initial version of fix pitorsion

examples/amoeba/data.ubiquitin

@@ -13,6 +13,8 @@ LAMMPS data file created from Tinker ubiquitin.xyz and amoeba_ubiquitin.prm file
 0 54.99 xlo xhi
 0 41.91 ylo yhi
 0 41.91 zlo zhi
+6 pitorsion types
+106 pitorsions
 
 Masses
 
@@ -26346,6 +26348,124 @@ UreyBradley Coeffs
 110 0.0 0.0
 111 -7.6 1.5537
 
+PiTorsions
+
+1 1 2 4 3 20 21 24
+2 1 21 23 22 37 38 41
+3 1 27 29 28 30 35 36
+4 1 38 40 39 56 57 60
+5 1 57 59 58 76 77 80
+6 2 62 65 63 64 66 71
+7 2 62 64 63 65 67 72
+8 2 63 71 64 66 68 73
+9 2 63 72 65 67 68 74
+10 2 64 73 66 68 67 75
+11 2 65 74 67 68 66 75
+12 1 77 79 78 92 93 96
+13 1 93 95 94 114 115 118
+14 1 115 117 116 128 129 132
+15 1 129 131 130 147 148 151
+16 1 148 150 149 161 162 165
+17 1 162 164 163 168 169 172
+18 1 169 171 170 190 191 194
+19 1 191 193 192 204 205 208
+20 1 205 207 206 223 224 227
+21 1 224 226 225 237 238 241
+22 1 238 240 239 256 257 260
+23 1 257 259 258 271 272 275
+24 1 272 274 273 287 288 291
+25 3 288 290 289 302 303 309
+26 1 303 305 304 316 317 320
+27 1 317 319 318 327 328 331
+28 1 328 330 329 339 340 343
+29 1 340 342 341 353 354 357
+30 1 354 356 355 372 373 376
+31 1 373 375 374 387 388 391
+32 1 388 390 389 401 402 405
+33 1 393 395 394 396 399 400
+34 1 402 404 403 417 418 421
+35 1 418 420 419 439 440 443
+36 1 440 442 441 449 450 453
+37 1 450 452 451 471 472 475
+38 1 472 474 473 490 491 494
+39 1 491 493 492 507 508 511
+40 1 497 499 498 500 505 506
+41 1 508 510 509 519 520 523
+42 1 520 522 521 541 542 545
+43 1 542 544 543 556 557 560
+44 1 557 559 558 563 564 567
+45 3 564 566 565 582 583 589
+46 3 583 585 584 596 597 603
+47 1 597 599 598 610 611 614
+48 1 611 613 612 622 623 626
+49 1 623 625 624 639 640 643
+50 1 629 631 630 632 637 638
+51 1 640 642 641 656 657 660
+52 1 646 648 647 649 654 655
+53 1 657 659 658 680 681 684
+54 1 681 683 682 699 700 703
+55 1 700 702 701 718 719 722
+56 1 719 721 720 738 739 742
+57 2 724 727 725 726 728 733
+58 2 724 726 725 727 729 734
+59 2 725 733 726 728 730 735
+60 2 725 734 727 729 730 736
+61 2 726 735 728 730 729 737
+62 2 727 736 729 730 728 737
+63 1 739 741 740 748 749 752
+64 1 749 751 750 755 756 759
+65 1 756 758 757 777 778 781
+66 1 778 780 779 794 795 798
+67 1 784 786 785 787 792 793
+68 1 795 797 796 813 814 817
+69 1 814 816 815 828 829 832
+70 1 829 831 830 840 841 844
+71 1 841 843 842 847 848 851
+72 1 848 850 849 871 872 875
+73 1 872 874 873 885 886 889
+74 1 886 888 887 904 905 908
+75 1 905 907 906 915 916 919
+76 1 916 918 917 927 928 931
+77 1 928 930 929 948 949 952
+78 2 933 936 934 935 937 943
+79 2 933 935 934 936 938 944
+80 2 934 943 935 937 939 945
+81 2 934 944 936 938 939 946
+82 2 935 945 937 939 938 940
+83 2 936 946 938 939 937 940
+84 1 949 951 950 962 963 966
+85 1 954 956 955 957 960 961
+86 1 963 965 964 981 982 985
+87 1 982 984 983 998 999 1002
+88 1 988 990 989 991 996 997
+89 1 999 1001 1000 1020 1021 1024
+90 1 1021 1023 1022 1035 1036 1039
+91 1 1036 1038 1037 1046 1047 1050
+92 1 1047 1049 1048 1060 1061 1064
+93 1 1061 1063 1062 1079 1080 1083
+94 1 1080 1082 1081 1097 1098 1101
+95 4 1085 1088 1086 1087 1089 1093
+96 5 1085 1087 1086 1088 1090 1094
+97 6 1086 1093 1087 1089 1090 1095
+98 4 1086 1094 1088 1090 1089 1096
+99 6 1087 1095 1089 1090 1088 1096
+100 1 1098 1100 1099 1116 1117 1120
+101 1 1117 1119 1118 1132 1133 1136
+102 1 1133 1135 1134 1151 1152 1155
+103 1 1152 1154 1153 1175 1176 1179
+104 1 1176 1178 1177 1194 1195 1198
+105 1 1195 1197 1196 1218 1219 1222
+106 1 1219 1221 1220 1225 1226 1229
+
+PiTorsion Coeffs
+
+1 6.85
+2 6.85
+3 6.85
+4 6.85
+5 6.85
+6 6.85
+
 Tinker Types
 
