i.e. the "TEMPCONTROL IONS" > should only be used > in the beginning to equilibrate the system. > > Hopefully this helps somewhat. > > Greetings, > > apsi > > -- > -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- > Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / > http://www.iki.fi/~apsi/ > Tel +41 1 635 44 97 / Fax +41 1 635 68 38 / GSM +41 > 79 719 09 35 > Anschrift: Physikalisch Chemisches Institut (PCI), > Universit?t Z?rich (UniZh) > Indirizzo: Winterthurerstra?e 190, CH-8057 Z?rich > Address: Schweiz / Svizzera / Suisse / Svizra / > Switzerland > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list __________________________________________________ Do you Yahoo!? HotJobs - Search new jobs daily now http://hotjobs.yahoo.com/ From proffess at mail.ru Fri Nov 8 15:34:26 2002 From: proffess at mail.ru (C=?koi8-r?Q?=C5=D2=C7=C5=CA=20=EC=C9=D3=C5=CE=CB=CF=D7?=) Date: Fri, 08 Nov 2002 17:34:26 +0300 Subject: [CPMD-list] problem with compiling CPMD Message-ID: Dear All, I have tried to compile CPMD code with IFC compiler. I have seen this error , but it did'n help me: ifc -O0 -c -O2 -tp p6 -axiM -O0 -pc64 -unroll -w90 -w95 ./BYLM_p.f -o ./BYLM_p.o ifc: Command line warning: overriding '-O0' with '-O2' ifc: Command line warning: overriding '-O2' with '-O0' external subroutine BYLMR119 $GK(2,IG)**6)*Sqrt(3357800061./(2.*Pi)))/(65536.*HG(IG)**9) ^ Warning 101 at (2647:./BYLM_p.f) : Constant truncated -- precision too great $17*GK(2,IG)**16)*GK(3,IG)*Sqrt(3357800061./(2.*Pi)))/ ^ Warning 101 at (2656:./BYLM_p.f) : Constant truncated -- precision too great $34*GK(3,IG)**2)*Sqrt(2398428615./Pi))/(8192.*HG(IG)**9) ^ Warning 101 at (2666:./BYLM_p.f) : Constant truncated -- precision too great $32*GK(3,IG)**2)*Sqrt(13591095485./(2.*Pi)))/(65536.*HG(IG)**9) ^ Warning 101 at (2675:./BYLM_p.f) : Constant truncated -- precision too great $320*GK(3,IG)**4)*Sqrt(3706662405./(2.*Pi)))/(65536.*HG(IG)**9) ^ Warning 101 at (2684:./BYLM_p.f) : Constant truncated -- precision too great $320*GK(3,IG)**4)*Sqrt(3706662405./(2.*Pi)))/(131072.*HG(IG)**9) ^ Warning 101 at (2994:./BYLM_p.f) : Constant truncated -- precision too great $32*GK(3,IG)**2)*Sqrt(13591095485./(2.*Pi)))/(65536.*HG(IG)**9) ^ Warning 101 at (3003:./BYLM_p.f) : Constant truncated -- precision too great $34*GK(3,IG)**2)*Sqrt(2398428615./Pi))/(131072.*HG(IG)**9) ^ Warning 101 at (3012:./BYLM_p.f) : Constant truncated -- precision too great $GK(2,IG)**16)*GK(3,IG)*Sqrt(3357800061./(2.*Pi)))/ ^ Warning 101 at (3021:./BYLM_p.f) : Constant truncated -- precision too great $GK(2,IG)**18)*Sqrt(3357800061./(2.*Pi)))/(131072.*HG(IG)**9) ^ Warning 101 at (3031:./BYLM_p.f) : Constant truncated -- precision too great $GK(2,IG)**6)*GK(3,IG)*Sqrt(14550466931./(2.*Pi)))/ ^ Warning 101 at (3049:./BYLM_p.f) : Constant truncated -- precision too great $34*GK(3,IG)**2)*Sqrt(1179767589./Pi))/(8192.*HG(IG)**9.5) ^ Warning 101 at (3069:./BYLM_p.f) : Constant truncated -- precision too great $192*GK(3,IG)**4)*Sqrt(2865149859./(2.*Pi)))/(65536.*HG(IG)**9.5) ^ Warning 101 at (3088:./BYLM_p.f) : Constant truncated -- precision too great $208*GK(3,IG)**6)*Sqrt(1823277183./(2.*Pi)))/(8192.*HG(IG)**9.5) ^ Warning 101 at (3109:./BYLM_p.f) : Constant truncated -- precision too great $208*GK(3,IG)**6)*Sqrt(1823277183./(2.*Pi)))/(32768.*HG(IG)**9.5) ^ Warning 101 at (3394:./BYLM_p.f) : Constant truncated -- precision too great $192*GK(3,IG)**4)*Sqrt(2865149859./(2.*Pi)))/(131072.*HG(IG)**9.5) ^ Warning 101 at (3414:./BYLM_p.f) : Constant truncated -- precision too great $34*GK(3,IG)**2)*Sqrt(1179767589./Pi))/(131072.*HG(IG)**9.5) ^ Warning 101 at (3433:./BYLM_p.f) : Constant truncated -- precision too great $GK(2,IG)**18)*GK(3,IG)*Sqrt(14550466931./(2.*Pi)))/ ^ Warning 101 at (3452:./BYLM_p.f) : Constant truncated -- precision too great 3500 Lines Compiled ifc: error: Fatal error in /opt/intel/compiler60/ia32/bin/f90com, terminated by terminate signal compilation aborted for ./BYLM_p.f (code 1) make: *** [BYLM_p.o] Error 1 Could you help me? Best. Sergey From hwsheng at jhu.edu Fri Nov 8 16:58:39 2002 From: hwsheng at jhu.edu (HW Sheng) Date: Fri, 08 Nov 2002 10:58:39 -0500 Subject: [CPMD-list] MPI jobs hang...for ever. Message-ID: <003b01c2873f$b4837a40$a567dc80@mrs.jhu.edu> Hi, Axel. How are you doing? Here is an update of the crash problem I posted one month ago. Thanks to your replies (and also discussions in other forums), I came to conclude that the NIC drivers are the culprits, although I was unable to pinpoint the exact problem. After upgrading the kernel to a higher version (currently 2.4.19), I am happy that the problem has been solved. Cheers, Howard > you're welcome, howard. sharing information on how to solve complicated > network problems is really important. studying the symptoms under varying > conditions can help to identify the real cause. it is of great importance to > me, to learn more about the characteristics of the 3c905 cards under linux, > since we employ about 30 of them in various desktops and single cpu > 'servers'. mind you, we run cpmd routinely only single-cpu, on the > SCI-clusters or on a gigabit ethernet single cpu cluster (with 3c996 cards). From eyvaz_isaev at yahoo.com Fri Nov 8 21:38:00 2002 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Fri, 8 Nov 2002 12:38:00 -0800 (PST) Subject: [CPMD-list] problem with compiling CPMD In-Reply-To: Message-ID: <20021108203800.57267.qmail@web80305.mail.yahoo.com> Dear Sergei, It is very strange that you have compiling problem. As a matter of fact there is no problem using IFC v.6 and CPMD v.3.5.3. If you still have problem, please let me know. Regards, Eyvaz Isaev Theoretical Physics Department Moscow Steel and Alloys Institute Tel: 2304506 (office) --- C????? ???????? wrote: > > Dear All, > > I have tried to compile CPMD code with IFC compiler. > I have seen this error , but it did'n help me: > ifc -O0 -c -O2 -tp p6 -axiM -O0 -pc64 -unroll -w90 > -w95 ./BYLM_p.f -o ./BYLM_p.o > ifc: Command line warning: overriding '-O0' with > '-O2' > ifc: Command line warning: overriding '-O2' with > '-O0' > external subroutine BYLMR119 > > > $GK(2,IG)**6)*Sqrt(3357800061./(2.*Pi)))/(65536.*HG(IG)**9) > ^ > Warning 101 at (2647:./BYLM_p.f) : Constant > truncated -- precision too great > > > $17*GK(2,IG)**16)*GK(3,IG)*Sqrt(3357800061./(2.*Pi)))/ > ^ > Warning 101 at (2656:./BYLM_p.f) : Constant > truncated -- precision too great > > > $34*GK(3,IG)**2)*Sqrt(2398428615./Pi))/(8192.*HG(IG)**9) > ^ > Warning 101 at (2666:./BYLM_p.f) : Constant > truncated -- precision too great > > > $32*GK(3,IG)**2)*Sqrt(13591095485./(2.*Pi)))/(65536.*HG(IG)**9) > ^ > Warning 101 at (2675:./BYLM_p.f) : Constant > truncated -- precision too great > > > $320*GK(3,IG)**4)*Sqrt(3706662405./(2.*Pi)))/(65536.*HG(IG)**9) > ^ > Warning 101 at (2684:./BYLM_p.f) : Constant > truncated -- precision too great > > > $320*GK(3,IG)**4)*Sqrt(3706662405./(2.*Pi)))/(131072.*HG(IG)**9) > ^ > Warning 101 at (2994:./BYLM_p.f) : Constant > truncated -- precision too great > > > $32*GK(3,IG)**2)*Sqrt(13591095485./(2.*Pi)))/(65536.*HG(IG)**9) > ^ > Warning 101 at (3003:./BYLM_p.f) : Constant > truncated -- precision too great > > > $34*GK(3,IG)**2)*Sqrt(2398428615./Pi))/(131072.*HG(IG)**9) > ^ > Warning 101 at (3012:./BYLM_p.f) : Constant > truncated -- precision too great > > > $GK(2,IG)**16)*GK(3,IG)*Sqrt(3357800061./(2.*Pi)))/ > ^ > Warning 101 at (3021:./BYLM_p.f) : Constant > truncated -- precision too great > > > $GK(2,IG)**18)*Sqrt(3357800061./(2.*Pi)))/(131072.*HG(IG)**9) > ^ > Warning 101 at (3031:./BYLM_p.f) : Constant > truncated -- precision too great > > > $GK(2,IG)**6)*GK(3,IG)*Sqrt(14550466931./(2.*Pi)))/ > ^ > Warning 101 at (3049:./BYLM_p.f) : Constant > truncated -- precision too great > > > $34*GK(3,IG)**2)*Sqrt(1179767589./Pi))/(8192.*HG(IG)**9.5) > ^ > Warning 101 at (3069:./BYLM_p.f) : Constant > truncated -- precision too great > > > $192*GK(3,IG)**4)*Sqrt(2865149859./(2.*Pi)))/(65536.*HG(IG)**9.5) > ^ > Warning 101 at (3088:./BYLM_p.f) : Constant > truncated -- precision too great > > > $208*GK(3,IG)**6)*Sqrt(1823277183./(2.*Pi)))/(8192.*HG(IG)**9.5) > ^ > Warning 101 at (3109:./BYLM_p.f) : Constant > truncated -- precision too great > > > $208*GK(3,IG)**6)*Sqrt(1823277183./(2.*Pi)))/(32768.*HG(IG)**9.5) > ^ > Warning 101 at (3394:./BYLM_p.f) : Constant > truncated -- precision too great > > > $192*GK(3,IG)**4)*Sqrt(2865149859./(2.*Pi)))/(131072.*HG(IG)**9.5) > ^ > Warning 101 at (3414:./BYLM_p.f) : Constant > truncated -- precision too great > > > $34*GK(3,IG)**2)*Sqrt(1179767589./Pi))/(131072.*HG(IG)**9.5) > ^ > Warning 101 at (3433:./BYLM_p.f) : Constant > truncated -- precision too great > > > $GK(2,IG)**18)*GK(3,IG)*Sqrt(14550466931./(2.*Pi)))/ > ^ > Warning 101 at (3452:./BYLM_p.f) : Constant > truncated -- precision too great > > 3500 Lines Compiled > ifc: error: Fatal error in > /opt/intel/compiler60/ia32/bin/f90com, terminated by > terminate signal > compilation aborted for ./BYLM_p.f (code 1) > make: *** [BYLM_p.o] Error 1 > > > > Could you help me? > > Best. > Sergey > > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list __________________________________________________ Do you Yahoo!? New DSL Internet Access from SBC & Yahoo! http://sbc.yahoo.com From rjsa at mail.shcnc.ac.cn Sat Nov 9 02:36:25 2002 From: rjsa at mail.shcnc.ac.cn (Rongjian Sa) Date: Sat, 9 Nov 2002 9:36:25 +0800 Subject: [CPMD-list] (no subject) Message-ID: <200211091634.gA9GYrFe025938@mail.shcnc.ac.cn> -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20021109/68f394aa/attachment.html -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/gif Size: 418 bytes Desc: not available Url : http://cpmd.org/pipermail/cpmd-list/attachments/20021109/68f394aa/attachment.gif From rjsa at mail.shcnc.ac.cn Sat Nov 9 04:17:01 2002 From: rjsa at mail.shcnc.ac.cn (Rongjian Sa) Date: Sat, 9 Nov 2002 11:17:1 +0800 Subject: [CPMD-list] TM pseudopotential Message-ID: <200211091815.gA9IFTFe026355@mail.shcnc.ac.cn> Hello, Everyone, I want to get some GGA TM pseudopotential, I want to know who can tell me where I can find them? Best wishes! -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20021109/73082953/attachment.html -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/gif Size: 418 bytes Desc: not available Url : http://cpmd.org/pipermail/cpmd-list/attachments/20021109/73082953/attachment.gif From proffess at mail.ru Sat Nov 9 11:25:26 2002 From: proffess at mail.ru (C=?koi8-r?Q?=C5=D2=C7=C5=CA=20=EC=C9=D3=C5=CE=CB=CF=D7?