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error out when reduced units are used with fix ipi or fix pimd

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This commit is contained in:
Axel Kohlmeyer
2022-11-24 10:14:09 -05:00
parent 7a4e1ed5bf
commit e36a360891
4 changed files with 71 additions and 55 deletions
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6
doc/src/fix_ipi.rst
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@ -90,6 +90,12 @@ coordinates are transferred. However, one could use this strategy to
define an external potential acting on the atoms that are moved by
i-PI.
Since the i-PI code uses atomic units internally, this fix needs to
convert LAMMPS data to and from its :doc:`specified units <units>`
accordingly when communicating with i-PI. This is not possible for
reduced units ("units lj") and thus *fix ipi* will stop with an error in
this case.
This fix is part of the MISC package. It is only enabled if
LAMMPS was built with that package. See the
:doc:`Build package <Build_package>` page for more info.

2
doc/src/fix_pimd.rst
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@ -156,6 +156,8 @@ This fix is part of the REPLICA package. It is only enabled if
LAMMPS was built with that package. See the
:doc:`Build package <Build_package>` page for more info.
Fix pid cannot be used with :doc:`lj units <units>`.
A PIMD simulation can be initialized with a single data file read via
the :doc:`read_data <read_data>` command. However, this means all
quasi-beads in a ring polymer will have identical positions and

