backport bugfixes for fix ipi from development branch

src/MISC/fix_ipi.cpp

@@ -48,6 +48,7 @@ using namespace FixConst;
 #ifndef _WIN32
 #include <netdb.h>
 #include <netinet/in.h>
+#include <netinet/tcp.h>
 #include <sys/socket.h>
 #include <sys/types.h>
 #include <sys/un.h>
@@ -78,7 +79,7 @@ static void open_socket(int &sockfd, int inet, int port, char *host, Error *erro
    error: pointer to a LAMMPS Error object
 */
 {
-  int ai_err;
+  int ai_err,flagNagle;
 
 #ifdef _WIN32
   error->one(FLERR, "i-PI socket implementation requires UNIX environment");
@@ -100,6 +101,11 @@ static void open_socket(int &sockfd, int inet, int port, char *host, Error *erro
     sockfd = socket(res->ai_family, res->ai_socktype, res->ai_protocol);
     if (sockfd < 0) error->one(FLERR, "Error creating socket for fix ipi");
 
+    // set TCP_NODELAY=1 to disable Nagle's algorithm as it slows down the small transactions for i-PI
+    flagNagle = 1;
+    int result_TCP = setsockopt(sockfd, IPPROTO_TCP, TCP_NODELAY, (char *)&flagNagle, sizeof(int));
+    if (result_TCP < 0) { perror("Error setting TCP_NODELAY"); }
+
     // makes connection
     if (connect(sockfd, res->ai_addr, res->ai_addrlen) < 0)
       error->one(FLERR, "Error opening INET socket: wrong port or server unreachable");
@@ -182,6 +188,7 @@ FixIPI::FixIPI(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), irregul
   master = (comm->me == 0) ? 1 : 0;
   inet = 1;
   reset_flag = 0;
+  firsttime = 1;
 
   int iarg = 5;
   while (iarg < narg) {
@@ -247,6 +254,7 @@ void FixIPI::init()
     ipisock = 0;
   // TODO: should check for success in socket opening,
   // but the current open_socket routine dies brutally if unsuccessful
+
   // tell lammps we have assigned a socket
   socketflag = 1;
 
@@ -363,17 +371,40 @@ void FixIPI::initial_integrate(int /*vflag*/)
   // has to be be done before invoking Irregular::migrate_atoms()
   //   since it requires atoms be inside simulation box
 
+  // folds atomic coordinates close to the origin
   if (domain->triclinic) domain->x2lamda(atom->nlocal);
   domain->pbc();
   domain->reset_box();
-  if (domain->triclinic) domain->lamda2x(atom->nlocal);
-
   // move atoms to new processors via irregular()
   // only needed if migrate_check() says an atom moves to far
-  if (domain->triclinic) domain->x2lamda(atom->nlocal);
   if (irregular->migrate_check()) irregular->migrate_atoms();
   if (domain->triclinic) domain->lamda2x(atom->nlocal);
 
+  // ensures continuity of trajectories relative to the
+  // snapshot at neighbor list creation, minimizing the
+  // number of neighbor list updates
+  auto xhold = neighbor->get_xhold();
+  if (xhold != NULL && !firsttime) {
+    // don't wrap if xhold is not used in the NL, or the
+    // first call (because the NL is initialized from the
+    // data file that might have nothing to do with the
+    // current structure
+    for (int i = 0; i < nlocal; i++) {
+      if (mask[i] & groupbit) {
+        auto delx = x[i][0] - xhold[i][0];
+        auto dely = x[i][1] - xhold[i][1];
+        auto delz = x[i][2] - xhold[i][2];
+
+        domain->minimum_image(delx, dely, delz);
+
+        x[i][0] = xhold[i][0] + delx;
+        x[i][1] = xhold[i][1] + dely;
+        x[i][2] = xhold[i][2] + delz;
+      }
+    }
+  }
+  firsttime = 0;
+
   // check if kspace solver is used
   if (reset_flag && kspace_flag) {
     // reset kspace, pair, angles, ... b/c simulation box might have changed.
@@ -452,6 +483,7 @@ void FixIPI::final_integrate()
   retstr[0]=0;
 
   if (master) {
+    // check for new messages
     while (true) {
       readbuffer(ipisock, header, MSGLEN, error); header[MSGLEN]=0;
 
@@ -464,6 +496,7 @@ void FixIPI::final_integrate()
       error->one(FLERR, "Got EXIT message from i-PI. Now leaving!");
 
     if (strcmp(header,"GETFORCE    ") == 0)  {
+      // return force and energy data
       writebuffer(ipisock,"FORCEREADY  ",MSGLEN, error);
       writebuffer(ipisock,(char*) &pot,8, error);
       writebuffer(ipisock,(char*) &nat,4, error);
@@ -478,5 +511,3 @@ void FixIPI::final_integrate()
 
   hasdata=0;
 }
-
-

src/MISC/fix_ipi.h

@@ -42,6 +42,7 @@ class FixIPI : public Fix {
   long bsize;
   int kspace_flag;
   int reset_flag;
+  int firsttime;
 
  private:
   class Irregular *irregular;