=) Date: Sat, 09 Nov 2002 13:25:26 +0300 Subject: [CPMD-list] Compiling CPMD using IFC and MKL Message-ID: Dear All, I have compiled CPMD code (3.5.2) using IFC compiler. In LFFLAGS I used only "-latlas $...". But I cannot compile this CPMD code using MKL library without ATLAS Library. What LFFLAGS or another FLAGS I must use? Best, Sergey From Ari.P.Seitsonen at iki.fi Sat Nov 9 19:31:36 2002 From: Ari.P.Seitsonen at iki.fi (Ari.P.Seitsonen at iki.fi) Date: Sat, 9 Nov 2002 19:31:36 +0100 Subject: [CPMD-list] MD at fixed tempeature In-Reply-To: <20021106204802.4395.qmail@web13204.mail.yahoo.com> (message from R Jkhurdakar on Wed, 6 Nov 2002 12:48:02 -0800 (PST)) References: <20021106204802.4395.qmail@web13204.mail.yahoo.com> Message-ID: <200211091831.gA9IVaR12062@magadino.cscs.ch> Dear Dr Jkhurdakar, > Thanks for suggestions. How much fluctuation from > the desired Temperature is generally accepted? For > example, for simulation at 300K for a system > containing > about 8 atoms, are the fluctuation of +-70K around > 300K acceptable? > If I've correctly understood your mail, I use the > following input for CPMD section to get the desired > initial TEMP. > > & CPMD > MOLECULAR DYNAMICS > QUENCH BO > TEMPERATURE > 300 > MAXSTEP > 10 > & > Then I rerun the simulation with the following > section. > > & CPMD > MOLECULAR DYNAMICS > RESTART WAVEFUNCTION COORDINATES VELOCITIES GEOFILE > QUENCH BO > MAXSTEP > 1000 > &END > And perform the averages after discarding first few > picoseconds for equilibration. Is this the correct way to > siumlate an isolated system at 300K with CPMD. First of all, in general you should not quench the electrons to the Born-Oppenheimer surface in Car-Parrinello dynamics, in the latter input when you do the restart. Secondly, the average fluctuation in microcanonical simulation is about dT = sqrt[2/(3*N)] * T_average, where N is the number of atoms. So in your case, provided that you start from an equilibrated geometry the final temperature would be around 300 K (please notice that for this you should have the initial temperature 600 K!), and the fluctuation ca. 87 K. Greetings from Rome, apsi -- -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ Tel +41 1 635 44 97 / Fax +41 1 635 68 38 / GSM +41 79 719 09 35 Anschrift: Physikalisch Chemisches Institut (PCI), Universit?t Z?rich (UniZh) Indirizzo: Winterthurerstra?e 190, CH-8057 Z?rich Address: Schweiz / Svizzera / Suisse / Svizra / Switzerland From eyvaz_isaev at yahoo.com Sat Nov 9 21:53:33 2002 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Sat, 9 Nov 2002 12:53:33 -0800 (PST) Subject: [CPMD-list] problem with compiling CPMD In-Reply-To: <3DCCC42A.000009.05528@ariel.yandex.ru> Message-ID: <20021109205333.51568.qmail@web80312.mail.yahoo.com> Dear Sergei, Please type "locate libcxa.so" in your command line. You will receive a message that looks like the next line /opt/intel/compiler50/ia32/lib/ (I have just checked it on my PC). Probably installation of IFC is not complete, and you should add the next line into your .bashrc file: LD_LIBRARY_PATH=/opt/intel/compiler60/ia32/lib If you have questions, welcome. Regards, Eyvaz. --- Sergei Lisenkov wrote: > Dear Eyvaz, > > Thank you for your e-mail. I just compiled CPMD code > 3.5.3 using IFC 6.0. I added new ATLAS library. But > I haveone problem. Could you help me? > > I wanted to run the CPMD code at the another > computer, but I got the message: > ./cpmd.x file.in PP_PATH > file.out > > ./cpmd.x : error cannot open shared library > libcxa.so.1: NO file or such directory. > > What does it mean? > > Best wishes, > > Sergey __________________________________________________ Do you Yahoo!? New DSL Internet Access from SBC & Yahoo! http://sbc.yahoo.com From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Sun Nov 10 09:49:45 2002 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Sun, 10 Nov 2002 09:49:45 +0100 Subject: [CPMD-list] problem with compiling CPMD In-Reply-To: <20021109205333.51568.qmail@web80312.mail.yahoo.com> Message-ID: <200211100849.gAA8njB18840@yello.theochem.ruhr-uni-bochum.de> On Sat, 9 Nov 2002 12:53:33 -0800 (PST) Eyvaz Isaev wrote: alternatively you can just link statically by adding '-static' to LFLAGS. this way you don't have to copy/install the ifc runtime to all the machines you want to run cpmd on. cheers, axel kohlmeyer. > Dear Sergei, > > Please type "locate libcxa.so" in your command line. > You will receive a message that looks like the next > line > > /opt/intel/compiler50/ia32/lib/ (I have just checked > it on my PC). > > Probably installation of IFC is not complete, and > you should add the next line into your .bashrc file: > > LD_LIBRARY_PATH=/opt/intel/compiler60/ia32/lib > > If you have questions, welcome. > > Regards, > Eyvaz. > > --- Sergei Lisenkov wrote: > > Dear Eyvaz, > > > > Thank you for your e-mail. I just compiled CPMD code > > 3.5.3 using IFC 6.0. I added new ATLAS library. But > > I haveone problem. Could you help me? > > > > I wanted to run the CPMD code at the another > > computer, but I got the message: > > ./cpmd.x file.in PP_PATH > file.out > > > > ./cpmd.x : error cannot open shared library > > libcxa.so.1: NO file or such directory. > > > > What does it mean? > > > > Best wishes, > > > > Sergey > > > __________________________________________________ > Do you Yahoo!? > New DSL Internet Access from SBC & Yahoo! > http://sbc.yahoo.com > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > -- ======================================================================= Axel Kohlmeyer e-mail: axel.kohlmeyer at theochem.ruhr-uni-bochum.de Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673 Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045 D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From mit at uni.udm.ru Sun Nov 10 10:11:07 2002 From: mit at uni.udm.ru (mit) Date: Sun, 10 Nov 2002 13:11:07 +0400 Subject: [CPMD-list] problem with compiling CPMD (Yu.Mitrokhin) In-Reply-To: References: Message-ID: <200211100912.KAA08628@internet-fence.zurich.ihost.com> 8 ?????? 2002 18:34, ?? ????????: > Dear All, > > I have tried to compile CPMD code with IFC compiler. I have seen this error > , but it did'n help me: ifc -O0 -c -O2 -tp p6 -axiM -O0 -pc64 -unroll -w90 > -w95 ./BYLM_p.f -o ./BYLM_p.o ifc: Command line warning: overriding '-O0' > with '-O2' > ifc: Command line warning: overriding '-O2' with '-O0' > external subroutine BYLMR119 > > $GK(2,IG)**6)*Sqrt(3357800061./(2.*Pi)))/(65536.*HG(IG)**9) > ^ > Could you help me? > > Best. > Sergey > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list Dear Sergey, if you take last version cpmd (3.5.3) and IFC 6.0 then you have no problem with modus blym_p.f and all others. Best regards Yurii Mitrokhin ------------------------------------------------ Yuriy Mitrokhin, Ph.D. Phone: +7 3412 753831 Department of Physics Fax: +7 3412 755866 Udmurt State University http://www.uni.udm.ru 1 Universitetskaia St. E-mail: mit at uni.udm.ru 426034 Izhevsk RUSSIA ------------------------------------------------- From proffess at mail.ru Sun Nov 10 13:48:19 2002 From: proffess at mail.ru (C=?koi8-r?Q?=C5=D2=C7=C5=CA=20=EC=C9=D3=C5=CE=CB=CF=D7?=) Date: Sun, 10 Nov 2002 15:48:19 +0300 Subject: [CPMD-list] Compiling CPMD 3.5.3. using IFC Message-ID: Dear All, I have one problem with compiling CPMD using IFC: ..... ^ Comment 15 at (424:./system.h) : This feature is obsolescent in Fortran 95 575 Lines Compiled rm -f proja.f /lib/cpp -P -C -traditional -D__Linux -D__PGI -DLAPACK -DFFT_DEFAULT -DLINUX_IFC ./proja.F ./proja.f /opt/intel/compiler60/ia32/bin/ifc -c -O3 -tp p6 -axiM -pc64 -unroll -w90 -w95 ./proja.f -o ./proja.o external subroutine PROJA POINTER(IP_IATPT,IATPT),(IP_IPEPT,IPEPT),(IP_IATPE,IATPE) ^ Warning 114 at (196:./system.h) : Pointer variable has already been declared - retyped as INTEGER ^ Warning 114 at (196:./system.h) : Pointer variable has already been declared - retyped as INTEGER ^ Warning 114 at (196:./system.h) : Pointer variable has already been declared - retyped as INTEGER CHARACTER*80 FPATH ^ Comment 15 at (424:./system.h) : This feature is obsolescent in Fortran 95 586 Lines Compiled rm -f atoms.f /lib/cpp -P -C -traditional -D__Linux -D__PGI -DLAPACK -DFFT_DEFAULT -DLINUX_IFC ./atoms.F ./atoms.f /opt/intel/compiler60/ia32/bin/ifc -c -O3 -tp p6 -axiM -pc64 -unroll -w90 -w95 ./atoms.f -o ./atoms.o external subroutine ATOMS CHARACTER*2 EL(99) ^ Comment 15 at (6:./adat.inc) : This feature is obsolescent in Fortran 95 CHARACTER*2 EL2(99) ^ Comment 15 at (13:./atoms.f) : This feature is obsolescent in Fortran 95 318 Lines Compiled ./atoms.f(290) : (col. 0) remark: LOOP WAS VECTORIZED. ./atoms.f(2) : (col. 0) remark: atoms_ has been targeted for automatic cpu dispatch. rm -f fitpack.f /lib/cpp -P -C -traditional -D__Linux -D__PGI -DLAPACK -DFFT_DEFAULT -DLINUX_IFC ./fitpack.F ./fitpack.f /opt/intel/compiler60/ia32/bin/ifc -c -O3 -tp p6 -axiM -pc64 -unroll -w90 -w95 ./fitpack.f -o ./fitpack.o external subroutine CURV1 5 sdiag1 = sdiag2 ^ Comment 9 at (176:./fitpack.f) : Terminating a DO loop with a statement other than CONTINUE or ENDDO is obsolescent in Fortran 90 and Fortran 95 7 yp(ibak) = yp(ibak)-temp(ibak)*yp(ibak+1) ^ Comment 9 at (184:./fitpack.f) : Terminating a DO loop with a statement other than CONTINUE or ENDDO is obsolescent in Fortran 90 and Fortran 95 external subroutine CURVS external function CURV2 external function CURVD external function CURVI external subroutine CURVP1 1 sdiag1 = sdiag2 ^ Comment 9 at (740:./fitpack.f) : Terminating a DO loop with a statement other than CONTINUE or ENDDO is obsolescent in Fortran 90 and Fortran 95 3 temp(ibak) =temp(npibak)-temp(ibak)*temp(ibak+1) ^ Comment 9 at (754:./fitpack.f) : Terminating a DO loop with a statement other than CONTINUE or ENDDO is obsolescent in Fortran 90 and Fortran 95 5 yp(i) = yp(i)+temp(i)*ypn ^ Comment 9 at (762:./fitpack.f) : Terminating a DO loop with a statement other than CONTINUE or ENDDO is obsolescent in Fortran 90 and Fortran 95 external subroutine CURVPS external function CURVP2 external function CURVPI external subroutine CEEZ external subroutine CURVPP 1 dim1 = di ^ Comment 9 at (1494:./fitpack.f) : Terminating a DO loop with a statement other than CONTINUE or ENDDO is obsolescent in Fortran 90 and Fortran 95 3 betap = beta ^ Comment 9 at (1535:./fitpack.f) : Terminating a DO loop with a statement other than CONTINUE or ENDDO is obsolescent in Fortran 90 and Fortran 95 4 sum = sum+((y(i)-con)/d(i))**2 ^ Comment 9 at (1543:./fitpack.f) : Terminating a DO loop with a statement other than CONTINUE or ENDDO is obsolescent in Fortran 90 and Fortran 95 hd(i) ^ Error 7 at (1559:./fitpack.f) : incomplete statement Error 38 : END statement is missing 2 Errors ./fitpack.f(45) : (col. 0) remark: curv1_ has been targeted for automatic