Unverified Commit 3e58ebea authored by Steve Plimpton's avatar Steve Plimpton Committed by GitHub
Browse files

Merge pull request #957 from akohlmey/collected_small_fixes 

Collected small changes and bugfixes for next patch release
parents 7a22612b 47482afb

potentials/ffield.reax.lg

+6 −68
Original line number Diff line number Diff line
@@ -39,7 +39,7 @@ DATE: 2012-01-06 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: Liu, 
    5.0000 !Molecular energy (not used)           

    0.0000 !Molecular energy (not used)           

    6.9784 !Valency angle conjugation parameter   

  7    ! Nr of atoms; cov.r; valency;a.m;Rvdw;Evdw;gammaEEM;cov.r2;#

  5    ! Nr of atoms; cov.r; valency;a.m;Rvdw;Evdw;gammaEEM;cov.r2;#

            alfa;gammavdW;valency;Eunder;Eover;chiEEM;etaEEM;n.u.               

            cov r3;Elp;Heat inc.;n.u.;n.u.;n.u.;n.u.                            

            ov/un;val1;n.u.;val3,vval4
@@ -68,17 +68,7 @@ DATE: 2012-01-06 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: Liu, 
      1.4703   9.4922  70.0338   8.5146  28.0801   8.5010   0.9745   0.0000

    -10.0773   2.7466   1.0338   6.2998   2.8793   1.8000   0.0000  14.0000

    180.0000   2.0783

 Si   2.0276   4.0000  28.0600   2.2042   0.1322   0.8218   1.5758   4.0000

     11.9413   2.0618   4.0000  11.8211 136.4845   1.8038   7.3852   0.0000

     -1.0000   0.0000 126.5331   6.4918   8.5961   0.2368   0.8563   0.0000

     -3.8112   3.1873   1.0338   4.0000   2.5791   0.0000   0.0000   0.0000

    180.0000   2.2042

 X   -0.1000   2.0000   1.0080   2.0000   0.0000   1.0000  -0.1000   6.0000

     10.0000   2.5000   4.0000   0.0000   0.0000   8.5000   1.5000   0.0000

     -0.1000   0.0000  -2.3700   8.7410  13.3640   0.6690   0.9745   0.0000

    -11.0000   2.7466   1.0338   4.0000   2.8793   0.0000   0.0000   0.0000

    180.0000   2.0000

 18      ! Nr of bonds; Edis1;LPpen;n.u.;pbe1;pbo5;13corr;pbo6      

 10      ! Nr of bonds; Edis1;LPpen;n.u.;pbe1;pbo5;13corr;pbo6      

                         pbe2;pbo3;pbo4;Etrip;pbo1;pbo2;ovcorr                  

  1  1 141.9346 113.4487  67.6027   0.1554  -0.3045   1.0000  30.4515   0.4283

         0.0801  -0.2113   8.5395   1.0000  -0.0933   6.6967   1.0000   0.0000
@@ -100,34 +90,14 @@ DATE: 2012-01-06 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: Liu, 
         5.1146   1.0000   0.0000   1.0000  -0.0532   5.1189   0.0000   0.0000

