source/unres/src-HCD-5D/lista.txt

   1 --------------------------------
   2  SOURCE FILE add.f
   3 --------------------------------
   4 --------------------------------
   5  SOURCE FILE arcos.f
   6 --------------------------------
   7 --------------------------------
   8  SOURCE FILE banach.f
   9 --------------------------------
  10 --------------------------------
  11  SOURCE FILE bank.F
  12 --------------------------------
  13 --------------------------------
  14  SOURCE FILE blas.f
  15 --------------------------------
  16 --------------------------------
  17  SOURCE FILE bond_move.f
  18 --------------------------------
  19 --------------------------------
  20  SOURCE FILE brown_step.F
  21 --------------------------------
  22 --------------------------------
  23  SOURCE FILE cartder.F
  24 --------------------------------
  25 --------------------------------
  26  SOURCE FILE cartprint.f
  27 --------------------------------
  28 --------------------------------
  29  SOURCE FILE chainbuild.F
  30 --------------------------------
  31 --------------------------------
  32  SOURCE FILE check_bond.f
  33 --------------------------------
  34 --------------------------------
  35  SOURCE FILE checkder_p.F
  36 --------------------------------
  37 --------------------------------
  38  SOURCE FILE check_sc_distr.f
  39 --------------------------------
  40 --------------------------------
  41  SOURCE FILE check_sc_map.f
  42 --------------------------------
  43 --------------------------------
  44  SOURCE FILE checkvar.f
  45 --------------------------------
  46 --------------------------------
  47  SOURCE FILE cinfo.f
  48 --------------------------------
  49 2c2
  50 < C 0 40360 116
  51 ---
  52 > C 0 40360 71
  53 6,7c6,7
  54 <       write(iout,*)'Version 0.40360 build 116'
  55 <       write(iout,*)'compiled Thu Apr  7 16:12:04 2016'
  56 ---
  57 >       write(iout,*)'Version 0.40360 build 71'
  58 >       write(iout,*)'compiled Sun Jan  3 21:03:16 2016'
  59 --------------------------------
  60  SOURCE FILE compare_s1.F
  61 --------------------------------
  62 --------------------------------
  63  SOURCE FILE contact.f
  64 --------------------------------
  65 --------------------------------
  66  SOURCE FILE convert.f
  67 --------------------------------
  68 --------------------------------
  69  SOURCE FILE cored.f
  70 --------------------------------
  71 --------------------------------
  72  SOURCE FILE csa.f
  73 --------------------------------
  74 --------------------------------
  75  SOURCE FILE diff12.f
  76 --------------------------------
  77 --------------------------------
  78  SOURCE FILE dihed_cons.F
  79 --------------------------------
  80 --------------------------------
  81  SOURCE FILE distfit.f
  82 --------------------------------
  83 --------------------------------
  84  SOURCE FILE djacob.f
  85 --------------------------------
  86 --------------------------------
  87  SOURCE FILE econstr_local.F
  88 --------------------------------
  89 --------------------------------
  90  SOURCE FILE ecorr_num.f
  91 --------------------------------
  92 --------------------------------
  93  SOURCE FILE eelec.F
  94 --------------------------------
  95 --------------------------------
  96  SOURCE FILE eigen.f
  97 --------------------------------
  98 --------------------------------
  99  SOURCE FILE elecont.f
 100 --------------------------------
 101 --------------------------------
 102  SOURCE FILE energy_p_new_barrier.F
 103 --------------------------------
 104 2817,2849c2817,2859
 105 <         cost1=dcos(theta(i-1))
 106 <         sint1=dsin(theta(i-1))
 107 <         sint1sq=sint1*sint1
 108 <         sint1cub=sint1sq*sint1
 109 <         sint1cost1=2*sint1*cost1
 110 <         do k=1,2
 111 <           b1k=bnew1(1,k,iti)+(bnew1(2,k,iti)+bnew1(3,k,iti)*cost1)*cost1
 112 <           b1(k,i-2)=sint1*b1k