cpu dispatch. ./fitpack.f(1262) : (col. 0) remark: ceez_ has been targeted for automatic cpu dispatch. ./fitpack.f(313) : (col. 0) remark: curv2_ has been targeted for automatic cpu dispatch. ./fitpack.f(389) : (col. 0) remark: curvd_ has been targeted for automatic cpu dispatch. ./fitpack.f(466) : (col. 0) remark: curvi_ has been targeted for automatic cpu dispatch. ./fitpack.f(634) : (col. 0) remark: curvp1_ has been targeted for automatic cpu dispatch. ./fitpack.f(903) : (col. 0) remark: curvp2_ has been targeted for automatic cpu dispatch. ./fitpack.f(986) : (col. 0) remark: curvpi_ has been targeted for automatic cpu dispatch. compilation aborted for ./fitpack.f (code 1) make: *** [fitpack.o] Error 1 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20021110/1ebc9024/attachment.html From eyvaz_isaev at yahoo.com Sun Nov 10 16:43:21 2002 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Sun, 10 Nov 2002 07:43:21 -0800 (PST) Subject: [CPMD-list] Compiling CPMD 3.5.3. using IFC In-Reply-To: Message-ID: <20021110154321.60709.qmail@web80312.mail.yahoo.com> Dear Sergei, According to your recent mail installation of the IFC is not correct. Warnings could be removed using "-w" flag. OK, I will send you an example of the .bashrs file and Makefile I used. Regards, Eyvaz --- C????? ???????? wrote: > Dear All, > > I have one problem with compiling CPMD using IFC: > > ..... > ^ > Comment 15 at (424:./system.h) : This feature is > obsolescent in Fortran 95 > > 575 Lines Compiled > rm -f proja.f > /lib/cpp -P -C -traditional -D__Linux -D__PGI > -DLAPACK -DFFT_DEFAULT -DLINUX_IFC ./proja.F > ./proja.f > /opt/intel/compiler60/ia32/bin/ifc -c -O3 -tp p6 > -axiM -pc64 -unroll -w90 -w95 ./proja.f -o ./proja.o > > external subroutine PROJA > > POINTER(IP_IATPT,IATPT),(IP_IPEPT,IPEPT),(IP_IATPE,IATPE) > > ^ > Warning 114 at (196:./system.h) : Pointer variable > has already been declared - retyped as INTEGER > ^ > Warning 114 at (196:./system.h) : Pointer variable > has already been declared - retyped as INTEGER > ^ > Warning 114 at (196:./system.h) : Pointer variable > has already been declared - retyped as INTEGER > > CHARACTER*80 FPATH > ^ > Comment 15 at (424:./system.h) : This feature is > obsolescent in Fortran 95 > > 586 Lines Compiled > rm -f atoms.f > /lib/cpp -P -C -traditional -D__Linux -D__PGI > -DLAPACK -DFFT_DEFAULT -DLINUX_IFC ./atoms.F > ./atoms.f > /opt/intel/compiler60/ia32/bin/ifc -c -O3 -tp p6 > -axiM -pc64 -unroll -w90 -w95 ./atoms.f -o ./atoms.o > > external subroutine ATOMS > > CHARACTER*2 EL(99) > ^ > Comment 15 at (6:./adat.inc) : This feature is > obsolescent in Fortran 95 > > CHARACTER*2 EL2(99) > ^ > Comment 15 at (13:./atoms.f) : This feature is > obsolescent in Fortran 95 > > 318 Lines Compiled > ./atoms.f(290) : (col. 0) remark: LOOP WAS > VECTORIZED. > ./atoms.f(2) : (col. 0) remark: atoms_ has been > targeted for automatic cpu dispatch. > rm -f fitpack.f > /lib/cpp -P -C -traditional -D__Linux -D__PGI > -DLAPACK -DFFT_DEFAULT -DLINUX_IFC ./fitpack.F > ./fitpack.f > /opt/intel/compiler60/ia32/bin/ifc -c -O3 -tp p6 > -axiM -pc64 -unroll -w90 -w95 ./fitpack.f -o > ./fitpack.o > external subroutine CURV1 > > 5 sdiag1 = sdiag2 > ^ > Comment 9 at (176:./fitpack.f) : Terminating a DO > loop with a statement other than CONTINUE or ENDDO > is obsolescent in Fortran 90 and Fortran 95 > > 7 yp(ibak) = yp(ibak)-temp(ibak)*yp(ibak+1) > ^ > Comment 9 at (184:./fitpack.f) : Terminating a DO > loop with a statement other than CONTINUE or ENDDO > is obsolescent in Fortran 90 and Fortran 95 > external subroutine CURVS > external function CURV2 > external function CURVD > external function CURVI > external subroutine CURVP1 > > 1 sdiag1 = sdiag2 > ^ > Comment 9 at (740:./fitpack.f) : Terminating a DO > loop with a statement other than CONTINUE or ENDDO > is obsolescent in Fortran 90 and Fortran 95 > > 3 temp(ibak) =temp(npibak)-temp(ibak)*temp(ibak+1) > ^ > Comment 9 at (754:./fitpack.f) : Terminating a DO > loop with a statement other than CONTINUE or ENDDO > is obsolescent in Fortran 90 and Fortran 95 > > 5 yp(i) = yp(i)+temp(i)*ypn > ^ > Comment 9 at (762:./fitpack.f) : Terminating a DO > loop with a statement other than CONTINUE or ENDDO > is obsolescent in Fortran 90 and Fortran 95 > external subroutine CURVPS > external function CURVP2 > external function CURVPI > external subroutine CEEZ > external subroutine CURVPP > > 1 dim1 = di > ^ > Comment 9 at (1494:./fitpack.f) : Terminating a DO > loop with a statement other than CONTINUE or ENDDO > is obsolescent in Fortran 90 and Fortran 95 > > 3 betap = beta > ^ > Comment 9 at (1535:./fitpack.f) : Terminating a DO > loop with a statement other than CONTINUE or ENDDO > is obsolescent in Fortran 90 and Fortran 95 > > 4 sum = sum+((y(i)-con)/d(i))**2 > ^ > Comment 9 at (1543:./fitpack.f) : Terminating a DO > loop with a statement other than CONTINUE or ENDDO > is obsolescent in Fortran 90 and Fortran 95 > > hd(i) > ^ > Error 7 at (1559:./fitpack.f) : incomplete statement > > Error 38 : END statement is missing > > 2 Errors > ./fitpack.f(45) : (col. 0) remark: curv1_ has been > targeted for automatic cpu dispatch. > ./fitpack.f(1262) : (col. 0) remark: ceez_ has been > targeted for automatic cpu dispatch. > ./fitpack.f(313) : (col. 0) remark: curv2_ has been > targeted for automatic cpu dispatch. > ./fitpack.f(389) : (col. 0) remark: curvd_ has been > targeted for automatic cpu dispatch. > ./fitpack.f(466) : (col. 0) remark: curvi_ has been > targeted for automatic cpu dispatch. > ./fitpack.f(634) : (col. 0) remark: curvp1_ has been > targeted for automatic cpu dispatch. > ./fitpack.f(903) : (col. 0) remark: curvp2_ has been > targeted for automatic cpu dispatch. > ./fitpack.f(986) : (col. 0) remark: curvpi_ has been > targeted for automatic cpu dispatch. > compilation aborted for ./fitpack.f (code 1) > make: *** [fitpack.o] Error 1 > > __________________________________________________ Do you Yahoo!? New DSL Internet Access from SBC & Yahoo! http://sbc.yahoo.com From eyvaz_isaev at yahoo.com Sun Nov 10 17:06:43 2002 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Sun, 10 Nov 2002 08:06:43 -0800 (PST) Subject: [CPMD-list] Re: compilin CPMD (3.5.3) using IFC In-Reply-To: <3DCE4D6E.000009.25195@soapbox.yandex.ru> Message-ID: <20021110160643.41712.qmail@web80313.mail.yahoo.com> Dear Sergei, Please find below the main part of the Makefile. An example of the .bashrc is attached. Regards, Eyvaz. P.S. Unfortunately it is not clear about terminal. Can you explain it in Russian, separately? #---------------------------------------------------------------------------- # Makefile for cpmd.x (plane wave electronic calculation) # Configuration: PC-IFC # Creation of Makefile: Aug 20 2002 # on Linux linux 2.4.10-64GB-SMP #1 SMP Fri Sep 28 17:26:36 GMT 2001 i686 unknown # Author: #---------------------------------------------------------------------------- # SHELL = /bin/sh # #--------------- Default Configuration for PC-IFC --------------- SRC = . DEST = . BIN = . #QMMM_FLAGS = -D__QMECHCOUPL #QMMM_LIBS = -L. -lmm FFLAGS = -pc64 -unroll -w90 -w95 LFLAGS = -L/home/isaev/LAPACK -llapack -lf77blas -latlas -Vaxlib $(QMMM_LIBS) CFLAGS = CPP = /lib/cpp -P -C -traditional CPPFLAGS = -D__Linux -D__PGI -DLAPACK -DFFT_DEFAULT -DLINUX_IFC CC = gcc -O2 -Wall FC = ifc -c -O3 -tp p6 -axiM -w LD = ifc -O3 -tp p6 -axiM AR = #---------------------------------------------------------------------------- --- Sergei Lisenkov wrote: > Dear Eyvaz, > > Thank you for your e-mails. Plese, send me copy of > .bashrc file. > > On my local PC the compiling of CPMD is succesfull. > But,... > > I am working also at the terminal of big linux > machine (do you understand > me?). On this terminal I have IFC compiler and only > user's permissions. I > would like to compile the CPMD code, but I have the > messages: > > ......... > 1547 Lines Compiled > rm -f response_p.f > /lib/cpp -P -C -traditional -D__Linux -D__PGI > -DLAPACK -DFFT_DEFAULT > -DLINUX_IFC ./response_p.F ./response_p.f > /opt/intel/compiler60/ia32/bin/ifc -c -O3 -tp p6 > -axiM -pc64 -unroll -w90 > -w95 ./response_p.f -o ./response_p.o > Error FCE09 : Read error on Program Unit Catalog > work.pc > compilation aborted for ./response_p.f (code 1) > make: *** [response_p.o] Error 1 > /users/sergey/CPMD/SOURCE 6 % > > > What does it mean? > My makefile is: > > #---------------------------------------------------------------------------- > # > SHELL = /bin/sh > # > #--------------- Default Configuration for PC-IFC > --------------- > SRC = . > DEST = . > BIN = . > #QMMM_FLAGS = -D__QMECHCOUPL > #QMMM_LIBS = -L. -lmm > FFLAGS = -pc64 -unroll -w90 -w95 > LFLAGS = /users/sergey/ - latlas -Vaxlib > $(QMMM_LIBS) > CFLAGS = > CPP = /lib/cpp -P -C -traditional > CPPFLAGS = -D__Linux -D__PGI -DLAPACK -DFFT_DEFAULT > -DLINUX_IFC > CC = gcc -O2 -Wall > FC = /opt/intel/compiler60/ia32/bin/ifc -c -O3 -tp > p6 -axiM > LD = /opt/intel/compiler60/ia32/bin/ifc -O3 -tp p6 > -axiM > AR = > > > Thank you for your help, > Best wishes, > Sergey __________________________________________________ Do you Yahoo!? New DSL Internet Access from SBC & Yahoo! http://sbc.yahoo.com -------------- next part -------------- A non-text attachment was scrubbed... Name: .bashrc_1 Type: application/octet-stream Size: 608 bytes Desc: .bashrc_1 Url : http://cpmd.org/pipermail/cpmd-list/attachments/20021110/d3281820/attachment.obj From mkosmows at mailbox.syr.edu Mon Nov 11 09:34:39 2002 From: mkosmows at mailbox.syr.edu (mkosmows) Date: Mon, 11 Nov 2002 03:34:39 -0500 Subject: [CPMD-list] Help with molecular crystals Message-ID: <3DE2C607@OrangeMail> Dear CPMD community: I'm trying to do a geometry optimization of a molecular crystal (with 2 molecules per cell). I entered the literature data into rpluto, filled the unit cell, and got rid of the atoms outside the unit cell. So I have one whole molecule and a bunch of lonely atoms due to the way the molecules pack into the cell. I chose the cell symmetry based on the geometry of the cell (all angles 90 degrees, so orthorhombic) and the point group based on the point group of the space group. The results were rather bizarre. There were many assumed bonds that made no sense and the geometry was very much distorted from observed. The next thing I tried was to manually CHANGE BONDS. This got rid of wrong bonds, but failed to add the right bonds that were not assumed. These bonds are the bonds that end up being spread across the ends of the cell due to packing. (In one cell these would be from two different molecules). I then tried to use two whole molecules even though they had atoms outside of the cell but got "Failure to symmetrise