115
src/MISC/fix_ipi.cpp
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@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -47,12 +46,12 @@ using namespace FixConst;
// socket interface
#ifndef _WIN32
#include <unistd.h>
#include <sys/types.h>
#include <sys/socket.h>
#include <netinet/in.h>
#include <sys/un.h>
#include <netdb.h>
#include <netinet/in.h>
#include <sys/socket.h>
#include <sys/types.h>
#include <sys/un.h>
#include <unistd.h>
#else
#ifndef WIN32_LEAN_AND_MEAN
#define WIN32_LEAN_AND_MEAN
@ -65,8 +64,7 @@ using namespace FixConst;
/* Utility functions to simplify the interface with POSIX sockets */
static void open_socket(int &sockfd, int inet, int port, char* host,
Error *error)
static void open_socket(int &sockfd, int inet, int port, char *host, Error *error)
/* Opens a socket.
Args:
@ -83,9 +81,9 @@ static void open_socket(int &sockfd, int inet, int port, char* host,
int ai_err;
#ifdef _WIN32
error->one(FLERR,"i-PI socket implementation requires UNIX environment");
error->one(FLERR, "i-PI socket implementation requires UNIX environment");
#else
if (inet>0) { // creates an internet socket
if (inet > 0) { // creates an internet socket
// fetches information on the host
struct addrinfo hints, *res;
@ -96,40 +94,39 @@ static void open_socket(int &sockfd, int inet, int port, char* host,
hints.ai_flags = AI_PASSIVE;
ai_err = getaddrinfo(host, std::to_string(port).c_str(), &hints, &res);
if (ai_err!=0)
error->one(FLERR,"Error fetching host data. Wrong host name?");
if (ai_err != 0) error->one(FLERR, "Error fetching host data. Wrong host name?");
// creates socket
sockfd = socket(res->ai_family, res->ai_socktype, res->ai_protocol);
if (sockfd < 0)
error->one(FLERR,"Error opening socket");
if (sockfd < 0) error->one(FLERR, "Error opening socket");
// makes connection
if (connect(sockfd, res->ai_addr, res->ai_addrlen) < 0)
error->one(FLERR,"Error opening INET socket: wrong port or server unreachable");
error->one(FLERR, "Error opening INET socket: wrong port or server unreachable");
freeaddrinfo(res);
} else { // creates a unix socket
} else { // creates a unix socket
struct sockaddr_un serv_addr;
// fills up details of the socket address
memset(&serv_addr, 0, sizeof(serv_addr));
serv_addr.sun_family = AF_UNIX;
strcpy(serv_addr.sun_path, "/tmp/ipi_");
strcpy(serv_addr.sun_path+9, host);
strcpy(serv_addr.sun_path + 9, host);
// creates the socket
sockfd = socket(AF_UNIX, SOCK_STREAM, 0);
// connects
if (connect(sockfd, (struct sockaddr *) &serv_addr, sizeof(serv_addr)) < 0)
error->one(FLERR,"Error opening UNIX socket: server may not be running "
error->one(FLERR,
"Error opening UNIX socket: server may not be running "
"or the path to the socket unavailable");
}
#endif
}
static void writebuffer(int sockfd, const char *data, int len, Error* error)
static void writebuffer(int sockfd, const char *data, int len, Error *error)
/* Writes to a socket.
Args:
@ -140,14 +137,11 @@ static void writebuffer(int sockfd, const char *data, int len, Error* error)
{
int n;
n = write(sockfd,data,len);
if (n < 0)
error->one(FLERR,"Error writing to socket: broken connection");
n = write(sockfd, data, len);
if (n < 0) error->one(FLERR, "Error writing to socket: broken connection");
}
static void readbuffer(int sockfd, char *data, int len, Error* error)
static void readbuffer(int sockfd, char *data, int len, Error *error)
/* Reads from a socket.
Args:
@ -158,44 +152,52 @@ static void readbuffer(int sockfd, char *data, int len, Error* error)
{
int n, nr;
n = nr = read(sockfd,data,len);
n = nr = read(sockfd, data, len);
while (nr>0 && n<len) {
nr=read(sockfd,&data[n],len-n);
n+=nr;
while (nr > 0 && n < len) {
nr = read(sockfd, &data[n], len - n);
n += nr;
}
if (n == 0)
error->one(FLERR,"Error reading from socket: broken connection");
if (n == 0) error->one(FLERR, "Error reading from socket: broken connection");
}
/* ---------------------------------------------------------------------- */
FixIPI::FixIPI(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), irregular(nullptr)
FixIPI::FixIPI(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), irregular(nullptr)
{
/* format for fix:
* fix num group_id ipi host port [unix]
*/
if (strcmp(style,"ipi") != 0 && narg < 5)
error->all(FLERR,"Illegal fix ipi command");
if (narg < 5) utils::missing_cmd_args(FLERR, "fix ipi", error);
if (atom->tag_enable == 0)
error->all(FLERR,"Cannot use fix ipi without atom IDs");
if (atom->tag_enable == 0) error->all(FLERR, "Cannot use fix ipi without atom IDs");
if (atom->tag_consecutive() == 0) error->all(FLERR, "Fix ipi requires consecutive atom IDs");
if (strcmp(update->unit_style, "lj") == 0) error->all(FLERR, "Fix ipi does not support lj units");
if (atom->tag_consecutive() == 0)
error->all(FLERR,"Fix ipi requires consecutive atom IDs");
if (strcmp(arg[1],"all") != 0)
error->warning(FLERR,"Fix ipi always uses group all");
if ((strcmp(arg[1], "all") != 0) && (comm->me == 0))
error->warning(FLERR, "Not using group 'all' with fix ipi can result in undefined behavior");
host = strdup(arg[3]);
port = utils::inumeric(FLERR,arg[4],false,lmp);
port = utils::inumeric(FLERR, arg[4], false, lmp);
inet = ((narg > 5) && (strcmp(arg[5],"unix") == 0) ) ? 0 : 1;
master = (comm->me==0) ? 1 : 0;
// check if forces should be reinitialized and set flag
reset_flag = ((narg > 6 && (strcmp(arg[5],"reset") == 0 )) || ((narg > 5) && (strcmp(arg[5],"reset") == 0)) ) ? 1 : 0;
master = (comm->me == 0) ? 1 : 0;
inet = 1;
reset_flag = 0;
int iarg = 5;
while (iarg < narg) {
if (strcmp(arg[iarg], "unix") == 0) {
inet = 0;
++iarg;
} else if (strcmp(arg[iarg], "reset") == 0) {
reset_flag = 1;
++iarg;
} else {
error->all(FLERR, "Unknown fix ipi keyword: {}", arg[iarg]);
}
}
// sanity check
if (inet && ((port <= 1024) || (port > 65536)))
error->all(FLERR, "Invalid port for fix ipi: {}", port);
hasdata = bsize = 0;
@ -223,7 +225,6 @@ FixIPI::~FixIPI()
delete irregular;
}
/* ---------------------------------------------------------------------- */
int FixIPI::setmask()
@ -240,9 +241,11 @@ void FixIPI::init()
{
//only opens socket on master process
if (master) {
if (!socketflag) open_socket(ipisock, inet, port, host, error);
} else ipisock=0;
//! should check for success in socket opening -- but the current open_socket routine dies brutally if unsuccessful
if (!socketflag) open_socket(ipisock, inet, port, host, error);
} else
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;
@ -252,11 +255,13 @@ void FixIPI::init()
kspace_flag = (force->kspace) ? 1 : 0;
// makes sure that neighbor lists are re-built at each step (cannot make assumptions when cycling over beads!)
// makes sure that neighbor lists are re-built at each step
// (cannot make assumptions when cycling over beads!)
neighbor->delay = 0;
neighbor->every = 1;
}
// clang-format off
void FixIPI::initial_integrate(int /*vflag*/)
{
/* This is called at the beginning of the integration loop,

3
src/REPLICA/fix_pimd.cpp
View File

@ -102,6 +102,9 @@ FixPIMD::FixPIMD(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
error->universe_all(FLERR, fmt::format("Unknown keyword {} for fix pimd", arg[i]));
}
if (strcmp(update->unit_style, "lj") == 0)
error->all(FLERR, "Fix pimd does not support lj units");
/* Initiation */
size_peratom_cols = 12 * nhc_nchain + 3;