 113 <           gtb1(k,i-2)=cost1*b1k-sint1sq*
 114 <      &              (bnew1(2,k,iti)+2*bnew1(3,k,iti)*cost1)
 115 <           b2k=bnew2(1,k,iti)+(bnew2(2,k,iti)+bnew2(3,k,iti)*cost1)*cost1
 116 <           b2(k,i-2)=sint1*b2k
 117 <           gtb2(k,i-2)=cost1*b2k-sint1sq*
 118 <      &              (bnew2(2,k,iti)+2*bnew2(3,k,iti)*cost1)
 119 <         enddo
 120 <         do k=1,2
 121 <           do l=1,2
 122 <             aux=eenew(1,l,k,iti)+eenew(2,l,k,iti)*cost1
 123 <             EE(l,k,i-2)=sint1sq*aux
 124 <             gtEE(l,k,i-2)=sint1cost1*aux-sint1cub*eenew(2,l,k,iti)
 125 <           enddo
 126 <         enddo
 127 <         EE(1,1,i-2)=EE(1,1,i-2)+e0new(1,iti)*cost1
 128 <         EE(1,2,i-2)=EE(1,2,i-2)+e0new(2,iti)+e0new(3,iti)*cost1
 129 <         EE(2,1,i-2)=EE(2,1,i-2)+e0new(2,iti)*cost1+e0new(3,iti)
 130 <         EE(2,2,i-2)=EE(2,2,i-2)-e0new(1,iti)
 131 <         gtEE(1,1,i-2)=gtEE(1,1,i-2)-e0new(1,iti)*sint1
 132 <         gtEE(1,2,i-2)=gtEE(1,2,i-2)-e0new(3,iti)*sint1
 133 <         gtEE(2,1,i-2)=gtEE(2,1,i-2)-e0new(2,iti)*sint1
 134 <         b1tilde(1,i-2)=b1(1,i-2)
 135 <         b1tilde(2,i-2)=-b1(2,i-2)
 136 <         b2tilde(1,i-2)=b2(1,i-2)
 137 <         b2tilde(2,i-2)=-b2(2,i-2)
 138 ---
 139 >         b1(1,i-2)=bnew1(1,1,iti)*dsin(theta(i-1)/2.0d0)
 140 >      &           +bnew1(2,1,iti)*dsin(theta(i-1))
 141 >      &           +bnew1(3,1,iti)*dcos(theta(i-1)/2.0d0)
 142 >         gtb1(1,i-2)=bnew1(1,1,iti)*dcos(theta(i-1)/2.0d0)/2.0d0
 143 >      &             +bnew1(2,1,iti)*dcos(theta(i-1))
 144 >      &             -bnew1(3,1,iti)*dsin(theta(i-1)/2.0d0)/2.0d0
 145 > c     &           +bnew1(3,1,iti)*sin(alpha(i))*cos(beta(i))
 146 > c     &*(cos(theta(i)/2.0)
 147 >         b2(1,i-2)=bnew2(1,1,iti)*dsin(theta(i-1)/2.0d0)
 148 >      &           +bnew2(2,1,iti)*dsin(theta(i-1))
 149 >      &           +bnew2(3,1,iti)*dcos(theta(i-1)/2.0d0)
 150 > c     &           +bnew2(3,1,iti)*sin(alpha(i))*cos(beta(i))
 151 > c     &*(cos(theta(i)/2.0)
 152 >         gtb2(1,i-2)=bnew2(1,1,iti)*dcos(theta(i-1)/2.0d0)/2.0d0
 153 >      &             +bnew2(2,1,iti)*dcos(theta(i-1))
 154 >      &             -bnew2(3,1,iti)*dsin(theta(i-1)/2.0d0)/2.0d0
 155 > c        if (ggb1(1,i).eq.0.0d0) then
 156 > c        write(iout,*) 'i=',i,ggb1(1,i),
 157 > c     &bnew1(1,1,iti)*cos(theta(i)/2.0)/2.0,
 158 > c     &bnew1(2,1,iti)*cos(theta(i)),
 159 > c     &bnew1(3,1,iti)*sin(theta(i)/2.0)/2.0
 160 > c        endif
 161 >         b1(2,i-2)=bnew1(1,2,iti)
 162 >         gtb1(2,i-2)=0.0
 163 >         b2(2,i-2)=bnew2(1,2,iti)
 164 >         gtb2(2,i-2)=0.0
 165 >         EE(1,1,i-2)=eenew(1,iti)*dcos(theta(i-1))
 166 >         EE(1,2,i-2)=eeold(1,2,iti)
 167 >         EE(2,1,i-2)=eeold(2,1,iti)
 168 >         EE(2,2,i-2)=eeold(2,2,iti)
 169 >         gtEE(1,1,i-2)=-eenew(1,iti)*dsin(theta(i-1))
 170 >         gtEE(1,2,i-2)=0.0d0
 171 >         gtEE(2,2,i-2)=0.0d0
 172 >         gtEE(2,1,i-2)=0.0d0
 173 > c        EE(2,2,iti)=0.0d0
 174 > c        EE(1,2,iti)=0.5d0*eenew(1,iti)
 175 > c        EE(2,1,iti)=0.5d0*eenew(1,iti)
 176 > c        b1(2,iti)=bnew1(1,2,iti)*sin(alpha(i))*sin(beta(i))
 177 > c        b2(2,iti)=bnew2(1,2,iti)*sin(alpha(i))*sin(beta(i))
 178 >        b1tilde(1,i-2)=b1(1,i-2)
 179 >        b1tilde(2,i-2)=-b1(2,i-2)
 180 >        b2tilde(1,i-2)=b2(1,i-2)
 181 >        b2tilde(2,i-2)=-b2(2,i-2)
 182 2853c2863
 183 <       enddo
 184 ---
 185 >        enddo
 186 7498d7507
 187 <       double precision c1(0:maxval_kcc),c2(0:maxval_kcc)
 188 7521a7531,7532
 189 >         sumnonchebyshev=0.0d0
 190 >         sumchebyshev=0.0d0
 191 7531a7543,7545
 192 > c Cosines of halves thetas
 193 >         costheti12=0.5d0*(1.0d0+costhet1)
 194 >         costheti22=0.5d0*(1.0d0+costhet2)
 195 7539,7547d7552
 196 <         nval=nterm_kcc_Tb(itori,itori1)
 197 <         c1(0)=0.0d0
 198 <         c2(0)=0.0d0
 199 <         c1(1)=1.0d0
 200 <         c2(1)=1.0d0