coordinates," leading to early termination. If anyone knows how to properly set up molecular crystals I would appreciate hearing about it. I'm using a 40ry cutoff with the Goedecker pseudopotentials downloaded from CPMD.org. I am also getting several ODIIS insufficient progress, reset messages throughout each run. I'm still trying to understand what the ODIIS is and any assistance in how to properly set the ODIIS variable would be nice! Thank's, Mark Kosmowski Chemistry Department Syracuse University mkosmows at syr.edu From proffess at mail.ru Mon Nov 11 10:26:43 2002 From: proffess at mail.ru (Sergey) Date: Mon, 11 Nov 2002 12:26:43 +0300 Subject: [CPMD-list] (no subject) Message-ID: Dear All, I have one question. I have tried to run one example, but I have received the message: ****** ****** **** **** ****** ******* ******* ********** ******* *** ** *** ** **** ** ** *** ** ** *** ** ** ** ** ** ** ******* ** ** ** ** *** ****** ** ** ** *** ******* ** ** ** ******* ****** ** ** ** ****** VERSION 3.5.3 COPYRIGHT IBM RESEARCH DIVISION MPI FESTKOERPERFORSCHUNG STUTTGART The CPMD consortium WWW: http://www.cpmd.org Mailinglist: cpmd-list at cpmd.org E-mail: cpmd at cpmd.org *** Nov 10 2002 -- 10:58:28 *** THE INPUT FILE IS: dimer_h20.in THIS JOB RUNS ON: arthur.ccs.uky.edu THE CURRENT DIRECTORY IS: /u/disk1/users/sergey/work THE TEMPORARY DIRECTORY IS: /u/disk1/users/sergey/work THE PROCESS ID IS: 19172 THE JOB WAS SUBMITTED BY: sergey OPTIMIZATION OF IONIC POSITIONS PATH TO THE RESTART FILES: ./ GRAM-SCHMIDT ORTHOGONALIZATION MAXIMUM NUMBER OF STEPS: 10000 STEPS PRINT INTERMEDIATE RESULTS EVERY 10001 STEPS STORE INTERMEDIATE RESULTS EVERY 10 STEPS STORE INTERMEDIATE RESULTS EVERY 10001 SELF-CONSISTENT STEPS NUMBER OF DISTINCT RESTART FILES: 1 TEMPERATURE IS CALCULATED ASSUMING EXTENDED BULK BEHAVIOR FICTITIOUS ELECTRON MASS: 400.0000 TIME STEP: 5.0000 CONVERGENCE CRITERIA FOR WAVEFUNCTION OPTIMIZATION: 1.0000E-06 WAVEFUNCTION OPTIMIZATION BY PRECONDITIONED DIIS THRESHOLD FOR THE WF-HESSIAN IS 0.5000 MAXIMUM NUMBER OF VECTORS RETAINED FOR DIIS: 10 FULL ELECTRONIC GRADIENT IS USED CONVERGENCE CRITERIA FOR GEOMETRY OPTIMIZATION: 5.000000E-06 GEOMETRY OPTIMIZATION BY QUASI-NEWTON UPDATE EMPIRICAL INITIAL HESSIAN (DISCO PARAMETRISATION) SPLINE INTERPOLATION IN G-SPACE FOR PSEUDOPOTENTIAL FUNCTIONS NUMBER OF SPLINE POINTS: 501 EXCHANGE CORRELATION FUNCTIONALS LDA EXCHANGE: NONE LDA XC THROUGH PADE APPROXIMATION S.GOEDECKER, J.HUTTER, M.TETER PRB 54 1703 (1996) GRADIENT CORRECTED FUNCTIONAL DENSITY THRESHOLD: 1.00000E-07 EXCHANGE ENERGY [A.D. BECKE, PHYS. REV. A 38, 3098 (1988)] PARAMETER BETA: 0.004200 CORRELATION ENERGY [J.P. PERDEW, PHYS. REV. B 33, 8822 (1986)] *** DETSP| THE NEW SIZE OF THE PROGRAM IS 1484 kBYTES *** !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! WARNING! XC FUNCTIONALS INCONSISTENT FOR O_SG_LDA !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! WARNING! XC FUNCTIONALS INCONSISTENT FOR H_SG_LDA !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! >>>>>>>> CENTER OF MASS HAS BEEN MOVED TO CENTER OF BOX <<<<<<<< AUTOMATIC DETERMINATION OF THE POINT GROUP: THE CRYSTAL SYSTEM IS CUBIC WITH 1 OPERATIONS: 1 THE SPACE GROUP OF THE CRYSTAL IS SYMMORPHIC THE POINT GROUP OF THE CRYSTAL IS 1(c1) [INDEX= 1] NUMBER OF PRIMITIVE CELL: 1 SYMMETRY UNIQUE (INEQUIVALENT) ATOMS: 6 REQUIRED PRECISION FOR SYMMETRY: 1.00E-06 NUMBER OF IRREDUCIBLE REPRESENTATIONS: 1 DIMENSION OF IR: 1 ***************************** ATOMS **************************** NR TYPE X(bohr) Y(bohr) Z(bohr) MBL 1 O 12.255182 9.448634 9.225004 3 2 O 6.778522 9.448618 9.659000 3 3 H 10.444350 9.448292 9.522282 3 4 H 13.016241 9.448711 10.876154 3 5 H 6.084422 10.899306 8.803308 3 6 H 6.083738 7.998335 8.803183 3 **************************************************************** NUMBER OF STATES: 8 NUMBER OF ELECTRONS: 16.00000 CHARGE: 0.00000 ELECTRON TEMPERATURE(KELVIN): 0.00000 OCCUPATION 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > OXYGEN LDA-PSEUDOPOTENTIAL (GOEDECKER TYPE) > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > HYDROGEN LDA-PSEUDOPOTENTIAL (GOEDECKER TYPE) > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> **************************************************************** * ATOM MASS RAGGIO NLCC PSEUDOPOTENTIAL * * O 15.9994 1.2000 NO GOEDECKER S NONLOCAL * * P LOCAL * * H 1.0080 1.2000 NO S LOCAL * **************************************************************** *** RGGEN| THE NEW SIZE OF THE PROGRAM IS 3308 kBYTES *** ************************** SUPERCELL *************************** THIS IS AN ISOLATED SYSTEM CALCULATION POISSON EQUATION SOLVER : HOCKNEY COULOMB SMOOTHING RADIUS : 1.350 SYMMETRY: SIMPLE CUBIC POINT GROUP : [CUBIC] 1 (c1) LATTICE CONSTANT(a.u.): 18.89726 CELL DIMENSION: 18.8973 1.0000 1.0000 0.0000 0.0000 0.0000 VOLUME(OMEGA IN BOHR^3): 6748.33304 LATTICE VECTOR A1(BOHR): 18.8973 0.0000 0.0000 LATTICE VECTOR A2(BOHR): 0.0000 18.8973 0.0000 LATTICE VECTOR A3(BOHR): 0.0000 0.0000 18.8973 RECIP. LAT. VEC. B1(2Pi/BOHR): 0.0529 0.0000 0.0000 RECIP. LAT. VEC. B2(2Pi/BOHR): 0.0000 0.0529 0.0000 RECIP. LAT. VEC. B3(2Pi/BOHR): 0.0000 0.0000 0.0529 REAL SPACE MESH: 48 48 48 WAVEFUNCTION CUTOFF(RYDBERG): 13.00000 DENSITY CUTOFF(RYDBERG): (DUAL= 4.00) 52.00000 NUMBER OF PLANE WAVES FOR WAVEFUNCTION CUTOFF: 2689 NUMBER OF PLANE WAVES FOR DENSITY CUTOFF: 21466 **************************************************************** ** Address Error ** End of diagnostics What Does it mean? Best. Sergey -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20021111/e5ad112b/attachment.html From natasa.mateljevic at yale.edu Mon Nov 11 17:38:45 2002 From: natasa.mateljevic at yale.edu (Natasa Mateljevic) Date: Mon, 11 Nov 2002 11:38:45 -0500 (EST) Subject: [CPMD-list] oxygen and graphite Message-ID: Dear List, when I dotn specify the multiplicity of oxygen or LSD on graphite, after geometry optimization oxygen moves. If I use triplet oxygen and LSD, oxygen stays in the same place after geometry optimization. I am using 8 carbon atoms to specigy my unit cell. Here is a sample input, any suggestions on LSD oe on this input. &CPMD OPTIMIZE GEOMETRY STRUCTURE BONDS ANGLES &END &SYSTEM CELL VECTORS 9.29640 0.0 0.0, 4.64820 8.05092 0.0, 0.0 0.0 1$ CUTOFF 25. TESR 4 &END &DFT FUNCTIONAL PBE GC-CUTOFF 1.0D-7 &END &ATOMS *006-C-gpbe--bm.uspp BINARY NEWF 8 2.32410 0.00000 0.00000 0.00000 1.34182 0.00000 4.64820 4.02546 0.00000 2.32410 5.36728 0.00000 6.97230 0.00000 0.00000 4.64820 1.34182 0.00000 9.29640 4.02546 0.00000 6.97230 5.36728 0.00000 *008-O-gpbe--bm.uspp BINARY NEWF LMAX=P 1 3.00000 4.000000 5.00000 &END Thanks for any advice, Natasa From natasa.mateljevic at yale.edu Mon Nov 11 17:41:54 2002 From: natasa.mateljevic at yale.edu (Natasa Mateljevic) Date: Mon, 11 Nov 2002 11:41:54 -0500 (EST) Subject: [CPMD-list] optimization Message-ID: Dear List, also in regards to the input I sent in the previous email, my gradients after geometry optimization are very high, can I fix this? ATOM COORDINATES GRADIENTS 1 C 2.6450 0.0082 -0.3823 0.839E-04 -0.296E-02 0.127E-02 2 C 0.3187 1.3301 -0.3272 -0.442E-02 0.150E-01 -0.254E-02 3 C 4.9720 4.0392 -0.1920 -0.564E-02 -0.406E-02 0.224E-02 4 C 2.6099 5.3931 -0.1871 0.131E-01 -0.774E-02 0.432E-02 5 C 7.2745 -0.0028 -0.0307 0.761E-02 0.779E-02 0.129E-02 6 C 4.9701 1.3417 -0.0277 -0.568E-02 0.730E-02 -0.153E-02 7 C 9.6155 4.0602 -0.4744 -0.771E-02 -0.194E-01 -0.186E-02 8 C 7.2834 5.3668 -0.5257 0.203E-02 0.402E-02 0.273E-03 9 O 1.1205 3.9494 6.6119 0.737E-03 0.213E-03 -0.195E-02 Thanks, Natasa From konopka at elf.stuba.sk Mon Nov 11 17:52:25 2002 From: konopka at elf.stuba.sk (Martin Konopka) Date: Mon, 11 Nov 2002 17:52:25 +0100 (MET) Subject: [CPMD-list] How to get the CONSTRAINT file? Message-ID: Dear CPMD community, can anybody tell me how to force CPMD to produce the CONSTRAINT file and to do constraint MD using the Blue Moon ensemble prescription? I am doing a Car-Parinello constraint simulation but I can not get the CONSTRAINT file. According to the manual, it should be produced in constraint MD runs automatically. I am using Vanderbilt pseudpotentials and the OLDCODE keyword. The program otherwise works, constraints are not ignored, the only problem is with the CONSTRAINT file. Below I put most of my input file. Thanks. Martin Konopka. &CPMD RESTART WAVEFUNCTIONS COORDINATES VELOCITIES NOSEP LATEST RESTFILE 2 STORE 200 MOLECULAR DYNAMICS CP MAXSTEP 5000 NOSE IONS MASSIVE 300.0D0 4000.0D0 NOSE PARAMETERS 3 3 0 6.0 15 4 EMASS 200.0D0 TIMESTEP 5.0D0 ISOLATED MOLECULE SPLINE POINTS QFUNCTIONS 2001 CENTER MOLECULE OFF MEMORY BIG LSD &END &DFT OLDCODE GRADIENT CORRECTION PBEX PBEC GC-CUTOFF 5.0D-5 &END &SYSTEM SYMMETRY 8 CELL ABSOLUTE 23.0D0 30.0D0 36.0D0 0.0D0 0.0D0 0.0D0 TESR 4 CUTOFF 25.0D0 CHARGE 0 &END &ATOMS *H.uspp BINARY NEWF TPSEU LMAX=S 5 ... (I have 4 species and 13 atoms in total.) ... CONSTRAINTS FIX ATOMS 1 12 FIX COORDINATES 1 6 1 1 0 END CONSTRAINTS &END ------------------------------------------------------------------------ Dr. Martin Konopka http://www.ccms.elf.stuba.sk/konopka.html Department of Physics tel: +421 (0)2 60291714 Slovak University of Technology (FEI STU) fax: +421 (0)2 65411483 Ilkovicova 3, 812 19 Bratislava, Slovakia ------------------------------------------------------------------------ From hutter at pci.unizh.ch Mon Nov 11 18:55:26 2002 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Mon, 11 Nov 2002 18:55:26 +0100 (MET) Subject: [CPMD-list] Help with molecular crystals In-Reply-To: <3DE2C607@OrangeMail> Message-ID: Hi there are often problems with the specification of coordinates and cell parameters in CPMD when taken from other programs or resources. The reason is that different definitions and standards are used. Some tricks to be used: 1) specify the 2 molecules with the coordinates such that the molecules are not "split". The atoms specified have not to be in the unit cell. 2) specify the cell using cell vectors, although orthorhombic should be easy enough to avoid errors 3) use POINT GROUP AUTO if the program doesn't find the correct point group your input is not correct or the coordinates not accurate enough 4) The add bonds feature is only for the empirical Hessian. It has no effect on the DFT calculation. For your system it is probably best to use HESSIAN UNIT. 5) Check the input by displaying the system with a graphics program. It most of the time easy to see when the box and coordinates are not maching. 