 1 234

examples/amoeba/in.ubiquitin

@@ -14,15 +14,16 @@ improper_style  amoeba
 # per-atom properties required by AMOEBA or HIPPO
 
 fix             amtype all property/atom i_amtype ghost yes
-#fix             pitorsion all pitorsion
+fix             pitorsion all pitorsion
 
 fix             extra all property/atom &
                 i_amgroup i_ired i_xaxis i_yaxis i_zaxis d_pval ghost yes
 fix             extra2 all property/atom i_polaxe
 
-read_data       data.ubiquitin fix amtype NULL "Tinker Types"
+#read_data       data.ubiquitin fix amtype NULL "Tinker Types"
-#read_data       data.ubiquitin fix amtype NULL "Tinker Types" &
+read_data       data.ubiquitin fix amtype NULL "Tinker Types" &
-#                fix pitorsion pitorsions PiTorsions
+                fix pitorsion "pitorsion types" "PiTorsion Coeffs" &
+                fix pitorsion pitorsions PiTorsions
 
 pair_style      amoeba
 pair_coeff      * * amoeba_ubiquitin.prm amoeba_ubiquitin.key

src/AMOEBA/angle_amoeba.cpp

@@ -103,10 +103,6 @@ void AngleAmoeba::compute(int eflag, int vflag)
 
   ev_init(eflag,vflag);
 
-  // DEBUG
-  int ubn = 0;
-  double eub = 0.0;
-
   for (n = 0; n < nanglelist; n++) {
     i1 = anglelist[n][0];
     i2 = anglelist[n][1];
@@ -131,17 +127,10 @@ void AngleAmoeba::compute(int eflag, int vflag)
     // Urey-Bradley H-H bond term within water molecules
 
     uflag = ubflag[type];
-
+    if (uflag) tinker_urey_bradley(i1,i3,type,eflag);
-    if (uflag) {
-      ubn++;
-      eub += tinker_urey_bradley(i1,i3,type,eflag);
   }
 }
 
-  // DEBUG
-  printf("UreyBradley n %d eng %g\n",ubn,eub);
-}
-
 /* ---------------------------------------------------------------------- */
 
 void AngleAmoeba::tinker_angle(int i1, int i2, int i3, int type, int eflag)
@@ -543,7 +532,7 @@ void AngleAmoeba::tinker_bondangle(int i1, int i2, int i3, int type, int eflag)
 