 201 <         do j=2,nval
 202 <           c1(j)=c1(j-1)*costhet1
 203 <           c2(j)=c2(j-1)*costhet2
 204 <         enddo
 205 7549a7555,7560
 206 >
 207 >           nval=nterm_kcc_Tb(itori,itori1)
 208 >           v1ij=v1_kcc(j,itori,itori1)
 209 >           v2ij=v2_kcc(j,itori,itori1)
 210 > c          write (iout,*) "i",i," j",j," v1",v1ij," v2",v2ij
 211 > C v1ij is c_n and d_n in euation above
 212 7554,7582c7565,7591
 213 <           sumvalc=0.0d0
 214 <           gradvalct1=0.0d0
 215 <           gradvalct2=0.0d0
 216 <           do k=1,nval
 217 <             do l=1,nval
 218 <               sumvalc=sumvalc+v1_kcc(l,k,j,itori1,itori)*c1(k)*c2(l)
 219 <               gradvalct1=gradvalct1+
 220 <      &           (k-1)*v1_kcc(l,k,j,itori1,itori)*c1(k-1)*c2(l)
 221 <               gradvalct2=gradvalct2+
 222 <      &           (l-1)*v1_kcc(l,k,j,itori1,itori)*c1(k)*c2(l-1)
 223 <             enddo
 224 <           enddo
 225 <           gradvalct1=-gradvalct1*sinthet1
 226 <           gradvalct2=-gradvalct2*sinthet2
 227 <           sumvals=0.0d0
 228 <           gradvalst1=0.0d0
 229 <           gradvalst2=0.0d0
 230 <           do k=1,nval
 231 <             do l=1,nval
 232 <               sumvals=sumvals+v2_kcc(l,k,j,itori1,itori)*c1(k)*c2(l)
 233 <               gradvalst1=gradvalst1+
 234 <      &           (k-1)*v2_kcc(l,k,j,itori1,itori)*c1(k-1)*c2(l)
 235 <               gradvalst2=gradvalst2+
 236 <      &           (l-1)*v2_kcc(l,k,j,itori1,itori)*c1(k)*c2(l-1)
 237 <             enddo
 238 <           enddo
 239 <           gradvalst1=-gradvalst1*sinthet1
 240 <           gradvalst2=-gradvalst2*sinthet2
 241 <           etori=etori+sint1t2n*(sumvalc*cosphi+sumvals*sinphi)
 242 ---
 243 >           sumth1tyb1=tschebyshev(1,nval,v11_chyb(1,j,itori,itori1),
 244 >      &        costheti12)
 245 >           gradth1tyb1=-0.5d0*sinthet1*gradtschebyshev(0,nval-1,
 246 >      &        v11_chyb(1,j,itori,itori1),costheti12)
 247 > c          write (iout,*) "v11",(v11_chyb(k,j,itori,itori1),k=1,nval),
 248 > c     &      " sumth1tyb1",sumth1tyb1," gradth1tyb1",gradth1tyb1
 249 >           sumth2tyb1=tschebyshev(1,nval,v21_chyb(1,j,itori,itori1),
 250 >      &        costheti22)
 251 >           gradth2tyb1=-0.5d0*sinthet2*gradtschebyshev(0,nval-1,
 252 >      &        v21_chyb(1,j,itori,itori1),costheti22)
 253 > c          write (iout,*) "v21",(v21_chyb(k,j,itori,itori1),k=1,nval),
 254 > c     &      " sumth2tyb1",sumth2tyb1," gradth2tyb1",gradth2tyb1
 255 >           sumth1tyb2=tschebyshev(1,nval,v12_chyb(1,j,itori,itori1),
 256 >      &        costheti12)
 257 >           gradth1tyb2=-0.5d0*sinthet1*gradtschebyshev(0,nval-1,
 258 >      &        v12_chyb(1,j,itori,itori1),costheti12)
 259 > c          write (iout,*) "v12",(v12_chyb(k,j,itori,itori1),k=1,nval),
 260 > c     &      " sumth1tyb2",sumth1tyb2," gradth1tyb2",gradth1tyb2
 261 >           sumth2tyb2=tschebyshev(1,nval,v22_chyb(1,j,itori,itori1),
 262 >      &        costheti22)
 263 >           gradth2tyb2=-0.5d0*sinthet2*gradtschebyshev(0,nval-1,
 264 >      &        v22_chyb(1,j,itori,itori1),costheti22)
 265 > c          write (iout,*) "v22",(v22_chyb(k,j,itori,itori1),k=1,nval),
 266 > c     &      " sumth2tyb2",sumth2tyb2," gradth2tyb2",gradth2tyb2
 267 > C          etors=etors+sint1t2n*(v1ij*cosphi+v2ij*sinphi)
 268 > C          if (energy_dec) etors_ii=etors_ii+
 269 > C     &                v1ij*cosphi+v2ij*sinphi
 270 7584c7593,7598
 271 <           glocig=glocig+j*sint1t2n*(sumvals*cosphi-sumvalc*sinphi)
 272 ---
 273 >           actval1=v1ij*cosphi*(1.0d0+sumth1tyb1+sumth2tyb1)
 274 >           actval2=v2ij*sinphi*(1.0d0+sumth1tyb2+sumth2tyb2)
 275 >           etori=etori+sint1t2n*(actval1+actval2)
 276 >           glocig=glocig+
 277 >      &        j*sint1t2n*(v2ij*cosphi*(1.0d0+sumth1tyb2+sumth2tyb2)
 278 >      &        -v1ij*sinphi*(1.0d0+sumth1tyb1+sumth2tyb1))
 279 7586,7589c7600,7621