  2  4 208.0443   0.0000   0.0000  -0.3923   0.0000   1.0000   6.0000   0.3221

        10.5505   1.0000   0.0000   1.0000  -0.0690   6.2949   0.0000   0.0000

  1  5 128.7959  56.4134  39.0716   0.0688  -0.4463   1.0000  31.1766   0.4530

         0.1955  -0.3587   6.2148   1.0000  -0.0770   6.6386   1.0000   0.0000

  2  5 128.6090   0.0000   0.0000  -0.5555   0.0000   1.0000   6.0000   0.4721

        10.8735   1.0000   0.0000   1.0000  -0.0242   9.1937   1.0000   0.0000

  3  5   0.0000   0.0000   0.0000   0.5563  -0.4038   1.0000  49.5611   0.6000

         0.4259  -0.4577  12.7569   1.0000  -0.1100   7.1145   1.0000   0.0000

  4  5   0.0000   0.0000   0.0000   0.4438  -0.2034   1.0000  40.3399   0.6000

         0.3296  -0.3153   9.1227   1.0000  -0.1805   5.6864   1.0000   0.0000

  5  5  96.1871  93.7006  68.6860   0.0955  -0.4781   1.0000  17.8574   0.6000

         0.2723  -0.2373   9.7875   1.0000  -0.0950   6.4757   1.0000   0.0000

  6  6 109.1904  70.8314  30.0000   0.2765  -0.3000   1.0000  16.0000   0.1583

         0.2804  -0.1994   8.1117   1.0000  -0.0675   8.2993   0.0000   0.0000

  2  6 137.1002   0.0000   0.0000  -0.1902   0.0000   1.0000   6.0000   0.4256

        17.7186   1.0000   0.0000   1.0000  -0.0377   6.4281   0.0000   0.0000

  3  6 191.1743  52.0733  43.3991  -0.2584  -0.3000   1.0000  36.0000   0.8764

         1.0248  -0.3658   4.2151   1.0000  -0.5004   4.2605   1.0000   0.0000

 10    ! Nr of off-diagonal terms; Ediss;Ro;gamma;rsigma;rpi;rpi2   

 6     ! Nr of off-diagonal terms; Ediss;Ro;gamma;rsigma;rpi;rpi2   

  1  2   0.0464   1.8296   9.9214   1.0029  -1.0000  -1.0000   0.0000

  2  3   0.0403   1.6913  10.4801   0.8774  -1.0000  -1.0000   0.0000

  2  4   0.0524   1.7325  10.1306   0.9982  -1.0000  -1.0000 294.9500

  1  3   0.1028   1.9277   9.1521   1.3399   1.1104   1.1609 631.8500

  1  4   0.2070   1.7366   9.5916   1.2960   1.2008   1.1262 650.0000

  3  4   0.0491   1.7025  10.6101   1.3036   1.1276   1.0173 880.0000

  2  6   0.0470   1.6738  11.6877   1.1931  -1.0000  -1.0000   0.0000

  3  6   0.1263   1.8163  10.6833   1.6266   1.2052  -1.0000   0.0000

  1  5   0.1408   1.8161   9.9393   1.7986   1.3021   1.4031   0.0000

  2  5   0.0895   1.6239  10.0104   1.4640  -1.0000  -1.0000   0.0000

 62    ! Nr of angles;at1;at2;at3;Thetao,o;ka;kb;pv1;pv2            

 41    ! Nr of angles;at1;at2;at3;Thetao,o;ka;kb;pv1;pv2            

  1  1  1  74.0317  32.2712   0.9501   0.0000   0.1780  10.5736   1.0400

  1  1  2  70.6558  14.3658   5.3224   0.0000   0.0058   0.0000   1.0400

  2  1  2  76.7339  14.4217   3.3631   0.0000   0.0127   0.0000   1.0400
@@ -164,33 +134,12 @@ DATE: 2012-01-06 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: Liu, 
  2  4  2  55.8679  14.2331   2.9225   0.0000   0.2000   0.0000   2.9932