 /* ---------------------------------------------------------------------- */
 
-double AngleAmoeba::tinker_urey_bradley(int i1, int i2, int type, int eflag)
+void AngleAmoeba::tinker_urey_bradley(int i1, int i2, int type, int eflag)
 {
   double delx,dely,delz;
   double rsq,r,dr,rk;
@@ -585,8 +574,6 @@ double AngleAmoeba::tinker_urey_bradley(int i1, int i2, int type, int eflag)
   }
 
   if (evflag) ev_tally2(i1,i2,nlocal,newton_bond,ebond,fbond,delx,dely,delz);
-  
-  return ebond;
 }
 
 /* ---------------------------------------------------------------------- */

src/AMOEBA/angle_amoeba.h

@@ -46,7 +46,7 @@ class AngleAmoeba : public Angle {
   void tinker_angle(int, int, int, int, int);
   void tinker_anglep(int, int, int, int, int);
   void tinker_bondangle(int, int, int, int, int);
-  double tinker_urey_bradley(int, int, int, int);
+  void tinker_urey_bradley(int, int, int, int);
   void allocate();
 };
 

src/AMOEBA/fix_pitorsion.cpp

@@ -89,6 +89,10 @@ FixPiTorsion::FixPiTorsion(LAMMPS *lmp, int narg, char **arg) :
   npitorsion_list = 0;
   max_pitorsion_list = 0;
   pitorsion_list = nullptr;
+
+  // pitorsion coeff
+
+  kpit = nullptr;
 }
 
 /* --------------------------------------------------------------------- */
@@ -114,6 +118,10 @@ FixPiTorsion::~FixPiTorsion()
   // compute list
 
   memory->destroy(pitorsion_list);
+
+  // coeff
+
+  memory->destroy(kpit);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -185,19 +193,19 @@ void FixPiTorsion::pre_neighbor()
   int i,m,atom1,atom2,atom3,atom4,atom5,atom6;
 
   // guesstimate initial length of local pitorsion list
-  // if npitorsion_global was not set (due to read_restart, no read_data),
+  // if npitorsions was not set (due to read_restart, no read_data),
   //   then list will grow by LISTDELTA chunks
 
   if (max_pitorsion_list == 0) {
-    if (nprocs == 1) max_pitorsion_list = npitorsion_global;
+    if (nprocs == 1) max_pitorsion_list = npitorsions;
     else max_pitorsion_list = 
-           static_cast<int> (LB_FACTOR*npitorsion_global/nprocs);
+           static_cast<int> (LB_FACTOR*npitorsions/nprocs);
     memory->create(pitorsion_list,max_pitorsion_list,7,
                    "pitorsion:pitorsion_list");
   }
 
   int nlocal = atom->nlocal;
-  pitorsion_list = 0;
+  npitorsion_list = 0;
 
   for (i = 0; i < nlocal; i++) {
     for (m = 0; m < num_pitorsion[i]; m++) {
@@ -209,7 +217,7 @@ void FixPiTorsion::pre_neighbor()
       atom6 = atom->map(pitorsion_atom6[i][m]);
 
       if (atom1 == -1 || atom2 == -1 || atom3 == -1 ||
-          atom4 == -1 || atom5 == -1)
+          atom4 == -1 || atom5 == -1 || atom6 == -1)
         error->one(FLERR,"PiTorsion atoms {} {} {} {} {} {} missing on "
                    "proc {} at step {}",
                    pitorsion_atom1[i][m],pitorsion_atom2[i][m],
@@ -531,7 +539,9 @@ double FixPiTorsion::compute_scalar()
 void FixPiTorsion::read_data_header(char *line)
 {
   if (strstr(line,"pitorsions")) {
-    sscanf(line,BIGINT_FORMAT,&npitorsion_global);
+    sscanf(line,BIGINT_FORMAT,&npitorsions);
+  } else if (strstr(line,"pitorsion types")) {
+    sscanf(line,"%d",&npitorsion_types);
   } else error->all(FLERR,"Invalid read data header line for fix pitorsion");
 