 280 <           glocit1=glocit1+sint1t2n*(gradvalct1*cosphi+gradvalst1*sinphi)
 281 <      &   +j*sint1t2n1*costhet1*sinthet2*(sumvalc*cosphi+sumvals*sinphi)
 282 <           glocit2=glocit2+sint1t2n*(gradvalct2*cosphi+gradvalst2*sinphi)
 283 <      &   +j*sint1t2n1*sinthet1*costhet2*(sumvalc*cosphi+sumvals*sinphi)
 284 ---
 285 >           glocit1=glocit1+
 286 >      &       j*sint1t2n1*costhet1*sinthet2*(actval1+actval2)+
 287 >      &       sint1t2n*(v1ij*cosphi*gradth1tyb1+v2ij*sinphi*gradth1tyb2)
 288 >           glocit2=glocit2+
 289 >      &       j*sint1t2n1*sinthet1*costhet2*(actval1+actval2)+
 290 >      &       sint1t2n*(v1ij*cosphi*gradth2tyb1+v2ij*sinphi*gradth2tyb2)
 291 >
 292 > C now the Czebyshev polinominal sum
 293 > c        do k=1,nterm_kcc_Tb(itori,itori1)
 294 > c         thybt1(k)=v1_chyb(k,j,itori,itori1)
 295 > c         thybt2(k)=v2_chyb(k,j,itori,itori1)
 296 > C         thybt1(k)=0.0
 297 > C         thybt2(k)=0.0
 298 > c        enddo
 299 > C        print *, sumth1thyb, gradthybt1, sumth2thyb, gradthybt2,
 300 > C     &         gradtschebyshev
 301 > C     &         (0,nterm_kcc_Tb(itori,itori1)-1,thybt2(1),
 302 > C     &         dcos(theti22)**2),
 303 > C     &         dsin(theti22)
 304 >
 305 > C now overal sumation
 306 > C         print *,"sumnon", sumnonchebyshev,sumth1thyb+sumth2thyb
 307 7645c7677
 308 <       double precision thybt1(maxang_kcc)
 309 ---
 310 >       double precision thybt1(maxtermkcc)
 311 7656,7659c7688,7691
 312 <         iti=iabs(itortyp_kcc(itype(i-1)))
 313 <         sinthet=dsin(theta(i))
 314 <         costhet=dcos(theta(i))
 315 <         do j=1,nbend_kcc_Tb(iti)
 316 ---
 317 >          iti=itortyp_kcc(itype(i-1))
 318 >         sinthet=dsin(theta(i)/2.0d0)
 319 >         costhet=dcos(theta(i)/2.0d0)
 320 >          do j=1,nbend_kcc_Tb(iti)
 321 7661,7663c7693,7695
 322 <         enddo
 323 <         sumth1thyb=v1bend_chyb(0,iti)+
 324 <      &    tschebyshev(1,nbend_kcc_Tb(iti),thybt1(1),costhet)
 325 ---
 326 >          enddo
 327 >          sumth1thyb=tschebyshev
 328 >      &         (1,nbend_kcc_Tb(iti),thybt1(1),costhet)
 329 7667c7699,7700
 330 <         gradthybt1=gradtschebyshev(0,ihelp,thybt1(1),costhet)
 331 ---
 332 >         gradthybt1=gradtschebyshev
 333 >      &         (0,ihelp,thybt1(1),costhet)
 334 7670c7703,7704
 335 <         gloc(nphi+i-2,icg)=gloc(nphi+i-2,icg)-wang*gradthybt1*sinthet
 336 ---
 337 >         gloc(nphi+i-2,icg)=gloc(nphi+i-2,icg)+wang*
 338 >      &   gradthybt1*sinthet*(-0.5d0)
 339 11698,11699c11732,11733
 340 <       vectube(2)=mod((c(2,i)+c(2,i+1))/2.0d0,boxxsize)
 341 <           if (vectube(2).lt.0) vectube(2)=vectube(2)+boxxsize
 342 ---
 343 >       vectube(2)=mod((c(2,i)+c(2,i+1))/2.0d0,boxysize)
 344 >           if (vectube(2).lt.0) vectube(2)=vectube(2)+boxysize
 345 11748,11749c11782,11783
 346 <           vectube(2)=mod(vectube(2),boxxsize)
 347 <           if (vectube(2).lt.0) vectube(2)=vectube(2)+boxxsize
 348 ---
 349 >           vectube(2)=mod(vectube(2),boxysize)
 350 >           if (vectube(2).lt.0) vectube(2)=vectube(2)+boxysize
 351 11833,11834c11867,11868
 352 <       vectube(2)=mod((c(2,i)+c(2,i+1))/2.0d0,boxxsize)
 353 <           if (vectube(2).lt.0) vectube(2)=vectube(2)+boxxsize
 354 ---
 355 >       vectube(2)=mod((c(2,i)+c(2,i+1))/2.0d0,boxysize)
 356 >           if (vectube(2).lt.0) vectube(2)=vectube(2)+boxysize
 357 11883,11884c11917,11918
 358 <           vectube(2)=mod(vectube(2),boxxsize)
 359 <           if (vectube(2).lt.0) vectube(2)=vectube(2)+boxxsize
 360 ---
 361 >           vectube(2)=mod(vectube(2),boxysize)
 362 >           if (vectube(2).lt.0) vectube(2)=vectube(2)+boxysize
 363 11906,11909c11940,11943
 364 <          gg_tube_SC(3,i)=gg_tube_SC(3,i)
 365 <      &+ssgradtube*tubetranene(itype(i))
 366 <          gg_tube(3,i-1)= gg_tube(3,i-1)
 367 <      &+ssgradtube*tubetranene(itype(i))
 368 ---
 369 > C         gg_tube_SC(3,i)=gg_tube_SC(3,i)