  1  2  3   0.0000   0.0019   6.0000   0.0000   0.0000   0.0000   1.0400

  1  2  4   0.0000   0.0019   6.0000   0.0000   0.0000   0.0000   1.0400

  1  2  5   0.0000   0.0019   6.0000   0.0000   0.0000   0.0000   1.0400

  3  2  3   0.0000   0.0019   6.0000   0.0000   0.0000   0.0000   1.0400

  3  2  4   0.0000   0.0019   6.0000   0.0000   0.0000   0.0000   1.0400

  4  2  4   0.0000   0.0019   6.0000   0.0000   0.0000   0.0000   1.0400

  2  2  3   0.0000   0.0019   6.0000   0.0000   0.0000   0.0000   1.0400

  2  2  4   0.0000   0.0019   6.0000   0.0000   0.0000   0.0000   1.0400

  1  1  5  74.4180  33.4273   1.7018   0.1463   0.5000   0.0000   1.6178

  1  5  1  79.7037  28.2036   1.7073   0.1463   0.5000   0.0000   1.6453

  2  1  5  63.3289  29.4225   2.1326   0.0000   0.5000   0.0000   3.0000

  1  5  2  85.9449  38.3109   1.2492   0.0000   0.5000   0.0000   1.1000

  1  5  5  85.6645  40.0000   2.9274   0.1463   0.5000   0.0000   1.3830

  2  5  2  83.8555   5.1317   0.4377   0.0000   0.5000   0.0000   3.0000

  2  5  5  97.0064  32.1121   2.0242   0.0000   0.5000   0.0000   2.8568

  6  6  6  69.3456  21.7361   1.4283   0.0000  -0.2101   0.0000   1.3241

  2  6  6  75.6168  21.5317   1.0435   0.0000   2.5179   0.0000   1.0400

  2  6  2  78.3939  20.9772   0.8630   0.0000   2.8421   0.0000   1.0400

  3  6  6  70.3016  15.4081   1.3267   0.0000   2.1459   0.0000   1.0400

  2  6  3  73.8232  16.6592   3.7425   0.0000   0.8613   0.0000   1.0400

  3  6  3  90.0344   7.7656   1.7264   0.0000   0.7689   0.0000   1.0400

  6  3  6  22.1715   3.6615   0.3160   0.0000   4.1125   0.0000   1.0400

  2  3  6  83.7634   5.6693   2.7780   0.0000   1.6982   0.0000   1.0400

  3  3  6  73.4663  25.0761   0.9143   0.0000   2.2466   0.0000   1.0400

  2  2  6   0.0000  47.1300   6.0000   0.0000   1.6371   0.0000   1.0400

  6  2  6   0.0000  31.5209   6.0000   0.0000   1.6371   0.0000   1.0400

  3  2  6   0.0000  31.0427   4.5625   0.0000   1.6371   0.0000   1.0400

  2  2  5   0.0000   0.0019   6.0000   0.0000   0.0000   0.0000   1.0400

 31    ! Nr of torsions;at1;at2;at3;at4;;V1;V2;V3;V2(BO);vconj;n.u;n

 25    ! Nr of torsions;at1;at2;at3;at4;;V1;V2;V3;V2(BO);vconj;n.u;n

  1  1  1  1   0.0000  48.4194   0.3163  -8.6506  -1.7255   0.0000   0.0000

  1  1  1  2   0.0000  63.3484   0.2210  -8.8401  -1.8081   0.0000   0.0000

  2  1  1  2   0.0000  45.2741   0.4171  -6.9800  -1.2359   0.0000   0.0000
@@ -205,12 +154,6 @@ DATE: 2012-01-06 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: Liu, 
  0  4  4  0   2.0000  75.3685  -0.7852  -9.0000  -2.0000   0.0000   0.0000

  0  1  1  0   0.0930  18.6070  -1.3191  -9.0000  -1.0000   0.0000   0.0000

  4  1  4  4  -2.0000  20.6655  -1.5000  -9.0000  -2.0000   0.0000   0.0000

  0  1  5  0   4.0885  78.7058   0.1174  -2.1639   0.0000   0.0000   0.0000

  0  5  5  0  -0.0170 -56.0786   0.6132  -2.2092   0.0000   0.0000   0.0000

  0  2  5  0   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000

  0  6  6  0   0.0000   0.0000   0.1200  -2.4426   0.0000   0.0000   0.0000

  0  2  6  0   0.0000   0.0000   0.1200  -2.4847   0.0000   0.0000   0.0000

  0  3  6  0   0.0000   0.0000   0.1200  -2.4703   0.0000   0.0000   0.0000

  1  1  3  3   1.2707  21.6200   1.5000  -9.0000  -2.0000   0.0000   0.0000

  1  3  3  1  -1.8804  79.9255  -1.5000  -4.1940  -2.0000   0.0000   0.0000

  3  1  3  3  -2.0000  22.5092   1.5000  -8.9500  -2.0000   0.0000   0.0000
@@ -222,13 +165,8 @@ DATE: 2012-01-06 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: Liu, 
  1  1  4  3  -2.0000  47.8326  -1.5000  -9.0000  -2.0000   0.0000   0.0000

  2  3  4  3  -0.2997 152.9040  -1.5000  -4.4564  -2.0000   0.0000   0.0000

  2  4  4  3   0.1040  70.1152   0.5284  -3.5026  -2.0000   0.0000   0.0000

  9    ! Nr of hydrogen bonds;at1;at2;at3;Rhb;Dehb;vhb1             

  4    ! Nr of hydrogen bonds;at1;at2;at3;Rhb;Dehb;vhb1             

  3  2  3   2.1845  -2.3549   3.0582  19.1627

  3  2  4   1.6658  -3.8907   3.0582  19.1627

  4  2  3   1.8738  -3.5421   3.0582  19.1627

  4  2  4   1.8075  -4.1846   3.0582  19.1627
 
  3  2  5   2.6644  -3.0000   3.0000   3.0000

  4  2  5   4.0476  -3.0000   3.0000   3.0000

  5  2  3   2.1126  -4.5790   3.0000   3.0000

  5  2  4   2.2066  -5.7038   3.0000   3.0000

  5  2  5   1.9461  -4.0000   3.0000   3.0000

src/USER-MISC/fix_smd.cpp

+12 −12
Original line number Diff line number Diff line
@@ -270,12 +270,12 @@ void FixSMD::smd_tether() 
        ftotal[2] -= fz*massfrac;