   // didn't set in constructor because this fix could be defined
@@ -549,6 +559,44 @@ void FixPiTorsion::read_data_header(char *line)
 void FixPiTorsion::read_data_section(char *keyword, int n, char *buf,
                                      tagint id_offset)
 {
+  int which;
+
+  if (strstr(keyword,"PiTorsions")) {
+    sscanf(keyword,BIGINT_FORMAT,&npitorsions);
+    which = 0;
+  } else if (strstr(keyword,"PiTorsion Coeffs")) {
+    sscanf(keyword,"%d",&npitorsion_types);
+    which = 1;
+  } else error->all(FLERR,"Invalid read data section for fix pitorsion");
+  
+  // loop over lines of PiTorsion Coeffs
+  // tokenize the line into values
+  // initialize kpit vector
+  
+  if (which == 1) {
+    int itype;
+    double value;
+    char *next;
+
+    memory->create(kpit,npitorsion_types+1,"pitorsion:kpit");
+
+    for (int i = 0; i < n; i++) {
+      next = strchr(buf,'\n');
+      *next = '\0';
+      sscanf(buf,"%d %g",&itype,&value);
+      if (itype <= 0 || itype > npitorsion_types)
+        error->all(FLERR,"Incorrect args for pitorsion coefficients");
+      kpit[itype] = value;
+      buf = next + 1;
+    }
+  }
+
+  // loop over lines of PiTorsions
+  // tokenize the line into values
+  // add PiTorsion to one or more of my atoms, depending on newton_bond
+
+  if (which == 0) {
+
     int m,tmp,itype;
     tagint atom1,atom2,atom3,atom4,atom5,atom6;
     char *next;
@@ -558,13 +606,9 @@ void FixPiTorsion::read_data_section(char *keyword, int n, char *buf,
     int nwords = utils::count_words(utils::trim_comment(buf));
     *next = '\n';
     
-  if (nwords != 7)
+    if (nwords != 8)
       error->all(FLERR,"Incorrect {} format in data file",keyword);
 
-  // loop over lines of PiTorsions
-  // tokenize the line into values
-  // add PiTorsion to one or more of my atoms, depending on newton_bond
-
     for (int i = 0; i < n; i++) {
       next = strchr(buf,'\n');
       *next = '\0';
@@ -579,31 +623,7 @@ void FixPiTorsion::read_data_section(char *keyword, int n, char *buf,
       atom5 += id_offset;
       atom6 += id_offset;
 
-    if ((m = atom->map(atom1)) >= 0) {
+      // atom3 owns the pitorsion when newton_bond on
-      if (num_pitorsion[m] == PITORSIONMAX)
-        error->one(FLERR,"Too many PiTorsions for one atom");
-      pitorsion_type[m][num_pitorsion[m]] = itype;
-      pitorsion_atom1[m][num_pitorsion[m]] = atom1;
-      pitorsion_atom2[m][num_pitorsion[m]] = atom2;
-      pitorsion_atom3[m][num_pitorsion[m]] = atom3;
-      pitorsion_atom4[m][num_pitorsion[m]] = atom4;
-      pitorsion_atom5[m][num_pitorsion[m]] = atom5;
-      pitorsion_atom6[m][num_pitorsion[m]] = atom6;
-      num_pitorsion[m]++;
-    }
-
-    if ((m = atom->map(atom2)) >= 0) {
-      if (num_pitorsion[m] == PITORSIONMAX)
-        error->one(FLERR,"Too many PiTorsions for one atom");
-      pitorsion_type[m][num_pitorsion[m]] = itype;
-      pitorsion_atom1[m][num_pitorsion[m]] = atom1;
-      pitorsion_atom2[m][num_pitorsion[m]] = atom2;
-      pitorsion_atom3[m][num_pitorsion[m]] = atom3;
-      pitorsion_atom4[m][num_pitorsion[m]] = atom4;
-      pitorsion_atom5[m][num_pitorsion[m]] = atom5;
-      pitorsion_atom6[m][num_pitorsion[m]] = atom6;
-      num_pitorsion[m]++;
-    }
 