6) ODIIS resets usually mean that either your trying to optimize a strange system (e.g. short bonds) or you have an otherwise difficult to optimize system. If all is correct, use the PCG MINIMZE obtimizer. This optimizer is slower than ODIIS but more robust. greetings Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4491 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at pci.unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Mon, 11 Nov 2002, mkosmows wrote: > Dear CPMD community: > > I'm trying to do a geometry optimization of a > molecular crystal (with 2 molecules per cell). I > entered the literature data into rpluto, filled the > unit cell, and got rid of the atoms outside the unit > cell. So I have one whole molecule and a bunch of > lonely atoms due to the way the molecules pack into > the cell. > > I chose the cell symmetry based on the geometry of > the cell (all angles 90 degrees, so orthorhombic) and > the point group based on the point group of the space > group. > > The results were rather bizarre. There were many > assumed bonds that made no sense and the geometry was > very much distorted from observed. > > The next thing I tried was to manually CHANGE BONDS. > This got rid of wrong bonds, but failed to add the > right bonds that were not assumed. These bonds are > the bonds that end up being spread across the ends of > the cell due to packing. (In one cell these would be > from two different molecules). > > I then tried to use two whole molecules even though > they had atoms outside of the cell but got "Failure > to symmetrise coordinates," leading to early > termination. If anyone knows how to properly set up > molecular crystals I would appreciate hearing about > it. > > I'm using a 40ry cutoff with the Goedecker > pseudopotentials downloaded from CPMD.org. > > I am also getting several ODIIS insufficient > progress, reset messages throughout each run. I'm > still trying to understand what the ODIIS is and any > assistance in how to properly set the ODIIS variable > would be nice! > > Thank's, > > Mark Kosmowski > > Chemistry Department > Syracuse University > mkosmows at syr.edu > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From hutter at pci.unizh.ch Mon Nov 11 19:05:23 2002 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Mon, 11 Nov 2002 19:05:23 +0100 (MET) Subject: [CPMD-list] How to get the CONSTRAINT file? In-Reply-To: Message-ID: Hi you are using "trivial" constraints. For this type of constraints (just fixed atomic coordinates) it is not necessary to perform SHAKE/RATTLE iterations. The constraint forces are equal to the calculated forces on the atom. This type of constraint is not often used in thermodynamic integration and CPMD is not writing the forces to the CONSTRAINT file. You can print the forces to the output file using the PRINT command or add a write statement in the forces routine. regards Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4491 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at pci.unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Mon, 11 Nov 2002, Martin Konopka wrote: > Dear CPMD community, > > can anybody tell me how to force CPMD to produce the CONSTRAINT file > and to do constraint MD using the Blue Moon ensemble prescription? > I am doing a Car-Parinello constraint simulation but I can not get > the CONSTRAINT file. According to the manual, it should be produced in > constraint MD runs automatically. > I am using Vanderbilt pseudpotentials and the OLDCODE keyword. > The program otherwise works, constraints are not ignored, the only > problem is with the CONSTRAINT file. > Below I put most of my input file. > Thanks. > > Martin Konopka. > > > &CPMD > RESTART WAVEFUNCTIONS COORDINATES VELOCITIES NOSEP LATEST > RESTFILE > 2 > STORE > 200 > MOLECULAR DYNAMICS CP > MAXSTEP > 5000 > NOSE IONS MASSIVE > 300.0D0 4000.0D0 > NOSE PARAMETERS > 3 3 0 6.0 15 4 > EMASS > 200.0D0 > TIMESTEP > 5.0D0 > ISOLATED MOLECULE > SPLINE POINTS QFUNCTIONS > 2001 > CENTER MOLECULE OFF > MEMORY BIG > LSD > &END > &DFT > OLDCODE > GRADIENT CORRECTION PBEX PBEC > GC-CUTOFF > 5.0D-5 > &END > &SYSTEM > SYMMETRY > 8 > CELL ABSOLUTE > 23.0D0 30.0D0 36.0D0 0.0D0 0.0D0 0.0D0 > TESR > 4 > CUTOFF > 25.0D0 > CHARGE > 0 > &END > &ATOMS > *H.uspp BINARY NEWF TPSEU > LMAX=S > 5 > ... (I have 4 species and 13 atoms in total.) > ... > CONSTRAINTS > FIX ATOMS > 1 > 12 > FIX COORDINATES > 1 > 6 1 1 0 > END CONSTRAINTS > &END > > ------------------------------------------------------------------------ > Dr. Martin Konopka http://www.ccms.elf.stuba.sk/konopka.html > Department of Physics tel: +421 (0)2 60291714 > Slovak University of Technology (FEI STU) fax: +421 (0)2 65411483 > Ilkovicova 3, 812 19 Bratislava, Slovakia > ------------------------------------------------------------------------ > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From yyteng at imr.ac.cn Tue Nov 12 15:35:49 2002 From: yyteng at imr.ac.cn (ÌÚÓ¢Ôª) Date: Tue, 12 Nov 2002 15:35:49 Subject: [CPMD-list] NiAl Message-ID: <200211120736.IAA08598@internet-fence.zurich.ihost.com> -------------- next part -------------- A non-text attachment was scrubbed... Name: NiAl.out Type: application/octet-stream Size: 20577 bytes Desc: not available Url : http://cpmd.org/pipermail/cpmd-list/attachments/20021112/0a4fe48c/attachment.obj From ZRLSRB at ch.ibm.com Tue Nov 12 09:17:18 2002 From: ZRLSRB at ch.ibm.com (Salomon Billeter) Date: Tue, 12 Nov 2002 09:17:18 +0100 Subject: [CPMD-list] Questions about MD Message-ID: Dear Yi, > If I RESTART WAVEFUNCTION, would I write the &system > and &atom again? If yes, are the coordinates in &atom > same as the coordinates in &atom of OPTIMIZATION > WAVEFUNCTION? yes, you have to include the &SYSTEM and &ATOM sections even if you are restarting. If you write RESTART COORDINATES, the coordinates in the RESTART file override the ones in the input. RESTART WAVEFUNCTION alone does not select the coordinates in the RESTART file. Best regards, Salomon From yi_gao_cn at yahoo.com Tue Nov 12 09:55:20 2002 From: yi_gao_cn at yahoo.com (Yi Gao) Date: Tue, 12 Nov 2002 00:55:20 -0800 (PST) Subject: [CPMD-list] About NPT Message-ID: <20021112085520.187.qmail@web21307.mail.yahoo.com> Dear everyone, Whether the CPMD can do the NPT MD? If yes, what's the keyword about the pressure controling? Yi Gao __________________________________________________ Do you Yahoo!? U2 on LAUNCH - Exclusive greatest hits videos http://launch.yahoo.com/u2 From chimaju at magnum.barc.ernet.in Tue Nov 12 10:38:19 2002 From: chimaju at magnum.barc.ernet.in (Chiranjib Majumder) Date: Tue, 12 Nov 2002 15:08:19 +0530 (IST) Subject: [CPMD-list] Liquid calculation (fwd) Message-ID: Dear apsi Thanks a lot for your reply. I am pleased to see that the fluctuations in the temperature is around 55 to 60 as you have predicted. I shall appreciate if can tell me how i should impose a periodic boundary condition. What parameters are required for that. It needs to be mentioned that I wanted to do a calculation for Na liquid (which you are mentioning as cluster). I suppose you have guessed this idea from my input. As I told you that this is my first calculation for a liquid system so I don't know what parameters I should fix for liquid calculation as special. What I have done is that the cell length is fixed according to the XYZ coordinates. Above all what exactly I want to know is what parameters I should use to do a calculation for an extended system like liquid or solid with only gamma point. Thanking you in advance Chiranjib On Tue, 5 Nov 2002 Ari.P.Seitsonen at iki.fi wrote: > > Dear Chiranjib, > > Please excuse me for the very late reply, I have had such a busy > time in the last days!! (E.g. yesterday cleaning my "new" apartment > for six hours etc, very scientific ;) > > > For the first time I am trying to run a liquid system. I have taken 32 > > atoms of Na and positioned them in a fcc lattice points. To learn the > > calculations, I thought it is better to try with single gamma point. > > When we do single gamma point for isolated systems like > > cluster we keep some vacuum between two clusters but I thought for an > > extended liquid I should not keep any vacuum. So my cell length is fixed > > accordingly. I really don't know if I am wrong. Pl. correct me. I didn't > > fix NOSE parameters and would like to take the default vales. > > > > Overall I told you about my problem and I need to know how best I can > > perform a finite temperature calculation using this CPMD. Also I don't > > know whether I need to use some parameters to vary the occupancies. > > > > My input file is attached herewith. This input file preceeds another input > > where I took the optimized wavefunctions for this atomic positions. > > > > I hope this information will be sufficient for you to answere my querries > > so that I could proceed further. > > > > Thanking you > > > > Chiranjib > > > > &CPMD > > MOLECULAR DYNAMICS > > RESTART WAVEFUNCTION COORDINATES VELOCITIES LATEST > > NOSE IONS > > 400 2000 > > NOSE ELECTRONS > > 0.0001 6000 > > MAXSTEP > > 20000 > > TRAJECTORY SAMPLE > > 10 > > &END > > > > &SYSTEM > > ANGSTORM > > SYMMETRY > > 1 > > CELL > > 10.97 1.0 1.0 0 0 0 > > CUTOFF > > 15.0 > > &END > > &ATOMS > > ISOTOPE > > 23.0 > > > > *NA_SGS KLEINMAN-BYLANDER > > LMAX=S > > 32 > > 0.000000000 0.000000000 0.000000000 > > 2.743362646 2.743362646 0.000000000 > > 0.000000000 2.743362646 2.743362646 > > 2.743362646 0.000000000 2.743362646 > > 5.486725291 0.000000000 0.000000000 > > 8.230087937 2.743362646 0.000000000 > > 5.486725291 2.743362646 2.743362646 > > 8.230087937 0.000000000 2.743362646 > > 0.000000000 5.486725291 0.000000000 > > 2.743362646 8.230087937 0.000000000 > > 0.000000000 8.230087937 2.743362646 > > 2.743362646 5.486725291 2.743362646 > > 5.486725291 5.486725291 0.000000000 > > 8.230087937 8.230087937 0.000000000 > > 5.486725291 8.230087937 2.743362646 > > 8.230087937 5.486725291 2.743362646 > > 0.000000000 0.000000000 5.486725291 > > 2.743362646 2.743362646 5.486725291 > > 0.000000000 2.743362646 8.230087937 > > 2.743362646 0.000000000 8.230087937 > > 5.486725291 0.000000000 5.486725291 > > 8.230087937 2.743362646 5.486725291 > > 5.486725291 2.743362646 8.230087937 > > 8.230087937 0.000000000 8.230087937 > > 0.000000000 5.486725291 5.486725291 > > 2.743362646 8.230087937 5.486725291 > > 0.000000000 8.230087937 8.230087937 > > 2.743362646 5.486725291 8.230087937 > > 5.486725291 5.486725291 5.486725291 > > 8.230087937 8.230087937 5.486725291 > > 5.486725291 8.230087937 8.230087937 > > 8.230087937 5.486725291 8.230087937 > > END > > > > &DFT > > NEWCODE > > FUNCTIONAL LDA > > LDA CORRELATION > > &END > > Hmm, I don't remember your original question well, was it why the > temperature fluctuates strongly even though you assign a Nose > thermostat for the ions? From what I guess, the characteristic > frequency for the ions is too