        if (evflag) {

          domain->unmap(x[i],image[i],unwrap);

          v[0] = fx*massfrac*unwrap[0];

          v[1] = fy*massfrac*unwrap[1];

          v[2] = fz*massfrac*unwrap[2];

          v[3] = fx*massfrac*unwrap[1];

          v[4] = fx*massfrac*unwrap[2];

          v[5] = fy*massfrac*unwrap[2];

          v[0] = -fx*massfrac*unwrap[0];

          v[1] = -fy*massfrac*unwrap[1];

          v[2] = -fz*massfrac*unwrap[2];

          v[3] = -fx*massfrac*unwrap[1];

          v[4] = -fx*massfrac*unwrap[2];

          v[5] = -fy*massfrac*unwrap[2];

          v_tally(i, v);

        }

      }
@@ -291,12 +291,12 @@ void FixSMD::smd_tether() 
        ftotal[2] -= fz*massfrac;

        if (evflag) {

          domain->unmap(x[i],image[i],unwrap);

          v[0] = fx*massfrac*unwrap[0];

          v[1] = fy*massfrac*unwrap[1];

          v[2] = fz*massfrac*unwrap[2];

          v[3] = fx*massfrac*unwrap[1];

          v[4] = fx*massfrac*unwrap[2];

          v[5] = fy*massfrac*unwrap[2];

          v[0] = -fx*massfrac*unwrap[0];

          v[1] = -fy*massfrac*unwrap[1];

          v[2] = -fz*massfrac*unwrap[2];

          v[3] = -fx*massfrac*unwrap[1];

          v[4] = -fx*massfrac*unwrap[2];

          v[5] = -fy*massfrac*unwrap[2];

          v_tally(i, v);

        }

      }

src/USER-REAXC/reaxc_ffield.cpp

+29 −3
Original line number Diff line number Diff line
@@ -157,6 +157,18 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax, 
    fgets( s, MAX_LINE, fp );

    c = Tokenize( s, &tmp );



    /* Sanity checks */

    if (c == 2 && !lgflag) {

      if (me == 0)

        fprintf(stderr, "Force field file requires using 'lgvdw yes'\n");

      MPI_Abort( comm, FILE_NOT_FOUND );

    }

    if (c < 9) {

      if (me == 0)

        fprintf(stderr, "Inconsistent ffield file (reaxc_ffield.cpp) \n");

      MPI_Abort( comm, FILE_NOT_FOUND );

    }



    for( j = 0; j < (int)(strlen(tmp[0])); ++j )

      reax->sbp[i].name[j] = toupper( tmp[0][j] );
@@ -174,6 +186,13 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax, 
    fgets( s, MAX_LINE, fp );

    c = Tokenize( s, &tmp );



    /* Sanity check */

    if (c < 8) {

      if (me == 0)

        fprintf(stderr, "Inconsistent ffield file (reaxc_ffield.cpp) \n");

      MPI_Abort( comm, FILE_NOT_FOUND );

    }



    val = atof(tmp[0]); reax->sbp[i].alpha      = val;

    val = atof(tmp[1]); reax->sbp[i].gamma_w    = val;

    val = atof(tmp[2]); reax->sbp[i].valency_boc= val;
@@ -187,6 +206,13 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax, 
    fgets( s, MAX_LINE, fp );

    c = Tokenize( s, &tmp );



    /* Sanity check */

    if (c < 8) {

      if (me == 0)

        fprintf(stderr, "Inconsistent ffield file (reaxc_ffield.cpp) \n");

      MPI_Abort( comm, FILE_NOT_FOUND );

    }



    val = atof(tmp[0]); reax->sbp[i].r_pi_pi    = val;

    val = atof(tmp[1]); reax->sbp[i].p_lp2      = val;

    val = atof(tmp[2]);
@@ -201,7 +227,7 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax, 
    c = Tokenize( s, &tmp );



    /* Sanity check */

    if (c < 3) {

    if (c < 8) {

      if (me == 0)

        fprintf(stderr, "Inconsistent ffield file (reaxc_ffield.cpp) \n");

      MPI_Abort( comm, FILE_NOT_FOUND );
@@ -222,9 +248,9 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax, 
      c = Tokenize( s, &tmp );



      /* Sanity check */

      if (c > 3) {

      if (c > 2) {

        if (me == 0)

          fprintf(stderr, "Inconsistent ffield file (reaxc_ffield.cpp) \n");

          fprintf(stderr, "Force field file incompatible with 'lgvdw yes'\n");

        MPI_Abort( comm, FILE_NOT_FOUND );

      }

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