       if ((m = atom->map(atom3)) >= 0) {
         if (num_pitorsion[m] == PITORSIONMAX)
@@ -618,6 +638,37 @@ void FixPiTorsion::read_data_section(char *keyword, int n, char *buf,
         num_pitorsion[m]++;
       }
 
+      if (newton_bond == 0) {
+        if ((m = atom->map(atom1)) >= 0) {
+          if (num_pitorsion[m] == PITORSIONMAX)
+            error->one(FLERR,"Too many PiTorsions for one atom");
+          pitorsion_type[m][num_pitorsion[m]] = itype;
+          pitorsion_atom1[m][num_pitorsion[m]] = atom1;
+          pitorsion_atom2[m][num_pitorsion[m]] = atom2;
+          pitorsion_atom3[m][num_pitorsion[m]] = atom3;
+          pitorsion_atom4[m][num_pitorsion[m]] = atom4;
+          pitorsion_atom5[m][num_pitorsion[m]] = atom5;
+          pitorsion_atom6[m][num_pitorsion[m]] = atom6;
+          num_pitorsion[m]++;
+        }
+      }
+
+      if (newton_bond == 0) {
+        if ((m = atom->map(atom2)) >= 0) {
+          if (num_pitorsion[m] == PITORSIONMAX)
+            error->one(FLERR,"Too many PiTorsions for one atom");
+          pitorsion_type[m][num_pitorsion[m]] = itype;
+          pitorsion_atom1[m][num_pitorsion[m]] = atom1;
+          pitorsion_atom2[m][num_pitorsion[m]] = atom2;
+          pitorsion_atom3[m][num_pitorsion[m]] = atom3;
+          pitorsion_atom4[m][num_pitorsion[m]] = atom4;
+          pitorsion_atom5[m][num_pitorsion[m]] = atom5;
+          pitorsion_atom6[m][num_pitorsion[m]] = atom6;
+          num_pitorsion[m]++;
+        }
+      }
+
+      if (newton_bond == 0) {
         if ((m = atom->map(atom4)) >= 0) {
           if (num_pitorsion[m] == PITORSIONMAX)
             error->one(FLERR,"Too many PiTorsions for one atom");
@@ -630,7 +681,9 @@ void FixPiTorsion::read_data_section(char *keyword, int n, char *buf,
           pitorsion_atom6[m][num_pitorsion[m]] = atom6;
           num_pitorsion[m]++;
         }
+      }
 
+      if (newton_bond == 0) {
         if ((m = atom->map(atom5)) >= 0) {
           if (num_pitorsion[m] == PITORSIONMAX)
             error->one(FLERR,"Too many PiTorsions for one atom");
@@ -643,7 +696,9 @@ void FixPiTorsion::read_data_section(char *keyword, int n, char *buf,
           pitorsion_atom6[m][num_pitorsion[m]] = atom6;
           num_pitorsion[m]++;
         }
+      }
 