 370 > C     &+ssgradtube*tubetranene(itype(i))
 371 > C         gg_tube(3,i-1)= gg_tube(3,i-1)
 372 > C     &+ssgradtube*tubetranene(itype(i))
 373 --------------------------------
 374  SOURCE FILE energy_p_new.F
 375 --------------------------------
 376 --------------------------------
 377  SOURCE FILE energy_p_new-sep_barrier.F
 378 --------------------------------
 379 --------------------------------
 380  SOURCE FILE energy_p_new-sep.F
 381 --------------------------------
 382 --------------------------------
 383  SOURCE FILE energy_split.F
 384 --------------------------------
 385 --------------------------------
 386  SOURCE FILE energy_split-sep.F
 387 --------------------------------
 388 --------------------------------
 389  SOURCE FILE entmcm.F
 390 --------------------------------
 391 --------------------------------
 392  SOURCE FILE fitsq.f
 393 --------------------------------
 394 --------------------------------
 395  SOURCE FILE gauss.f
 396 --------------------------------
 397 --------------------------------
 398  SOURCE FILE gen_rand_conf.F
 399 --------------------------------
 400 --------------------------------
 401  SOURCE FILE geomout.F
 402 --------------------------------
 403 --------------------------------
 404  SOURCE FILE gnmr1.f
 405 --------------------------------
 406 --------------------------------
 407  SOURCE FILE gradient_p.F
 408 --------------------------------
 409 --------------------------------
 410  SOURCE FILE indexx.f
 411 --------------------------------
 412 --------------------------------
 413  SOURCE FILE initialize_p.F
 414 --------------------------------
 415 --------------------------------
 416  SOURCE FILE intcartderiv.F
 417 --------------------------------
 418 --------------------------------
 419  SOURCE FILE intcor.f
 420 --------------------------------
 421 --------------------------------
 422  SOURCE FILE intlocal.f
 423 --------------------------------
 424 --------------------------------
 425  SOURCE FILE int_to_cart.f
 426 --------------------------------
 427 --------------------------------
 428  SOURCE FILE isnan.f
 429 --------------------------------
 430 --------------------------------
 431  SOURCE FILE kinetic_lesyng.f
 432 --------------------------------
 433 --------------------------------
 434  SOURCE FILE lagrangian_lesyng.F
 435 --------------------------------
 436 --------------------------------
 437  SOURCE FILE local_move.f
 438 --------------------------------
 439 --------------------------------
 440  SOURCE FILE map.f
 441 --------------------------------
 442 --------------------------------
 443  SOURCE FILE matmult.f
 444 --------------------------------
 445 --------------------------------
 446  SOURCE FILE mc.F
 447 --------------------------------
 448 --------------------------------
 449  SOURCE FILE mcm.F
 450 --------------------------------
 451 --------------------------------
 452  SOURCE FILE MD_A-MTS.F
 453 --------------------------------
 454 1655a1656
 455 >       call enerprint(potEcomp)
 456 --------------------------------
 457  SOURCE FILE MD.F
 458 --------------------------------
 459 --------------------------------
 460  SOURCE FILE minimize_p.F
 461 --------------------------------
 462 413d412
 463 <       include 'COMMON.CONTROL'
 464 488,493d486
 465 < c-----
 466 <       write (iout,*) "checkgrad before SUMSL"
 467 <       icheckgrad=1
 468 <       aincr=1.0d-7
 469 <       call exec_checkgrad
 470 < c-----
 471 496,499d488
 472 < c-----
 473 <       write (iout,*) "checkgrad after SUMSL"
 474 <       call exec_checkgrad
 475 < c-----
 476 --------------------------------
 477  SOURCE FILE minim_jlee.F
 478 --------------------------------
 479 --------------------------------
 480  SOURCE FILE minim_mcmf.F
 481 --------------------------------
 482 --------------------------------
 483  SOURCE FILE misc.f
 484 --------------------------------