high, I don't think that you'd have the > ions oscillating at 2000 wave numbers in a sodium cluster, that's > namely the frequency of strong, covalent bonds like C-O (carbon > monoxide) or heavy water (deuterated water). Do you have some > estimate, e.g. from smaller clusters? Then you could take e.g. 90 % of > the highest frequency, or some frequency which is close to the maximum > in the vibrational density of states. > > The second point is more physical: In such a small cluster the > temperature necessarily would oscillate, and even though the Nose > thermostat would dampen it, it's not necessarily physical. For > example, the trajectory of the ions is somewhat affected. The > thermostat means that there's an external "force" or ensemble which > transfers energy to or from the systems, e.g. a molecule inserted in > water. However, if you just would like to have the properties of a > single molecule in vacuum the constant temperature is not well > defined, it's more an average temperature, also in experiments. A > collegue once showed (it's certainly something trivial to do the > derivation) me that the mean oscillation of a system with N atoms is > > dT = sqrt [ 2 / ( 3 N ) ] * T_wanted > > so if you have 32 atoms at 400 K the fluctuations would be about 58 K. > > Hopefully this helps you somewhat! > > Greetings from Zurich!, > > apsi > > -- > -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- > Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ > Tel +41 1 635 44 97 / Fax +41 1 635 68 38 / GSM +41 79 719 09 35 > Anschrift: Physikalisch Chemisches Institut (PCI), Universit?t Z?rich (UniZh) > Indirizzo: Winterthurerstra?e 190, CH-8057 Z?rich > Address: Schweiz / Svizzera / Suisse / Svizra / Switzerland > From jglee at nemo.physics.ncsu.edu Tue Nov 12 22:37:46 2002 From: jglee at nemo.physics.ncsu.edu (Jung Goo Lee) Date: Tue, 12 Nov 2002 16:37:46 -0500 Subject: [CPMD-list] Corrupted memory message on IBM-SP3 Message-ID: <3DD174AA.8070102@nemo.physics.ncsu.edu> Hi! I was running a DIPOLE DYNAMICS for 64 water molecules in order to compute the dipole moment on IBM-SP3 using 8 CPU's. The part of my input looks like; ******** &CPMD MOLECULAR DYNAMICS RESTART WAVEFUNCTION COORDINATES LATEST TEMPERATURE 0 QUENCH IONS QUENCH BO DIPOLE DYNAMICS WANNIER WANNIER OPTIMIZATION TRAJECTORY SAMPLE 1 MAXSTEP 10 STRUCTURE BONDS ANGLES TIMESTEP 4 EMASS 900 &END &ATOMS *008-O-gpbe--bm.uspp NEWF BINARY LMAX=P 64 -0.17126 -5.41610 0.28145 ******* But I got a CORRUPTED MEMORY message (PROGRAM STOPS IN SUBROUTINE MEMORY_CHECK| CORRUPTED MEMORY [PROC= 3]) . What shoud be changed? P.S. Part of Makefile of CPMDv3.5.3 looks like this; *** #--------------- Default Configuration for IBM-SP3 --------------- SRC = . DEST = . BIN = . #QMMM_FLAGS = -D__QMECHCOUPL #QMMM_LIBS = -L. -lmm FFLAGS = -O3 -qstrict -qxlf77=leadzero -qmaxmem=32768 -qarch=pwr3 LFLAGS = -L/usr/local/lapack -llapack_pwr3 -lessl -llapack_pwr3 \ -bbinder:/usr/lib/bind -bmaxdata:2048000000 -qarch=pwr3 $(QMMM_LIBS) CFLAGS = -O3 -qstrict -qarch=pwr3 CPP = /usr/ccs/lib/cpp -P CPPFLAGS = -D__IBM -DLAPACK -DPARALLEL -DMP_LIBRARY=__MPI -DFFT_ESSL CC = cc FC = mpxlf -c -O3 -qstrict LD = mpxlf -O3 -qstrict AR = /usr/bin/ar #---------------------------------------------------------------------------- *** Jung G. Lee From hutter at pci.unizh.ch Wed Nov 13 08:20:56 2002 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Wed, 13 Nov 2002 08:20:56 +0100 (MET) Subject: [CPMD-list] Corrupted memory message on IBM-SP3 In-Reply-To: <3DD174AA.8070102@nemo.physics.ncsu.edu> Message-ID: Hi DIPOLE DYNAMICS (i.e. the calculation of the dipole moment using the Berry phase algorithm) is not implemented with Vanderbilt ultra-soft PP. Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4491 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at pci.unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Tue, 12 Nov 2002, Jung Goo Lee wrote: > > Hi! > > I was running a DIPOLE DYNAMICS for 64 water molecules in order to compute > the dipole moment on IBM-SP3 using 8 CPU's. > The part of my input looks like; > > ******** > &CPMD > MOLECULAR DYNAMICS > RESTART WAVEFUNCTION COORDINATES LATEST > TEMPERATURE > 0 > QUENCH IONS > QUENCH BO > DIPOLE DYNAMICS WANNIER > WANNIER OPTIMIZATION > TRAJECTORY SAMPLE > 1 > MAXSTEP > 10 > STRUCTURE BONDS ANGLES > TIMESTEP > 4 > EMASS > 900 > &END > > > &ATOMS > *008-O-gpbe--bm.uspp NEWF BINARY > LMAX=P > 64 > -0.17126 -5.41610 0.28145 > > ******* > > But I got a CORRUPTED MEMORY message > (PROGRAM STOPS IN SUBROUTINE MEMORY_CHECK| CORRUPTED MEMORY [PROC= 3]) . > > What shoud be changed? > > P.S. Part of Makefile of CPMDv3.5.3 looks like this; > *** > #--------------- Default Configuration for IBM-SP3 --------------- > SRC = . > DEST = . > BIN = . > #QMMM_FLAGS = -D__QMECHCOUPL > #QMMM_LIBS = -L. -lmm > FFLAGS = -O3 -qstrict -qxlf77=leadzero -qmaxmem=32768 -qarch=pwr3 > LFLAGS = -L/usr/local/lapack -llapack_pwr3 -lessl -llapack_pwr3 \ > -bbinder:/usr/lib/bind -bmaxdata:2048000000 -qarch=pwr3 > $(QMMM_LIBS) > CFLAGS = -O3 -qstrict -qarch=pwr3 > CPP = /usr/ccs/lib/cpp -P > CPPFLAGS = -D__IBM -DLAPACK -DPARALLEL -DMP_LIBRARY=__MPI -DFFT_ESSL > CC = cc > FC = mpxlf -c -O3 -qstrict > LD = mpxlf -O3 -qstrict > AR = /usr/bin/ar > #---------------------------------------------------------------------------- > *** > > Jung G. Lee > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From yi_gao_cn at yahoo.com Wed Nov 13 14:40:06 2002 From: yi_gao_cn at yahoo.com (Yi Gao) Date: Wed, 13 Nov 2002 05:40:06 -0800 (PST) Subject: [CPMD-list] pseudopotential files Message-ID: <20021113134006.39548.qmail@web21310.mail.yahoo.com> Dear Sir or Madam, Where can I find the pseudopotential files of the transitional metals for CPMD? Yi Gao __________________________________________________ Do you Yahoo!? U2 on LAUNCH - Exclusive greatest hits videos http://launch.yahoo.com/u2 From proffess at mail.ru Fri Nov 15 11:54:41 2002 From: proffess at mail.ru (Sergey) Date: Fri, 15 Nov 2002 13:54:41 +0300 Subject: [CPMD-list] problem with IFC and MKL Message-ID: Dear All, I cannot compile CPMD code (3.5.3) on Pentium 4 using IFC and MKL library. The code indicated errors. I think I must add some flags or some library. What I must do? Best wishes, Sergey From julia at physc.su.se Fri Nov 15 13:16:40 2002 From: julia at physc.su.se (Julia Khalack) Date: Fri, 15 Nov 2002 13:16:40 +0100 Subject: [CPMD-list] [Fwd: Charge calculation] Message-ID: <3DD4E5A8.3020505@physc.su.se> -------------- next part -------------- An embedded message was scrubbed... From: Julia Khalack Subject: Charge calculation Date: Wed, 13 Nov 2002 14:53:32 +0100 Size: 3834 Url: http://cpmd.org/pipermail/cpmd-list/attachments/20021115/59806f1d/attachment.mht From hutter at pci.unizh.ch Fri Nov 15 14:16:06 2002 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Fri, 15 Nov 2002 14:16:06 +0100 (MET) Subject: [CPMD-list] [Fwd: Charge calculation] In-Reply-To: <3DD4E5A8.3020505@physc.su.se> Message-ID: Hi please try the following bug fix: Replace the last subroutine in proppt.F by the following code: C ================================================================== SUBROUTINE GIVE_SCR_ESPC(LESPC,TAG) C ==--------------------------------------------------------------== IMPLICIT NONE INCLUDE 'system.h' !NHG INCLUDE 'elct.inc' !N INCLUDE 'pslo.inc' !TIVAN C Arguments INTEGER LESPC CHARACTER TAG*30 C Variables INTEGER IL_QPHI, LRNLSM C ==--------------------------------------------------------------== CALL GIVE_QPHI(IL_QPHI) IF(TIVAN) THEN CALL GIVE_SCR_RNLSM(LRNLSM,TAG,N,.FALSE.) ELSE LRNLSM=0 ENDIF LESPC=MAX(2*NHG+IL_QPHI,LRNLSM) TAG='2*NHG+IL_QPHI' C ==--------------------------------------------------------------== RETURN END C ================================================================== ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4491 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at pci.unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Fri, 15 Nov 2002, Julia Khalack wrote: > > From hwsheng at jhu.edu Fri Nov 15 17:13:07 2002 From: hwsheng at jhu.edu (HW Sheng) Date: Fri, 15 Nov 2002 11:13:07 -0500 Subject: [CPMD-list] How to set the NOSE ELECTRONS parameters. Message-ID: <005901c28cc1$f4d56e00$a567dc80@mrs.jhu.edu> Dear all, For an isobaric-isothermal MD simulation, I need to set the target electron kinetic energy. According to the manual, it's suggested to perform a short run without thermostats, and then take the "natural" electron kinetic energy as the target value (see, e.g, the CPMD manual, version 3.5.2 pp 62). Still, I found this "target" value very capricious. After all, I arbitrarily set the kinetic energy to be 0.0001 a.u . During simulation I found that the output EKINC (the fictitious electron kinetic energy, ~ 0.007 a.u. after 1000 time steps) differs significantly from this desired kinetic energy 0.0001 a.u. I think this is abnormal, because EKINC should fluctuate around the desired (also predefined) kinetic energy. Can anyone tell me why? The ion temperature is also a pain in the neck. I have tried a number of NOSE parameters, but the temperature fluctuation is still too much. For example, the target ion temperature is 5000 Kelvin, and the fluctuation reaches as much as 1000 K. A possible reason is that the target electron kinetic energy is set too small and causes the damping of the ions. Do I make any sense? Besides, any rule-of-thumb to set the CELL kinetic energy? In a nutshell, I wish to have a guidance in choosing the Nose-Hover chain parameters. I appreciate your help. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20021115/290ecbd7/attachment.html From hwsheng at jhu.edu Fri Nov 15 17:31:49 2002 From: hwsheng at jhu.edu (HW Sheng) Date: Fri, 15 Nov 2002 11:31:49 -0500 Subject: [CPMD-list] How to set the NOSE ELECTRONS parameters. References: <005901c28cc1$f4d56e00$a567dc80@mrs.jhu.edu> Message-ID: <007c01c28cc4$80856660$a567dc80@mrs.jhu.edu> Dear all, attached please find the input file. For an isobaric-isothermal MD simulation, I need to set the target electron kinetic energy. According to the manual, it's suggested to perform a short run without thermostats, and then take the "natural" electron kinetic energy as the target value (see, e.g, the CPMD manual, version 3.5.2 pp 62). Still, I found this "target" value very capricious. After all, I arbitrarily set the kinetic energy to be 0.0001 a.u . During simulation I found that the output EKINC (the fictitious electron kinetic energy, ~ 0.007 a.u. after 1000 time steps) differs significantly from this desired kinetic energy 0.0001 a.u. I think this is abnormal, because EKINC should fluctuate around the desired (also predefined) kinetic energy. Can anyone tell me why? The ion temperature is also a pain in the neck. I have tried a number of NOSE parameters, but the temperature fluctuation is still too much. For example, the target ion temperature is 5000 Kelvin, and the fluctuation reaches as much as 1000 K. A possible reason is that the target electron kinetic energy is set too small and causes the damping of the ions. Do I make any sense? Besides, any rule-of-thumb to set the CELL kinetic energy? In a nutshell, I wish to have a guidance in choosing the Nose-Hover chain parameters. I appreciate your help. &CPMD MOLECULAR DYNAMICS PARRINELLO-RAHMAN NPT RESTART LATEST ALL NOSE IONS 5000 2000 NOSE ELECTRONS 0.0003 6000 NOSE CELL 0.5 1000 NOSE PARAMETERS 8 8 4 6 25 2 CMASS 4000 MAXSTEP 500 TIMESTEP 3.0 SPLINE RANGE 4.0 SPLINE POINTS 5000 MOVIE SAMPLE 10 &END &SYSTEM ANGSTROM SYMMETRY 1 ISOTROPIC CELL CELL 9.9 1.0 1.0 0 0 0 CUTOFF 70.0 TESR 4 &END &ATOMS ISOTOPE 92.91 *Nb-q5 GOEDECKER LMAX=D 54 -3.3000 -3.3000 -3.3000 -3.3000 -3.3000 0.0000 -3.3000 -3.3000 3.3000 -3.3000 -0.0000 -3.3000 -3.3000 0.0000 0.0000 -3.3000 0.0000 3.3000 -3.3000 3.3000 -3.3000 -3.3000 3.3000 0.0000 -3.3000 3.3000 3.3000 -0.0000 -3.3000 -3.3000 -0.0000 -3.3000 0.0000 0.0000 -3.3000 3.3000 -0.0000 -0.0000 -3.3000 0.0000 0.0000 0.0000 0.0000 0.0000 3.3000 0.0000 3.3000 -3.3000 0.0000 3.3000 0.0000 0.0000 3.3000 3.3000 3.3000 -3.3000 -3.3000 3.3000 -3.3000 0.0000 3.3000 -3.3000 3.3000 3.3000 -0.0000 -3.3000 3.3000 0.0000 0.0000 3.3000 0.0000 3.3000 3.3000 3.3000 -3.3000 3.3000 3.3000 0.0000 3.3000 3.3000 3.3000 -4.9500 -4.9500 -4.9500 -4.9500 -4.9500 -1.6500 -4.9500 -4.9500 1.6500 -4.9500 -1.6500 -4.9500 -4.9500 -1.6500 -1.6500 -4.9500 -1.6500 1.6500 -4.9500 1.6500 -4.9500 -4.9500 1.6500 -1.6500 -4.9500 1.6500 1.6500 -1.6500 -4.9500 -4.9500 -1.6500 -4.9500 -1.6500 -1.6500 -4.9500 1.6500 -1.6500 -1.6500 -4.9500 -1.6500 -1.6500 -1.6500 -1.6500 -1.6500 1.6500 -1.6500 1.6500 -4.9500 -1.6500 1.6500 -1.6500 -1.6500 1.6500 1.6500 1.6500 -4.9500 -4.9500 1.6500 -4.9500 -1.6500 1.6500 -4.9500 1.6500 1.6500 -1.6500 -4.9500 1.6500 -1.6500 -1.6500 1.6500 -1.6500 1.6500 1.6500 1.6500 -4.9500 1.6500 1.6500 -1.6500 1.6500 1.6500 1.6500 &END &DFT NEWCODE FUNCTIONAL PADE &END -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20021115/c566d6ca/attachment.html From rjsa at mail.shcnc.ac.cn Sat Nov 16 06:05:29 2002 From: rjsa at mail.shcnc.ac.cn (Rongjian Sa) Date: Sat, 16 Nov 2002 13:05:29 +0800 Subject: [CPMD-list] how to calculate the H monovalent cation Message-ID: <001d01c28d2d$c8e71f70$cf137fca@pc26> Dear CPMD list, I want to calculate some properties of H monovalent cation. But all my attempt was failed. However, when I changed the charge from 1 to 0, the calculation was succeed. Would you please tell me what I should do to get my calculation succeed? Sincerely yours, Rongjian -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20021116/61ec8b27/attachment.html From proffess at mail.ru Sat Nov 16 10:51:12 2002 From: proffess at mail.ru (Sergey) Date: Sat, 16 Nov 2002 12:51:12 +0300 Subject: [CPMD-list] Compiling Using IFC and MKL Message-ID: Dear all, I have tried to compile CPMD code (3.5.3)on Pentium 3 PC using IFC compiler (6.0) and MKL library. But I have errors: rm -f timetag.f /lib/cpp -P -C -traditional -DMKL -D__Linux -D__PGI -DLAPACK -DFFT_DEFAULT -DLINUX_IFC -DADD_BLAS_ONE_UNDERSCORE ./timetag.F ./timetag.f ifc -c -O3 -tp p6 -axiM -pc64 -unroll -w90 -w95 ./timetag.f external subroutine TIMETAG 13 Lines Compiled rm -f cpmd.x if [ "." != "." ]; then ln -s ./cpmd.x cpmd.x; fi ifc -O3 -tp p6 -axiM -o ./cpmd.x timetag.o cpmd.o softex.o envir.o setcnst.o control.o control_def.o control_pri.o control_bcast.o control_test.o header.o inscan.o memory.o freem.o readsr.o timer.o ttimp.o timec.o stopgm.o util.o dftin.o sysin.o ratom.o recpnew.o ghermit.o detsp.o coninp.o prmem.o setsys.o genxc.o setsc.o numpw.o cry.o latgen.o recips.o functionals.o lsd_func.o rinit.o rinforce.o fftprp.o rggen.o formf.o rnlset.o ylmr.o glopar.o rnlin.o sort.o radin.o bessm.o ylmr2.o pbc.o ortho.o finalp.o forcep.o rhopri.o phfac.o wrener.o rrane.o ranp.o rinitwf.o mltfft.o wrgeo.o rnlsm1.o rnlsm2.o fft.o ffts.o fftsg.o forces.o lowdin.o rgs.o rgsvan.o atomwf.o atrho.o xcener.o graden.o gcener.o hesele.o noforce.o rhoofr.o vpsi.o nlforce.o rotate.o hnlmat.o ovlap.o dotp.o fnonloc.o gsize.o csize.o rscpot.o csmat.o ksmat.o vofrho.o vofrhoa.o vofrhob.o vofrhoh.o vofrhot.o initclust.o jacobi.o rnlrh.o rnlfor.o potfor.o ppener.o reigs.o geofile.o rpiiint.o eicalc.o testex.o densto.o proja.o atoms.o fitpack.o wv30.o rv30.o wr30wfn.o setbasis.o gfft.o fftchk.o nfunc.o gcxctbl.o rhoofr_c.o jacobi_c.o velocitinp.o setirec.o compress.o interp3d.o ptheory.o clinbcg.o elstpo.o exterp.o mulliken.o espchg.o atomc.o eextern.o interpt.o egointer.o fileopen.o scratch.o forcedr.o initrun.o ldos.o fnlalloc.o dqgalloc.o anneal.o ylmr3.o rnlsm.o vofrhos.o get_addr.o teststore.o loadse.o rnlsmd.o wfnio.o density_functionals.o wfopts.o rwfopt.o updwf.o odiis.o pcgrad.o gmopts.o rgmopt.o fstart.o struc.o empfor.o puttau.o constr.o rrfo.o rbfgs.o rgdiis.o sdion.o hessin.o hessout.o hessup.o dum2.o detdof.o cnstfc.o fixcom.o cnstpr.o moverho.o elf.o lsd_elf.o mdpt.o mdmain.o dynit.o shake.o rattle.o resetac.o dispp.o nosalloc.o noseinit.o nospinit.o noseng.o nosepa.o noseup.o enosmove.o pnosmove.o ekinpp.o freqs.o printave.o printp.o rekine.o rinvel.o rscvp.o rscve.o deort.o quenbo.o velupa.o velupi.o posupa.o posupi.o rortog.o rortv.o crotwf.o noscinit.o prpcnosmove.o prpcmove.o prpnosmove.o prcnosmove.o ddipo.o opeigr.o sample.o! sd_wannier.o wannier_center.o wannier_print.o purge.o wc_dos.o fusion.o mdshop.o davidson.o ksdiag.o vgsortho.o hpsi.o spsi.o gsortho.o rhov1.o secdpt.o secder.o sdlinres.o sd_ii.o sd_loc2.o sd_nl2.o rnlsm_2d.o nl_res.o sd_loc.o sd_nl.o rho1ofr.o v1ofrho1.o lr_force.o opt_lr.o lr_upd.o dd_xc.o eind_ii.o eind_loc.o eind_nl.o lr_in.o lr_xcpot.o lr_ortho.o lr_pcg.o canon.o proppt.o prowfn.o dipo.o lodipo.o exdipo.o cmaos.o difrho.o conduct.o polarise.o calc_pij.o localize.o jrotation.o orbhard.o ohfd.o ohlr.o specpt.o td_dav.o td_nhdav.o lr_diag.o vhk.o gettrans.o rho1pri.o rw_linres.o td_force.o tdnlfor.o td_pcg.o orbrot.o vtd2.o stcop.o readvan.o aainit.o vdbinit.o rhov.o qvan1.o qvan2.o newd.o rnlfl.o augchg.o readvdb.o nlccset.o copot.o corec.o cofor.o nlccstr.o startpa.o loadpa.o sumfnl.o glosum.o summat.o my_para.o glomax.o glomin.o groups.o hipin.o hip.o mtin.o stress.o vlocst.o htrstr.o xcstr.o drhov.o nlsl.o nlsm1_s.o dqvan2.o dylmr.o ffsum.o qrada_s.o totstr.o putbet.o ranc.o newcell.o sdcell.o prpt.o prcpmd.o npt_md.o symmetry.o chksym.o symtrz.o multtb.o molsym.o lsfbtr.o friesner.o friesner_c.o ehpsi.o rrandd.o updrho.o anderson.o adjmu.o forces_diag.o mddiag.o extrap.o bogol.o calc_alm.o vbeta.o rhodiis.o rwswap.o frsblk.o frsblk_c.o mixing_r.o mixing_g.o broyden.o enbandpri.o rkpnt.o k290.o k290_2.o kpclean.o pi_cntl.o pi_init.o pi_mdpt.o pi_wf.o pi_md.o pi_diag.o rreadf.o repgen.o fharm.o global.o stagetrans.o pinmtrans.o getfu.o getfnm.o getgyr.o getcor.o prtgyr.o evirial.o wr_temps.o cl_init.o mdclas.o readff.o clas_force.o h0psi1_p.o v1ofrho_p.o fnonloc_p.o do_gga_p.o mddiag-interaction_p.o gndstate_p.o legendre_p.o interaction_p.o rotate_my_wannier_p.o BYLM_p.o hess_eta_p.o inr_dr.o lanc_phon_p.o dmudn_p.o hesele_p.o do_perturbation_p.o pcgrad_p.o rnlsm_p.o vpsi_p.o perturbation_p.o eigensystem_p.o phonons_p.o rwfopt_p.o d_mat_p.o updwf_p.o forces_p.o rhoofr_p.o raman_p.o opeigr_p.o nmr_p.o nmr_util_p.o nmr_chi_p.o nmr_shift_p.o nmr_current_p.o nmr_para_p.o h! ardness_p.o respin_p.o response_p.o kdp_diag.o kdp_prep.o kdp_rho.o kdp_stress_kin.o kdpoints.o rhoofr_kdp.o mm_detsp.o mm_init.o mm_dim.o mm_qmmm_forcedr.o mm_mdmain.o mm_coninp.o mm_cpmd_add_MM_forces_f77.o mm_cpmd_esp_charges_f77.o mm_cpmd_ext_pot_f77.o sysdepend.o shmemory.o /opt/intel/mkl/lib/32/libmkl_lapack.a /opt/intel/mkl/lib/32/libmkl_p3.a -Vaxlib /opt/intel/mkl/lib/32/libmkl_lapack.a(dgetrf_omp.o): In function `DGETRF_OMP_304__parallel_6': dgetrf_omp.o(.text+0x41): undefined reference to `__kmpc_for_static_init_4' dgetrf_omp.o(.text+0x124): undefined reference to `__kmpc_for_static_fini' /opt/intel/mkl/lib/32/libmkl_lapack.a(dgetrf_omp.o): In function `DGETRF_OMP_254__parallel_4': dgetrf_omp.o(.text+0x171): undefined reference to `__kmpc_for_static_init_4' dgetrf_omp.o(.text+0x385): undefined reference to `__kmpc_for_static_fini' /opt/intel/mkl/lib/32/libmkl_lapack.a(dgetrf_omp.o): In function `__MKL_LAPACK__dgetrf': dgetrf_omp.o(.text+0x419): undefined reference to `omp_get_max_threads' dgetrf_omp.o(.text+0x420): undefined reference to `omp_get_num_procs' /opt/intel/mkl/lib/32/libmkl_lapack.a(dgetrf_omp.o): In function `DGETRF_OMP': dgetrf_omp.o(.text+0x485): undefined reference to `__kmpc_global_thread_num' dgetrf_omp.o(.text+0x62a): undefined reference to `__kmpc_ok_to_fork' dgetrf_omp.o(.text+0x695): undefined reference to `__kmpc_fork_call' dgetrf_omp.o(.text+0x6aa): undefined reference to `__kmpc_serialized_parallel' dgetrf_omp.o(.text+0x719): undefined reference to `__kmpc_end_serialized_parallel' dgetrf_omp.o(.text+0x88a): undefined reference to `__kmpc_ok_to_fork' dgetrf_omp.o(.text+0x8d0): undefined reference to `__kmpc_fork_call' dgetrf_omp.o(.text+0x8df): undefined reference to `__kmpc_serialized_parallel' dgetrf_omp.o(.text+0x929): undefined reference to `__kmpc_end_serialized_parallel' /opt/intel/mkl/lib/32/libmkl_lapack.a(dpotrf_omp.o): In function `pkdpotrf_1': dpotrf_omp.o(.text+0x25): undefined reference to `mpptid' dpotrf_omp.o(.text+0x27a): undefined reference to `mppioa' dpotrf_omp.o(.text+0x298): undefined reference to `mppioa' dpotrf_omp.o(.text+0x2ba): undefined reference to `mppioa' dpotrf_omp.o(.text+0x2dc): undefined reference to `mppioa' dpotrf_omp.o(.text+0x2fe): undefined reference to `mppioa' /opt/intel/mkl/lib/32/libmkl_lapack.a(dpotrf_omp.o)(.text+0x320): more undefined references to `mppioa' follow /opt/intel/mkl/lib/32/libmkl_lapack.a(dpotrf_omp.o): In function `pk__MKL_LAPACK__dpotrf': dpotrf_omp.o(.text+0x385): undefined reference to `mpptid' dpotrf_omp.o(.text+0x5f9): undefined reference to `mppioa' dpotrf_omp.o(.text+0x61e): undefined reference to `mppioa' dpotrf_omp.o(.text+0x639): undefined reference to `mppioa' dpotrf_omp.o(.text+0x65b): undefined reference to `mppioa' dpotrf_omp.o(.text+0x67d): undefined reference to `mppioa' /opt/intel/mkl/lib/32/libmkl_lapack.a(dpotrf_omp.o)(.text+0x69f): more undefined references to `mppioa' follow /opt/intel/mkl/lib/32/libmkl_lapack.a(dpotrf_omp.o): In function `__MKL_LAPACK__dpotrf': dpotrf_omp.o(.text+0x708): undefined