+      if (newton_bond == 0) {
         if ((m = atom->map(atom6)) >= 0) {
           if (num_pitorsion[m] == PITORSIONMAX)
             error->one(FLERR,"Too many PiTorsions for one atom");
@@ -656,16 +711,20 @@ void FixPiTorsion::read_data_section(char *keyword, int n, char *buf,
           pitorsion_atom6[m][num_pitorsion[m]] = atom6;
           num_pitorsion[m]++;
         }
+      }
 
       buf = next + 1;
     }
   }
+}
 
 /* ---------------------------------------------------------------------- */
 
-bigint FixPiTorsion::read_data_skip_lines(char * /*keyword*/)
+bigint FixPiTorsion::read_data_skip_lines(char *keyword)
 {
-  return npitorsion_global;
+  if (strcmp(keyword,"PiTorsions") == 0) return npitorsions;
+  if (strcmp(keyword,"PiTorsion Coeffs") == 0) return (bigint) npitorsion_types;
+  return 0;
 }
 
 /* ----------------------------------------------------------------------
@@ -673,9 +732,11 @@ bigint FixPiTorsion::read_data_skip_lines(char * /*keyword*/)
    only called by proc 0
 ------------------------------------------------------------------------- */
 
-void FixPiTorsion::write_data_header(FILE *fp, int /*mth*/)
+void FixPiTorsion::write_data_header(FILE *fp, int mth)
 {
-  fprintf(fp,BIGINT_FORMAT " pitorsions\n",npitorsion_global);
+  if (mth == 0) fprintf(fp,BIGINT_FORMAT " pitorsions\n",npitorsions);
+  else if (mth == 1) 
+    fprintf(fp,BIGINT_FORMAT " pitorsion types\n",npitorsion_types);
 }
 
 /* ----------------------------------------------------------------------
@@ -686,7 +747,7 @@ void FixPiTorsion::write_data_header(FILE *fp, int /*mth*/)
    ny = columns = type + 6 atom IDs
 ------------------------------------------------------------------------- */
 
-void FixPiTorsion::write_data_section_size(int /*mth*/, int &nx, int &ny)
+void FixPiTorsion::write_data_section_size(int mth, int &nx, int &ny)
 {
   int i,m;
 
@@ -708,7 +769,7 @@ void FixPiTorsion::write_data_section_size(int /*mth*/, int &nx, int &ny)
    buf allocated by caller as owned PiTorsions by 7
 ------------------------------------------------------------------------- */
 
-void FixPiTorsion::write_data_section_pack(int /*mth*/, double **buf)
+void FixPiTorsion::write_data_section_pack(int mth, double **buf)
 {
   int i,m;
 
@@ -741,9 +802,10 @@ void FixPiTorsion::write_data_section_pack(int /*mth*/, double **buf)
    only called by proc 0
 ------------------------------------------------------------------------- */
 
-void FixPiTorsion::write_data_section_keyword(int /*mth*/, FILE *fp)
+void FixPiTorsion::write_data_section_keyword(int mth, FILE *fp)
 {
-  fprintf(fp,"\nPiTorsion\n\n");
+  if (mth == 0) fprintf(fp,"\nPiTorsions\n\n");
+  else if (mth == 1) fprintf(fp,"\nPiTorsion Coeffs\n\n");
 }
 
 /* ----------------------------------------------------------------------
@@ -753,7 +815,7 @@ void FixPiTorsion::write_data_section_keyword(int /*mth*/, FILE *fp)
    only called by proc 0
 ------------------------------------------------------------------------- */
 
-void FixPiTorsion::write_data_section(int /*mth*/, FILE *fp,
+void FixPiTorsion::write_data_section(int mth, FILE *fp,
                                   int n, double **buf, int index)
 {
   for (int i = 0; i < n; i++)
@@ -779,7 +841,7 @@ void FixPiTorsion::write_restart(FILE *fp)
   if (comm->me == 0) {
     int size = sizeof(bigint);
     fwrite(&size,sizeof(int),1,fp);
-    fwrite(&npitorsion_global,sizeof(bigint),1,fp);
+    fwrite(&npitorsions,sizeof(bigint),1,fp);
   }
 }
 