 485 --------------------------------
 486  SOURCE FILE moments.f
 487 --------------------------------
 488 --------------------------------
 489  SOURCE FILE MP.F
 490 --------------------------------
 491 --------------------------------
 492  SOURCE FILE MREMD.F
 493 --------------------------------
 494 --------------------------------
 495  SOURCE FILE MREMD_nosy1traj.F
 496 --------------------------------
 497 --------------------------------
 498  SOURCE FILE muca_md.f
 499 --------------------------------
 500 --------------------------------
 501  SOURCE FILE newconf.f
 502 --------------------------------
 503 --------------------------------
 504  SOURCE FILE parmread.F
 505 --------------------------------
 506 36d35
 507 <       character*3 string
 508 788c787
 509 < C read valence-torsional parameters
 510 ---
 511 > C read Czybyshev torsional parameters
 512 790d788
 513 <       write (iout,*) "nkcctyp",nkcctyp
 514 792d789
 515 <       write (iout,*) "itortyp_kcc",(itortyp_kcc(i),i=1,ntyp)
 516 796,797c793,794
 517 <       do i=-nkcctyp+1,nkcctyp-1
 518 <         do j=-nkcctyp+1,nkcctyp-1
 519 ---
 520 >       do i=0,nkcctyp
 521 >         do j=0,nkcctyp
 522 799,800d795
 523 <           read (itorkcc,'(13x,a)',end=121,err=121) string
 524 <           write (iout,*) i,j,string
 525 806,809c801,807
 526 <               do ll=1,nterm_kcc_Tb(j,i)
 527 <               read (itorkcc,*,end=121,err=121) ii,jj,kk,
 528 <      &          v1_kcc(ll,l,k,j,i),v2_kcc(ll,l,k,j,i)
 529 <               enddo
 530 ---
 531 >               read (itorkcc,*,end=121,err=121) v11_chyb(l,k,j,i)
 532 >             enddo
 533 >             do l=1,nterm_kcc_Tb(j,i)
 534 >               read (itorkcc,*,end=121,err=121) v21_chyb(l,k,j,i)
 535 >             enddo
 536 >             do l=1,nterm_kcc_Tb(j,i)
 537 >               read (itorkcc,*,end=121,err=121) v12_chyb(l,k,j,i)
 538 810a809,813
 539 >             do l=1,nterm_kcc_Tb(j,i)
 540 >               read (itorkcc,*,end=121,err=121) v22_chyb(l,k,j,i)
 541 >             enddo
 542 >             read (itorkcc,*,end=121,err=121) v1_kcc(k,j,i)
 543 >             read (itorkcc,*,end=121,err=121) v2_kcc(k,j,i)
 544 818,819c821,822
 545 <         do i=-nkcctyp+1,nkcctyp-1
 546 <         do j=-nkcctyp+1,nkcctyp-1
 547 ---
 548 >         do i=0,nkcctyp
 549 >         do j=0,nkcctyp
 550 821c824
 551 <         write (iout,'(3a5,2a15)') "itor","ival","jval","v_kcc","v2_kcc"
 552 ---
 553 >         write (iout,'(2a20,a15)') "v_kcc","v1_chyb","v2_chyb"
 554 823,827c826,836
 555 <           do l=1,nterm_kcc_Tb(j,i)
 556 <             do ll=1,nterm_kcc_Tb(j,i)
 557 <                write (iout,'(3i5,2f15.4)')
 558 <      &            k,l-1,ll-1,v1_kcc(ll,l,k,j,i),v2_kcc(ll,l,k,j,i)
 559 <             enddo
 560 ---
 561 >           write (iout,'(i5,f15.10,i5,2f15.10)')
 562 >      &      k,v1_kcc(k,j,i),1,v11_chyb(1,k,j,i),v21_chyb(1,k,j,i)
 563 >           do l=2,nterm_kcc_Tb(j,i)
 564 >             write (iout,'(20x,i5,2f15.10)')
 565 >      &        l,v11_chyb(l,k,j,i),v21_chyb(l,k,j,i)
 566 >           enddo
 567 >           write (iout,'(i5,f15.10,i5,2f15.10)')
 568 >      &      k,v2_kcc(k,j,i),1,v12_chyb(1,k,j,i),v22_chyb(1,k,j,i)
 569 >           do l=2,nterm_kcc_Tb(j,i)
 570 >             write (iout,'(20x,i5,2f15.10)')
 571 >      &        l,v12_chyb(l,k,j,i),v22_chyb(l,k,j,i)
 572 828a838
 573 >           write (iout,'(a)')
 574 835,836c845
 575 <       read (ithetkcc,*) ijunk
 576 <       do i=-nkcctyp+1,nkcctyp-1
 577 ---
 578 >       do i=0,nkcctyp
 579 838,839c847,848
 580 <         do j=0,nbend_kcc_Tb(i)
 581 <           read (ithetkcc,*,end=121,err=121) ijunk,v1bend_chyb(j,i)
 582 ---
 583 >         do j=1,nbend_kcc_Tb(i)
 584 >           read (ithetkcc,*,end=121,err=121) v1bend_chyb(j,i)
 585 845c854
 586 <         do i=-nkcctyp+1,nkcctyp-1
 587 ---
 588 >         do i=0,nkcctyp
 589 847,848c856,857
 590 <         do k=0,nbend_kcc_Tb(i)