reference to `mpptid' dpotrf_omp.o(.text+0x7a9): undefined reference to `omp_get_max_threads_' dpotrf_omp.o(.text+0xa9b): undefined reference to `mppfkd' dpotrf_omp.o(.text+0xaaf): undefined reference to `mptepa' dpotrf_omp.o(.text+0xd06): undefined reference to `mpofrk' dpotrf_omp.o(.text+0xf88): undefined reference to `mppfkd' dpotrf_omp.o(.text+0xf9c): undefined reference to `mptepa' dpotrf_omp.o(.text+0x1203): undefined reference to `mpofrk' dpotrf_omp.o(.text+0x12ca): undefined reference to `mptxpa' dpotrf_omp.o(.text+0x12f6): undefined reference to `mptxpa' /opt/intel/mkl/lib/32/libmkl_lapack.a(zgetrf_omp.o): In function `ZGETRF_OMP_304__parallel_6': zgetrf_omp.o(.text+0x41): undefined reference to `__kmpc_for_static_init_4' zgetrf_omp.o(.text+0x124): undefined reference to `__kmpc_for_static_fini' /opt/intel/mkl/lib/32/libmkl_lapack.a(zgetrf_omp.o): In function `ZGETRF_OMP_254__parallel_4': zgetrf_omp.o(.text+0x171): undefined reference to `__kmpc_for_static_init_4' zgetrf_omp.o(.text+0x383): undefined reference to `__kmpc_for_static_fini' /opt/intel/mkl/lib/32/libmkl_lapack.a(zgetrf_omp.o): In function `__MKL_LAPACK__zgetrf': zgetrf_omp.o(.text+0x419): undefined reference to `omp_get_max_threads' zgetrf_omp.o(.text+0x420): undefined reference to `omp_get_num_procs' /opt/intel/mkl/lib/32/libmkl_lapack.a(zgetrf_omp.o): In function `ZGETRF_OMP': zgetrf_omp.o(.text+0x485): undefined reference to `__kmpc_global_thread_num' zgetrf_omp.o(.text+0x679): undefined reference to `__kmpc_ok_to_fork' zgetrf_omp.o(.text+0x6e4): undefined reference to `__kmpc_fork_call' zgetrf_omp.o(.text+0x6f9): undefined reference to `__kmpc_serialized_parallel' zgetrf_omp.o(.text+0x768): undefined reference to `__kmpc_end_serialized_parallel' zgetrf_omp.o(.text+0x8f1): undefined reference to `__kmpc_ok_to_fork' zgetrf_omp.o(.text+0x93d): undefined reference to `__kmpc_fork_call' zgetrf_omp.o(.text+0x94c): undefined reference to `__kmpc_serialized_parallel' zgetrf_omp.o(.text+0x99c): undefined reference to `__kmpc_end_serialized_parallel' /opt/intel/mkl/lib/32/libmkl_lapack.a(zpotrf_omp.o): In function `pkzpotrf_1': zpotrf_omp.o(.text+0x25): undefined reference to `mpptid' zpotrf_omp.o(.text+0x275): undefined reference to `mppioa' zpotrf_omp.o(.text+0x293): undefined reference to `mppioa' zpotrf_omp.o(.text+0x2b5): undefined reference to `mppioa' zpotrf_omp.o(.text+0x2d7): undefined reference to `mppioa' zpotrf_omp.o(.text+0x2f9): undefined reference to `mppioa' /opt/intel/mkl/lib/32/libmkl_lapack.a(zpotrf_omp.o)(.text+0x31b): more undefined references to `mppioa' follow /opt/intel/mkl/lib/32/libmkl_lapack.a(zpotrf_omp.o): In function `pk__MKL_LAPACK__zpotrf': zpotrf_omp.o(.text+0x385): undefined reference to `mpptid' zpotrf_omp.o(.text+0x5f0): undefined reference to `mppioa' zpotrf_omp.o(.text+0x60e): undefined reference to `mppioa' zpotrf_omp.o(.text+0x630): undefined reference to `mppioa' zpotrf_omp.o(.text+0x652): undefined reference to `mppioa' zpotrf_omp.o(.text+0x674): undefined reference to `mppioa' /opt/intel/mkl/lib/32/libmkl_lapack.a(zpotrf_omp.o)(.text+0x696): more undefined references to `mppioa' follow /opt/intel/mkl/lib/32/libmkl_lapack.a(zpotrf_omp.o): In function `__MKL_LAPACK__zpotrf': zpotrf_omp.o(.text+0x6f8): undefined reference to `mpptid' zpotrf_omp.o(.text+0x799): undefined reference to `omp_get_max_threads_' zpotrf_omp.o(.text+0xa84): undefined reference to `mppfkd' zpotrf_omp.o(.text+0xa98): undefined reference to `mptepa' zpotrf_omp.o(.text+0xcf6): undefined reference to `mpofrk' zpotrf_omp.o(.text+0xf6c): undefined reference to `mppfkd' zpotrf_omp.o(.text+0xf80): undefined reference to `mptepa' zpotrf_omp.o(.text+0x11c3): undefined reference to `mpofrk' zpotrf_omp.o(.text+0x128a): undefined reference to `mptxpa' zpotrf_omp.o(.text+0x12b6): undefined reference to `mptxpa' /opt/intel/mkl/lib/32/libmkl_p3.a(dgemm_omp.o): In function `____MKL_BLAS__dgemm_234__parallel_6': dgemm_omp.o(.text+0x5c): undefined reference to `__kmpc_for_static_init_4' dgemm_omp.o(.text+0x1e1): undefined reference to `__kmpc_for_static_fini' /opt/intel/mkl/lib/32/libmkl_p3.a(dgemm_omp.o): In function `____MKL_BLAS__dgemm_216__parallel_4': dgemm_omp.o(.text+0x24c): undefined reference to `__kmpc_for_static_init_4' dgemm_omp.o(.text+0x3cb): undefined reference to `__kmpc_for_static_fini' /opt/intel/mkl/lib/32/libmkl_p3.a(dgemm_omp.o): In function `____MKL_BLAS__dgemm': dgemm_omp.o(.text+0x3f1): undefined reference to `__kmpc_global_thread_num' dgemm_omp.o(.text+0x44c): undefined reference to `omp_in_parallel_' dgemm_omp.o(.text+0x45f): undefined reference to `omp_get_max_threads_' dgemm_omp.o(.text+0x489): undefined reference to `kmp_set_stacksize_' dgemm_omp.o(.text+0x4e6): undefined reference to `__kmpc_ok_to_fork' dgemm_omp.o(.text+0x586): undefined reference to `__kmpc_fork_call' dgemm_omp.o(.text+0x5a4): undefined reference to `__kmpc_serialized_parallel' dgemm_omp.o(.text+0x646): undefined reference to `__kmpc_end_serialized_parallel' dgemm_omp.o(.text+0x69a): undefined reference to `__kmpc_ok_to_fork' dgemm_omp.o(.text+0x73a): undefined reference to `__kmpc_fork_call' dgemm_omp.o(.text+0x758): undefined reference to `__kmpc_serialized_parallel' dgemm_omp.o(.text+0x7fa): undefined reference to `__kmpc_end_serialized_parallel' /opt/intel/mkl/lib/32/libmkl_p3.a(dsymm_omp.o): In function `____MKL_BLAS__dsymm_174__parallel_6': dsymm_omp.o(.text+0x5c): undefined reference to `__kmpc_for_static_init_4' dsymm_omp.o(.text+0x1ce): undefined reference to `__kmpc_for_static_fini' /opt/intel/mkl/lib/32/libmkl_p3.a(dsymm_omp.o): In function `____MKL_BLAS__dsymm_144__parallel_4': dsymm_omp.o(.text+0x23c): undefined reference to `__kmpc_for_static_init_4' dsymm_omp.o(.text+0x3be): undefined reference to `__kmpc_for_static_fini' /opt/intel/mkl/lib/32/libmkl_p3.a(dsymm_omp.o): In function `____MKL_BLAS__dsymm': dsymm_omp.o(.text+0x3ef): undefined reference to `__kmpc_global_thread_num' dsymm_omp.o(.text+0x5f6): undefined reference to `omp_get_num_procs_' dsymm_omp.o(.text+0x63d): undefined reference to `omp_in_parallel_' dsymm_omp.o(.text+0x650): undefined reference to `omp_get_max_threads_' dsymm_omp.o(.text+0x6c0): undefined reference to `__kmpc_ok_to_fork' dsymm_omp.o(.text+0x752): undefined reference to `__kmpc_fork_call' dsymm_omp.o(.text+0x770): undefined reference to `__kmpc_serialized_parallel' dsymm_omp.o(.text+0x804): undefined reference to `__kmpc_end_serialized_parallel' dsymm_omp.o(.text+0x82f): undefined reference to `__kmpc_ok_to_fork' dsymm_omp.o(.text+0x8c1): undefined reference to `__kmpc_fork_call' dsymm_omp.o(.text+0x8df): undefined reference to `__kmpc_serialized_parallel' dsymm_omp.o(.text+0x973): undefined reference to `__kmpc_end_serialized_parallel' /opt/intel/mkl/lib/32/libmkl_p3.a(dsyr2k_omp.o): In function `____MKL_BLAS__dsyr2k_187__parallel_6': dsyr2k_omp.o(.text+0x5c): undefined reference to `__kmpc_for_static_init_4' dsyr2k_omp.o(.text+0x1ef): undefined reference to `__kmpc_for_static_fini' /opt/intel/mkl/lib/32/libmkl_p3.a(dsyr2k_omp.o): In function `____MKL_BLAS__dsyr2k_109__parallel_4': dsyr2k_omp.o(.text+0x25c): undefined reference to `__kmpc_for_static_init_4' dsyr2k_omp.o(.text+0x3df): undefined reference to `__kmpc_for_static_fini' /opt/intel/mkl/lib/32/libmkl_p3.a(dsyr2k_omp.o): In function `____MKL_BLAS__dsyr2k': dsyr2k_omp.o(.text+0x412): undefined reference to `__kmpc_global_thread_num' dsyr2k_omp.o(.text+0x574): undefined reference to `omp_get_num_procs_' dsyr2k_omp.o(.text+0x5c7): undefined reference to `omp_in_parallel_' dsyr2k_omp.o(.text+0x5da): undefined reference to `omp_get_max_threads_' dsyr2k_omp.o(.text+0x64f): undefined reference to `__kmpc_ok_to_fork' dsyr2k_omp.o(.text+0x6e1): undefined reference to `__kmpc_fork_call' dsyr2k_omp.o(.text+0x702): undefined reference to `__kmpc_serialized_parallel' dsyr2k_omp.o(.text+0x79c): undefined reference to `__kmpc_end_serialized_parallel' dsyr2k_omp.o(.text+0xabc): undefined reference to `__kmpc_ok_to_fork' dsyr2k_omp.o(.text+0xb4e): undefined reference to `__kmpc_fork_call' dsyr2k_omp.o(.text+0xb6f): undefined reference to `__kmpc_serialized_parallel' dsyr2k_omp.o(.text+0xc09): undefined reference to `__kmpc_end_serialized_parallel' /opt/intel/mkl/lib/32/libmkl_p3.a(dsyrk_omp.o): In function `____MKL_BLAS__dsyrk_153__parallel_6': dsyrk_omp.o(.text+0x5c): undefined reference to `__kmpc_for_static_init_4' dsyrk_omp.o(.text+0x1c9): undefined reference to `__kmpc_for_static_fini' /opt/intel/mkl/lib/32/libmkl_p3.a(dsyrk_omp.o): In function `____MKL_BLAS__dsyrk_95__parallel_4': dsyrk_omp.o(.text+0x23c): undefined reference to `__kmpc_for_static_init_4' dsyrk_omp.o(.text+0x3a1): undefined reference to `__kmpc_for_static_fini' /opt/intel/mkl/lib/32/libmkl_p3.a(dsyrk_omp.o): In function `____MKL_BLAS__dsyrk': dsyrk_omp.o(.text+0x3c4): undefined reference to `__kmpc_global_thread_num' dsyrk_omp.o(.text+0x4ca): undefined reference to `omp_get_num_procs_' dsyrk_omp.o(.text+0x50e): undefined reference to `omp_in_parallel_' dsyrk_omp.o(.text+0x521): undefined reference to `omp_get_max_threads_' dsyrk_omp.o(.text+0x590): undefined reference to `__kmpc_ok_to_fork' dsyrk_omp.o(.text+0x610): undefined reference to `__kmpc_fork_call' dsyrk_omp.o(.text+0x62e): undefined reference to `__kmpc_serialized_parallel' dsyrk_omp.o(.text+0x6b4): undefined reference to `__kmpc_end_serialized_parallel' dsyrk_omp.o(.text+0x8af): undefined reference to `__kmpc_ok_to_fork' dsyrk_omp.o(.text+0x92f): undefined reference to `__kmpc_fork_call' dsyrk_omp.o(.text+0x94d): undefined reference to `__kmpc_serialized_parallel' dsyrk_omp.o(.text+0x9d3): undefined reference to `__kmpc_end_serialized_parallel' /opt/intel/mkl/lib/32/libmkl_p3.a(dtrmm_omp.o): In function `____MKL_BLAS__dtrmm_146__parallel_6': dtrmm_omp.o(.text+0x5c): undefined reference to `__kmpc_for_static_init_4' dtrmm_omp.o(.text+0x1b9): undefined reference to `__kmpc_for_static_fini' /opt/intel/mkl/lib/32/libmkl_p3.a(dtrmm_omp.o): In function `____MKL_BLAS__dtrmm_122__parallel_4': dtrmm_omp.o(.text+0x22c): undefined reference to `__kmpc_for_static_init_4' dtrmm_omp.o(.text+0x391): undefined reference to `__kmpc_for_static_fini' /opt/intel/mkl/lib/32/libmkl_p3.a(dtrmm_omp.o): In function `____MKL_BLAS__dtrmm': dtrmm_omp.o(.text+0x3bf): undefined reference to `__kmpc_global_thread_num' dtrmm_omp.o(.text+0x53b): undefined reference to `omp_get_num_procs_' dtrmm_omp.o(.text+0x582): undefined reference to `omp_in_parallel_' dtrmm_omp.o(.text+0x595): undefined reference to `omp_get_max_threads_' dtrmm_omp.o(.text+0x605): undefined reference to `__kmpc_ok_to_fork' dtrmm_omp.o(.text+0x690): undefined reference to `__kmpc_fork_call'