@@ -789,7 +851,7 @@ void FixPiTorsion::write_restart(FILE *fp)
 
 void FixPiTorsion::restart(char *buf)
 {
-  npitorsion_global = *((bigint *) buf);
+  npitorsions = *((bigint *) buf);
 }
 
 /* ----------------------------------------------------------------------

src/AMOEBA/fix_pitorsion.h

@@ -68,7 +68,8 @@ class FixPiTorsion : public Fix {
   int nprocs, me;
   int newton_bond, eflag_caller;
   int ilevel_respa;
-  bigint npitorsion_global;
+  bigint npitorsions;
+  int npitorsion_types;
   double epitorsion;
 
   double *kpit;

src/modify.cpp

@@ -810,7 +810,7 @@ Fix *Modify::add_fix(int narg, char **arg, int trysuffix)
 
   const char *exceptions[] =
     {"GPU", "OMP", "INTEL", "property/atom", "cmap", "cmap3", "rx",
-     "deprecated", "STORE/KIM", nullptr};
+     "deprecated", "STORE/KIM", "pitorsion", nullptr};
 
   if (domain->box_exist == 0) {
     int m;

src/read_data.cpp

@@ -729,7 +729,6 @@ void ReadData::command(int narg, char **arg)
             if (firstpass) fix(fix_index[i],keyword);
             else skip_lines(modify->fix[fix_index[i]]->
                             read_data_skip_lines(keyword));
-            parse_keyword(0);
             break;
           }
         if (i == nfix)

tools/tinker/tinker2lmp.py

@@ -718,7 +718,7 @@ for atom1 in id:
 
 # DEBUG - if uncommented, no PiTorsions appear in data file
 
-pitorsionlist = []
+#pitorsionlist = []
 
 # ----------------------------------------
 # create lists of bond/angle/dihedral/improper types
@@ -1055,6 +1055,7 @@ for m,params in enumerate(prm.pitorsionparams):
 flags = len(prm.pitorsionparams)*[0]
 pitorsiontype = []
 pitorsionparams = []
+pitorsionlist_reduced = []
 
 for tmp1,tmp2,atom1,atom2,tmp3,tmp4 in pitorsionlist:
   type1 = type[atom1-1]
@@ -1062,15 +1063,13 @@ for tmp1,tmp2,atom1,atom2,tmp3,tmp4 in pitorsionlist:
   c1 = classes[type1-1]
   c2 = classes[type2-1]
 
+  # 6-tuple is only a PiTorsion if central 2 atoms math an entry in PRM file
+  # pitorsionlist_reduced = list of just these 6-tuples
+  
+  if (c1,c2) in pitdict or (c2,c1) in pitdict:
     if (c1,c2) in pitdict: m,params = pitdict[(c1,c2)]
-  elif (c2,c1) in pitdict: m,params = pitdict[(c2,c1)]
+    else: m,params = pitdict[(c2,c1)]
-  else:
+    pitorsionlist_reduced.append((tmp1,tmp2,atom1,atom2,tmp3,tmp4))
-    # NOTE: probably this PiT should be deleted from enumeration list
-    #       similar to olist for impropers above
-    # IMPORTANT: look at other errors and messages t2lmp.py is producing
-    error("PiTorsion not found: %d %d: %d %d" % (atom1,atom2,c1,c2))
-    pitorsiontype.append(0)
-    continue
 
     if not flags[m]:
       v1 = params[2:]
@@ -1078,9 +1077,9 @@ for tmp1,tmp2,atom1,atom2,tmp3,tmp4 in pitorsionlist:
       flags[m] = len(pitorsionparams)
     pitorsiontype.append(flags[m])
     
-print "PRM pitor param",len(prm.pitorsionparams)
+# replace original pitorsionlist with reduced version
-print "PiTor list",len(pitorsionlist)
+
-#print "Flags",flags
+pitorsionlist = pitorsionlist_reduced
 
 # ----------------------------------------
 # assign each atom to a Tinker group