 591 <           write(iout,'(i5,f15.5)') k,v1bend_chyb(k,i)
 592 ---
 593 >         do k=1,nbend_kcc_Tb(i)
 594 >           write(iout,'(i5,f15.10)') k,v1bend_chyb(k,i)
 595 1018,1100d1026
 596 < #ifdef NEWCORR
 597 <       do i=0,nloctyp-1
 598 <         read (ifourier,*,end=115,err=115)
 599 <         do ii=1,3
 600 <           do j=1,2
 601 <             read (ifourier,*,end=115,err=115) bnew1(ii,j,i)
 602 <           enddo
 603 <         enddo
 604 <         do ii=1,3
 605 <           do j=1,2
 606 <             read (ifourier,*,end=115,err=115) bnew2(ii,j,i)
 607 <           enddo
 608 <         enddo
 609 <         do kk=1,2
 610 <           read (ifourier,*,end=115,err=115) ccnew(kk,1,i)
 611 <           read (ifourier,*,end=115,err=115) ccnew(kk,2,i)
 612 <         enddo
 613 <         do kk=1,2
 614 <           read (ifourier,*,end=115,err=115) ddnew(kk,1,i)
 615 <           read (ifourier,*,end=115,err=115) ddnew(kk,2,i)
 616 <         enddo
 617 <         do ii=1,2
 618 <           do jj=1,2
 619 <             do kk=1,2
 620 <               read (ifourier,*,end=115,err=115) eenew(ii,jj,kk,i)
 621 <             enddo
 622 <           enddo
 623 <         enddo
 624 <         do ii=1,3
 625 <           read (ifourier,*,end=115,err=115) e0new(ii,i)
 626 <         enddo
 627 <       enddo
 628 <       do i=1,nloctyp-1
 629 <         do ii=1,3
 630 <           bnew1(ii,1,-i)= bnew1(ii,1,i)
 631 <           bnew1(ii,2,-i)=-bnew1(ii,2,i)
 632 <           bnew2(ii,1,-i)= bnew2(ii,1,i)
 633 <           bnew2(ii,2,-i)=-bnew2(ii,2,i)
 634 <         enddo
 635 <         do ii=1,2
 636 <           ccnew(ii,1,-i)=ccnew(ii,1,i)
 637 <           ccnew(ii,2,-i)=-ccnew(ii,2,i)
 638 <           ddnew(ii,1,-i)=ddnew(ii,1,i)
 639 <           ddnew(ii,2,-i)=-ddnew(ii,2,i)
 640 <         enddo
 641 <         e0new(1,-i)= e0new(1,i)
 642 <         e0new(2,-i)=-e0new(2,i)
 643 <         e0new(3,-i)=-e0new(3,i)
 644 <         do kk=1,2
 645 <           eenew(kk,1,1,-i)= eenew(kk,1,1,i)
 646 <           eenew(kk,1,2,-i)=-eenew(kk,1,2,i)
 647 <           eenew(kk,2,1,-i)=-eenew(kk,2,1,i)
 648 <           eenew(kk,2,2,-i)= eenew(kk,2,2,i)
 649 <         enddo
 650 <       enddo
 651 <       if (lprint) then
 652 <         write (iout,'(a)') "Coefficients of the multibody terms"
 653 <         do i=-nloctyp+1,nloctyp-1
 654 <           write (iout,*) "Type: ",onelet(iloctyp(i))
 655 <           write (iout,*) "Coefficients of the expansion of B1"
 656 <           do j=1,2
 657 <             write (iout,'(3hB1(,i1,1h),3f10.5)') j,(bnew1(k,j,i),k=1,3)
 658 <           enddo
 659 <           write (iout,*) "Coefficients of the expansion of B2"
 660 <           do j=1,2
 661 <             write (iout,'(3hB2(,i1,1h),3f10.5)') j,(bnew2(k,j,i),k=1,3)
 662 <           enddo
 663 <           write (iout,*) "Coefficients of the expansion of C"
 664 <           write (iout,'(3hC11,2f10.5)') (ccnew(j,1,i),j=1,2)
 665 <           write (iout,'(3hC12,2f10.5)') (ccnew(j,2,i),j=1,2)
 666 <           write (iout,*) "Coefficients of the expansion of D"
 667 <           write (iout,'(3hD11,2f10.5)') (ddnew(j,1,i),j=1,2)
 668 <           write (iout,'(3hD12,2f10.5)') (ddnew(j,2,i),j=1,2)
 669 <           write (iout,*) "Coefficients of the expansion of E"
 670 <           write (iout,'(2hE0,3f10.5)') (e0new(j,i),j=1,3)
 671 <           do j=1,2
 672 <             do k=1,2
 673 <               write (iout,'(1hE,2i1,2f10.5)') j,k,(eenew(l,j,k,i),l=1,2)
 674 <             enddo
 675 <           enddo
 676 <         enddo
 677 <       endif
 678 < #else
 679 1103a1030,1036
 680 > #ifdef NEWCORR
 681 >         read (ifourier,*,end=115,err=115) (bnew1(ii,1,i),ii=1,3)
 682 >         read (ifourier,*,end=115,err=115) (bnew2(ii,1,i),ii=1,3)
 683 >         read (ifourier,*,end=115,err=115) (bnew1(ii,2,i),ii=1,1)
 684 >         read (ifourier,*,end=115,err=115) (bnew2(ii,2,i),ii=1,1)
 685 >         read (ifourier,*,end=115,err=115) (eenew(ii,i),ii=1,1)
 686 > #endif
 687 1226c1159
 688 < #endif
 689 ---
 690 >
 691 1430d1362
 692 < #ifdef TUBE
 693 1432c1364
 694 <       read(itube,*) epspeptube,sigmapeptube
 695 ---
 696 >       read(itube,*) epspeptube,sigmapeptube,tubetranenepep
 697 1440c1372
 698 <        read(itube,*) epssctube,sigmasctube
 699 ---
 700 >        read(itube,*) epssctube,sigmasctube,tubetranene(i)
 701 1448d1379
 702 < #endif
 703 --------------------------------
 704  SOURCE FILE permut.F
 705 --------------------------------
 706 --------------------------------
 707  SOURCE FILE pinorm.f
 708 --------------------------------
 709 --------------------------------
 710  SOURCE FILE printmat.f
 711 --------------------------------
 712 --------------------------------
 713  SOURCE FILE prng_32.F
 714 --------------------------------
 715 --------------------------------
 716  SOURCE FILE q_measure1.F
 717 --------------------------------
 718 --------------------------------
 719  SOURCE FILE q_measure3.F
 720 --------------------------------
 721 --------------------------------
 722  SOURCE FILE q_measure.F
 723 --------------------------------
 724 --------------------------------
 725  SOURCE FILE randgens.f
 726 --------------------------------
 727 --------------------------------
 728  SOURCE FILE ran.f
 729 --------------------------------
 730 --------------------------------
 731  SOURCE FILE rattle.F
 732 --------------------------------
 733 --------------------------------
 734  SOURCE FILE readpdb.F
 735 --------------------------------
 736 --------------------------------
 737  SOURCE FILE readrtns_CSA.F
 738 --------------------------------
 739 2299,2300d2298
 740 <       write (iout,*) "Torsion-valence parameter file  : ",
 741 <      &  torkccname(:ilen(torkccname))
 742 2307c2305
 743 <       write (iout,*) "Bending-torsion parameter file  : ",
 744 ---
 745 >       write (iout,*) "Bending parameter file          : ",
 746 2309,2310d2306
 747 <       write (iout,*) "Bending-only parameter file     : ",
 748 <      &  thetkccname(:ilen(thetkccname))
 749 --------------------------------
 750  SOURCE FILE refsys.f
 751 --------------------------------
 752 --------------------------------
 753  SOURCE FILE regularize.F
 754 --------------------------------
 755 --------------------------------
 756  SOURCE FILE rescode.f
 757 --------------------------------
 758 --------------------------------
 759  SOURCE FILE restbin2asc.F
 760 --------------------------------
 761 --------------------------------
 762  SOURCE FILE rmdd.f
 763 --------------------------------
 764 --------------------------------
 765  SOURCE FILE rmsd.F
 766 --------------------------------
 767 --------------------------------
 768  SOURCE FILE sc_move.F
 769 --------------------------------
 770 --------------------------------
 771  SOURCE FILE shift.F
 772 --------------------------------
 773 --------------------------------
 774  SOURCE FILE sort.f
 775 --------------------------------
 776 --------------------------------
 777  SOURCE FILE ssMD.F
 778 --------------------------------
 779 --------------------------------
 780  SOURCE FILE stochfric.F
 781 --------------------------------
 782 --------------------------------
 783  SOURCE FILE sumsld.f
 784 --------------------------------
 785 --------------------------------
 786  SOURCE FILE surfatom.f
 787 --------------------------------
 788 --------------------------------
 789  SOURCE FILE test.F
 790 --------------------------------
 791 --------------------------------
 792  SOURCE FILE thread.F
 793 --------------------------------
 794 --------------------------------
 795  SOURCE FILE timing.F
 796 --------------------------------
 797 --------------------------------
 798  SOURCE FILE together.F
 799 --------------------------------
 800 --------------------------------
 801  SOURCE FILE unres.F
 802 --------------------------------